format-version: 1.2 data-version: releases/2016-09-27 date: 26:09:2016 17:34 saved-by: tb auto-generated-by: TermGenie 1.0 subsetdef: goantislim_grouping "Grouping classes that can be excluded" subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation" subsetdef: gocheck_do_not_manually_annotate "Term not to be used for direct manual annotation" subsetdef: goslim_aspergillus "Aspergillus GO slim" subsetdef: goslim_candida "Candida GO slim" subsetdef: goslim_chembl "ChEMBL protein targets summary" subsetdef: goslim_generic "Generic GO slim" subsetdef: goslim_goa "GOA and proteome slim" subsetdef: goslim_metagenomics "Metagenomics GO slim" subsetdef: goslim_pir "PIR GO slim" subsetdef: goslim_plant "Plant GO slim" subsetdef: goslim_pombe "Fission yeast GO slim" subsetdef: goslim_synapse "synapse GO slim" subsetdef: goslim_virus "Viral GO slim" subsetdef: goslim_yeast "Yeast GO slim" subsetdef: gosubset_prok "Prokaryotic GO subset" subsetdef: mf_needs_review "Catalytic activity terms in need of attention" subsetdef: termgenie_unvetted "Terms created by TermGenie that do not follow a template and require additional vetting by editors" subsetdef: virus_checked "Viral overhaul terms" synonymtypedef: syngo_official_label "label approved by the SynGO project" synonymtypedef: systematic_synonym "Systematic synonym" EXACT default-namespace: gene_ontology remark: cvs version: $Revision: 35842 $ ontology: go [Term] id: GO:0000001 name: mitochondrion inheritance namespace: biological_process def: "The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton." [GOC:mcc, PMID:10873824, PMID:11389764] synonym: "mitochondrial inheritance" EXACT [] is_a: GO:0048308 ! organelle inheritance is_a: GO:0048311 ! mitochondrion distribution [Term] id: GO:0000002 name: mitochondrial genome maintenance namespace: biological_process def: "The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome." [GOC:ai, GOC:vw] is_a: GO:0007005 ! mitochondrion organization [Term] id: GO:0000003 name: reproduction namespace: biological_process alt_id: GO:0019952 alt_id: GO:0050876 def: "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." [GOC:go_curators, GOC:isa_complete, GOC:jl, ISBN:0198506732] subset: goslim_chembl subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "reproductive physiological process" EXACT [] xref: Wikipedia:Reproduction is_a: GO:0008150 ! biological_process disjoint_from: GO:0044848 ! biological phase [Term] id: GO:0000005 name: obsolete ribosomal chaperone activity namespace: molecular_function def: "OBSOLETE. Assists in the correct assembly of ribosomes or ribosomal subunits in vivo, but is not a component of the assembled ribosome when performing its normal biological function." [GOC:jl, PMID:12150913] comment: This term was made obsolete because it refers to a class of gene products and a biological process rather than a molecular function. synonym: "ribosomal chaperone activity" EXACT [] is_obsolete: true consider: GO:0042254 consider: GO:0044183 consider: GO:0051082 [Term] id: GO:0000006 name: high-affinity zinc uptake transmembrane transporter activity namespace: molecular_function def: "Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Zn2+(out) = Zn2+(in), probably powered by proton motive force. In high-affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations." [TC:2.A.5.1.1] synonym: "high affinity zinc uptake transmembrane transporter activity" EXACT [] is_a: GO:0005385 ! zinc ion transmembrane transporter activity [Term] id: GO:0000007 name: low-affinity zinc ion transmembrane transporter activity namespace: molecular_function def: "Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Zn2+ = Zn2+, probably powered by proton motive force. In low-affinity transport the transporter is able to bind the solute only if it is present at very high concentrations." [GOC:mtg_transport, ISBN:0815340729] is_a: GO:0005385 ! zinc ion transmembrane transporter activity [Term] id: GO:0000008 name: obsolete thioredoxin namespace: molecular_function alt_id: GO:0000013 def: "OBSOLETE. A small disulfide-containing redox protein that serves as a general protein disulfide oxidoreductase. Interacts with a broad range of proteins by a redox mechanism, based on the reversible oxidation of 2 cysteine thiol groups to a disulfide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulfide and a dithiol." [GOC:kd] comment: This term was made obsolete because it represents gene products. synonym: "thioredoxin" EXACT [] is_obsolete: true consider: GO:0003756 consider: GO:0015036 [Term] id: GO:0000009 name: alpha-1,6-mannosyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a mannose residue to an oligosaccharide, forming an alpha-(1->6) linkage." [GOC:mcc, PMID:2644248] synonym: "1,6-alpha-mannosyltransferase activity" EXACT [] xref: EC:2.4.1.- xref: Reactome:REACT_22295 "Addition of a third mannose to the N-glycan precursor by Alg2, Saccharomyces cerevisiae" xref: Reactome:REACT_22383 "Addition of a third mannose to the N-glycan precursor by ALG2, Homo sapiens" is_a: GO:0000030 ! mannosyltransferase activity [Term] id: GO:0000010 name: trans-hexaprenyltranstransferase activity namespace: molecular_function def: "Catalysis of the reaction: all-trans-hexaprenyl diphosphate + isopentenyl diphosphate = all-trans-heptaprenyl diphosphate + diphosphate." [KEGG:R05612, RHEA:20839] subset: gosubset_prok xref: KEGG:R05612 xref: RHEA:20839 is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups [Term] id: GO:0000011 name: vacuole inheritance namespace: biological_process def: "The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton." [GOC:mcc, PMID:10873824, PMID:14616069] is_a: GO:0007033 ! vacuole organization is_a: GO:0048308 ! organelle inheritance [Term] id: GO:0000012 name: single strand break repair namespace: biological_process def: "The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair." [http://www.ultranet.com/~jkimball/BiologyPages/D/DNArepair.html] subset: gosubset_prok is_a: GO:0006281 ! DNA repair [Term] id: GO:0000014 name: single-stranded DNA endodeoxyribonuclease activity namespace: molecular_function def: "Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks." [GOC:mah] synonym: "single-stranded DNA specific endodeoxyribonuclease activity" RELATED [] synonym: "ssDNA-specific endodeoxyribonuclease activity" RELATED [GOC:mah] is_a: GO:0004520 ! endodeoxyribonuclease activity [Term] id: GO:0000015 name: phosphopyruvate hydratase complex namespace: cellular_component def: "A multimeric enzyme complex, usually a dimer or an octamer, that catalyzes the conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and water." [GOC:jl, ISBN:0198506732] subset: goslim_metagenomics subset: gosubset_prok synonym: "enolase complex" EXACT [] is_a: GO:0044445 ! cytosolic part is_a: GO:1902494 ! catalytic complex [Term] id: GO:0000016 name: lactase activity namespace: molecular_function def: "Catalysis of the reaction: lactose + H2O = D-glucose + D-galactose." [EC:3.2.1.108] synonym: "lactase-phlorizin hydrolase activity" BROAD [EC:3.2.1.108] synonym: "lactose galactohydrolase activity" EXACT [EC:3.2.1.108] xref: EC:3.2.1.108 xref: MetaCyc:LACTASE-RXN xref: Reactome:REACT_100439 "lactose + H2O => D-glucose + D-galactose, Gallus gallus" xref: Reactome:REACT_104113 "lactose + H2O => D-glucose + D-galactose, Rattus norvegicus" xref: Reactome:REACT_105850 "lactose + H2O => D-glucose + D-galactose, Bos taurus" xref: Reactome:REACT_109208 "lactose + H2O => D-glucose + D-galactose, Taeniopygia guttata" xref: Reactome:REACT_109391 "lactose + H2O => D-glucose + D-galactose, Sus scrofa" xref: Reactome:REACT_109447 "lactose + H2O => D-glucose + D-galactose, Danio rerio" xref: Reactome:REACT_112431 "lactose + H2O => D-glucose + D-galactose, Caenorhabditis elegans" xref: Reactome:REACT_114967 "lactose + H2O => D-glucose + D-galactose, Drosophila melanogaster" xref: Reactome:REACT_30821 "lactose + H2O => D-glucose + D-galactose, Mus musculus" xref: Reactome:REACT_78084 "lactose + H2O => D-glucose + D-galactose, Canis familiaris" xref: Reactome:REACT_78754 "lactose + H2O => D-glucose + D-galactose, Xenopus tropicalis" xref: Reactome:REACT_9455 "lactose + H2O => D-glucose + D-galactose, Homo sapiens" xref: RHEA:10079 is_a: GO:0004553 ! hydrolase activity, hydrolyzing O-glycosyl compounds [Term] id: GO:0000017 name: alpha-glucoside transport namespace: biological_process def: "The directed movement of alpha-glucosides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Alpha-glucosides are glycosides in which the sugar group is a glucose residue, and the anomeric carbon of the bond is in an alpha configuration." [GOC:jl, http://www.biochem.purdue.edu/, ISBN:0198506732] is_a: GO:0042946 ! glucoside transport [Term] id: GO:0000018 name: regulation of DNA recombination namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents." [GOC:go_curators, ISBN:0198506732] subset: gosubset_prok is_a: GO:0051052 ! regulation of DNA metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006310 ! DNA recombination relationship: regulates GO:0006310 ! DNA recombination [Term] id: GO:0000019 name: regulation of mitotic recombination namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA recombination during mitosis." [GOC:go_curators] synonym: "regulation of recombination within rDNA repeats" NARROW [] is_a: GO:0000018 ! regulation of DNA recombination intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006312 ! mitotic recombination relationship: regulates GO:0006312 ! mitotic recombination [Term] id: GO:0000020 name: obsolete negative regulation of recombination within rDNA repeats namespace: biological_process def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of genetic recombination within the DNA of the genes coding for ribosomal RNA." [GOC:go_curators, ISBN:0198506732] comment: This term was made obsolete because it describes a substrate-specific process. synonym: "negative regulation of recombination within rDNA repeats" EXACT [] is_obsolete: true consider: GO:0045950 [Term] id: GO:0000022 name: mitotic spindle elongation namespace: biological_process def: "The cell cycle process in which the distance is lengthened between poles of the mitotic spindle. Mitotic spindle elongation begins during mitotic prophase and ends during mitotic anaphase B." [GOC:mtg_cell_cycle, GOC:vw] synonym: "spindle elongation during mitosis" EXACT [] is_a: GO:0051231 ! spindle elongation is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0051231 ! spindle elongation intersection_of: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0000070 ! mitotic sister chromatid segregation relationship: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0007052 ! mitotic spindle organization [Term] id: GO:0000023 name: maltose metabolic process namespace: biological_process def: "The chemical reactions and pathways involving the disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose), an intermediate in the catabolism of glycogen and starch." [GOC:jl, ISBN:0198506732] subset: gosubset_prok synonym: "malt sugar metabolic process" EXACT [] synonym: "malt sugar metabolism" EXACT [] synonym: "maltose metabolism" EXACT [] is_a: GO:0005984 ! disaccharide metabolic process [Term] id: GO:0000024 name: maltose biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of the disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose)." [GOC:jl, ISBN:0198506732] subset: gosubset_prok synonym: "malt sugar biosynthesis" EXACT [] synonym: "malt sugar biosynthetic process" EXACT [] synonym: "maltose anabolism" EXACT [] synonym: "maltose biosynthesis" EXACT [] synonym: "maltose formation" EXACT [] synonym: "maltose synthesis" EXACT [] is_a: GO:0000023 ! maltose metabolic process is_a: GO:0046351 ! disaccharide biosynthetic process [Term] id: GO:0000025 name: maltose catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of the disaccharide maltose (4-O-alpha-D-glucopyranosyl-D-glucopyranose)." [GOC:jl, ISBN:0198506732] subset: gosubset_prok synonym: "malt sugar catabolic process" EXACT [] synonym: "malt sugar catabolism" EXACT [] synonym: "maltose breakdown" EXACT [] synonym: "maltose degradation" EXACT [] synonym: "maltose hydrolysis" NARROW [] xref: MetaCyc:MALTOSECAT-PWY is_a: GO:0000023 ! maltose metabolic process is_a: GO:0046352 ! disaccharide catabolic process [Term] id: GO:0000026 name: alpha-1,2-mannosyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a mannose residue to an oligosaccharide, forming an alpha-(1->2) linkage." [GOC:mcc, PMID:10521541] xref: EC:2.4.1.- xref: Reactome:REACT_22123 "Addition of the seventh mannose to the N-glycan precursor by ALG9, inside the ER lumen, Homo sapiens" xref: Reactome:REACT_22156 "Addition of a fourth and fifth mannose to the N-glycan precursor by ALG11, Homo sapiens" xref: Reactome:REACT_22220 "Addition of the fourth and fifth mannose to the N-glycan precursor skeleton by Alg11, Saccharomyces cerevisiae" xref: Reactome:REACT_22307 "Addition of the last mannose to the N-glycan precursor by ALG3, inside the ER lumen., Homo sapiens" is_a: GO:0000030 ! mannosyltransferase activity [Term] id: GO:0000027 name: ribosomal large subunit assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the large ribosomal subunit." [GOC:jl] subset: gosubset_prok synonym: "50S ribosomal subunit assembly" NARROW [GOC:mah] synonym: "60S ribosomal subunit assembly" NARROW [GOC:mah] is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0042255 ! ribosome assembly relationship: part_of GO:0042273 ! ribosomal large subunit biogenesis [Term] id: GO:0000028 name: ribosomal small subunit assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the small ribosomal subunit." [GOC:jl] subset: gosubset_prok synonym: "30S ribosomal subunit assembly" NARROW [GOC:mah] synonym: "40S ribosomal subunit assembly" NARROW [GOC:mah] is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0042255 ! ribosome assembly relationship: part_of GO:0042274 ! ribosomal small subunit biogenesis [Term] id: GO:0000030 name: mannosyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a mannosyl group to an acceptor molecule, typically another carbohydrate or a lipid." [GOC:ai, GOC:cjm] subset: gosubset_prok xref: EC:2.4.1.- xref: Reactome:REACT_1018 "glucosaminyl-acyl-PI + dolichol phosphate D-mannose -> mannose(al1-4)glucosaminyl-acyl-PI + dolichol phosphate, Homo sapiens" xref: Reactome:REACT_105204 "glucosaminyl-acyl-PI + dolichol phosphate D-mannose -> mannose(al1-4)glucosaminyl-acyl-PI + dolichol phosphate, Dictyostelium discoideum" xref: Reactome:REACT_2179 "mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI -> mannose (a1) mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI, Homo sapiens" xref: Reactome:REACT_22117 "Addition of the eighth mannose to the N-glycan precursor by ALG12, inside the ER lumen, Homo sapiens" xref: Reactome:REACT_30252 "glucosaminyl-acyl-PI + dolichol phosphate D-mannose -> mannose(al1-4)glucosaminyl-acyl-PI + dolichol phosphate, Rattus norvegicus" xref: Reactome:REACT_34702 "glucosaminyl-acyl-PI + dolichol phosphate D-mannose -> mannose(al1-4)glucosaminyl-acyl-PI + dolichol phosphate, Danio rerio" xref: Reactome:REACT_63412 "glucosaminyl-acyl-PI + dolichol phosphate D-mannose -> mannose(al1-4)glucosaminyl-acyl-PI + dolichol phosphate, Mus musculus" xref: Reactome:REACT_87972 "glucosaminyl-acyl-PI + dolichol phosphate D-mannose -> mannose(al1-4)glucosaminyl-acyl-PI + dolichol phosphate, Canis familiaris" xref: Reactome:REACT_95740 "glucosaminyl-acyl-PI + dolichol phosphate D-mannose -> mannose(al1-4)glucosaminyl-acyl-PI + dolichol phosphate, Gallus gallus" is_a: GO:0016758 ! transferase activity, transferring hexosyl groups relationship: part_of GO:0097502 ! mannosylation [Term] id: GO:0000031 name: mannosylphosphate transferase activity namespace: molecular_function def: "Catalysis of the transfer of a mannosylphosphate group from one compound to another." [GOC:jl] is_a: GO:0016740 ! transferase activity [Term] id: GO:0000032 name: cell wall mannoprotein biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of cell wall mannoproteins, any cell wall protein that contains covalently bound mannose residues." [GOC:ai] subset: gosubset_prok synonym: "cell wall mannoprotein anabolism" EXACT [] synonym: "cell wall mannoprotein biosynthesis" EXACT [] synonym: "cell wall mannoprotein formation" EXACT [] synonym: "cell wall mannoprotein synthesis" EXACT [] is_a: GO:0006057 ! mannoprotein biosynthetic process is_a: GO:0031506 ! cell wall glycoprotein biosynthetic process [Term] id: GO:0000033 name: alpha-1,3-mannosyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a mannose residue to an oligosaccharide, forming an alpha-(1->3) linkage." [GOC:mcc, PMID:10521541] xref: EC:2.4.1.- xref: Reactome:REACT_22347 "Addition of a second mannose to the N-glycan precursor by ALG2, Homo sapiens" xref: Reactome:REACT_22415 "Addition of the sixth mannose to the N-glycan precursor by ALG3., Homo sapiens" is_a: GO:0000030 ! mannosyltransferase activity [Term] id: GO:0000034 name: adenine deaminase activity namespace: molecular_function def: "Catalysis of the reaction: adenine + H2O = hypoxanthine + NH3." [EC:3.5.4.2] subset: gosubset_prok synonym: "ADase activity" EXACT [EC:3.5.4.2] synonym: "adenase activity" EXACT [EC:3.5.4.2] synonym: "adenine aminase activity" EXACT [EC:3.5.4.2] synonym: "adenine aminohydrolase activity" EXACT [EC:3.5.4.2] xref: EC:3.5.4.2 xref: MetaCyc:ADENINE-DEAMINASE-RXN xref: RHEA:23691 is_a: GO:0016814 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines is_a: GO:0019239 ! deaminase activity [Term] id: GO:0000035 name: acyl binding namespace: molecular_function def: "Interacting selectively and non-covalently with an acyl group, any group formally derived by removal of the hydroxyl group from the acid function of a carboxylic acid." [GOC:curators, ISBN:0198506732] subset: gosubset_prok synonym: "acyl-CoA or acyl binding" BROAD [] is_a: GO:0005488 ! binding [Term] id: GO:0000036 name: ACP phosphopantetheine attachment site binding involved in fatty acid biosynthetic process namespace: molecular_function def: "Interacting selectively and non-covalently with the attachment site of the phosphopantetheine prosthetic group of an acyl carrier protein (ACP) as part of the process of fatty acid biosynthesis." [CHEBI:22221, GOC:jl, GOC:vw] comment: Note that this term was moved from transporter to binding because we decided that ACP is not a true transporter, but instead tethers the growing entity that is acted on to make the fatty acid, so binding is the more correct parent. July 2012. subset: gosubset_prok synonym: "acyl carrier activity" EXACT [] is_a: GO:0044620 ! ACP phosphopantetheine attachment site binding intersection_of: GO:0044620 ! ACP phosphopantetheine attachment site binding intersection_of: part_of GO:0006633 ! fatty acid biosynthetic process relationship: part_of GO:0006633 ! fatty acid biosynthetic process [Term] id: GO:0000038 name: very long-chain fatty acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a fatty acid which has a chain length greater than C22." [CHEBI:27283, GOC:hjd] subset: gosubset_prok synonym: "very long chain fatty acid metabolic process" EXACT [GOC:bf] synonym: "very-long-chain fatty acid metabolic process" EXACT [] synonym: "very-long-chain fatty acid metabolism" EXACT [] is_a: GO:0006631 ! fatty acid metabolic process [Term] id: GO:0000039 name: obsolete plasma membrane long-chain fatty acid transporter namespace: molecular_function def: "OBSOLETE (was not defined before being made obsolete)." [GOC:ai] comment: This term was made obsolete because it describes a gene product and it contains component information. synonym: "plasma membrane long-chain fatty acid transporter" EXACT [] is_obsolete: true consider: GO:0005324 consider: GO:0005886 [Term] id: GO:0000040 name: low-affinity iron ion transmembrane transport namespace: biological_process def: "A process in which an iron ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore. In low-affinity transport the transporter is able to bind the solute only if it is only present at very low concentrations." [GOC:mah] synonym: "low affinity iron ion transport" BROAD [] synonym: "low-affinity iron ion transport" BROAD [] is_a: GO:0034755 ! iron ion transmembrane transport [Term] id: GO:0000041 name: transition metal ion transport namespace: biological_process def: "The directed movement of transition metal ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver." [ISBN:0198506732] subset: gosubset_prok synonym: "transition metal transport" EXACT [] is_a: GO:0030001 ! metal ion transport [Term] id: GO:0000042 name: protein targeting to Golgi namespace: biological_process def: "The process of directing proteins towards the Golgi; usually uses signals contained within the protein." [GOC:ai, GOC:mah] synonym: "protein-Golgi targeting" EXACT [] is_a: GO:0000301 ! retrograde transport, vesicle recycling within Golgi is_a: GO:0006605 ! protein targeting is_a: GO:0034067 ! protein localization to Golgi apparatus is_a: GO:0072600 ! establishment of protein localization to Golgi [Term] id: GO:0000044 name: obsolete ascorbate stabilization namespace: biological_process def: "OBSOLETE. The reduction of the ascorbate free radical to a stable form." [GOC:ai, GOC:mtg_electron_transport] comment: This term was made obsolete because it is defined as a function term and is in the process ontology. synonym: "ascorbate stabilization" EXACT [] synonym: "vitamin C stabilization" EXACT [] is_obsolete: true [Term] id: GO:0000045 name: autophagosome assembly namespace: biological_process def: "The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm." [GOC:autophagy, PMID:9412464] synonym: "autophagic vacuole assembly" EXACT [GOC:autophagy] synonym: "autophagic vacuole formation" RELATED [GOC:mah] synonym: "autophagosome biosynthesis" EXACT [] synonym: "autophagosome formation" EXACT [] synonym: "PAS formation" NARROW [] is_a: GO:0070925 ! organelle assembly is_a: GO:1905037 ! autophagosome organization [Term] id: GO:0000047 name: obsolete Rieske iron-sulfur protein namespace: molecular_function def: "OBSOLETE (was not defined before being made obsolete)." [GOC:ai] comment: This term was made obsolete because it represents a gene product. synonym: "Rieske iron-sulfur protein" EXACT [] synonym: "Rieske iron-sulphur protein" EXACT [] is_obsolete: true consider: GO:0009055 [Term] id: GO:0000048 name: peptidyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: peptidyl-tRNA(1) + aminoacyl-tRNA(2) = tRNA(1) + peptidylaminoacyl-tRNA(2)." [EC:2.3.2.12, PMID:11433365, PMID:9242921] synonym: "peptidyl-tRNA:aminoacyl-tRNA N-peptidyltransferase activity" EXACT [EC:2.3.2.12] xref: EC:2.3.2.12 xref: MetaCyc:PEPTIDYLTRANSFERASE-RXN xref: Reactome:REACT_102632 "Peptide transfer from P-site tRNA to the A-site tRNA, Saccharomyces cerevisiae" xref: Reactome:REACT_104123 "Peptide transfer from P-site tRNA to the A-site tRNA, Schizosaccharomyces pombe" xref: Reactome:REACT_112282 "Peptide transfer from P-site tRNA to the A-site tRNA, Gallus gallus" xref: Reactome:REACT_115501 "Peptide transfer from P-site tRNA to the A-site tRNA, Rattus norvegicus" xref: Reactome:REACT_1227 "Peptide transfer from P-site tRNA to the A-site tRNA, Homo sapiens" xref: Reactome:REACT_28090 "Peptide transfer from P-site tRNA to the A-site tRNA, Arabidopsis thaliana" xref: Reactome:REACT_31656 "Peptide transfer from P-site tRNA to the A-site tRNA, Taeniopygia guttata" xref: Reactome:REACT_33679 "Peptide transfer from P-site tRNA to the A-site tRNA, Dictyostelium discoideum" xref: Reactome:REACT_77497 "Peptide transfer from P-site tRNA to the A-site tRNA, Oryza sativa" xref: Reactome:REACT_81539 "Peptide transfer from P-site tRNA to the A-site tRNA, Drosophila melanogaster" xref: Reactome:REACT_87719 "Peptide transfer from P-site tRNA to the A-site tRNA, Mus musculus" xref: Reactome:REACT_90185 "Peptide transfer from P-site tRNA to the A-site tRNA, Danio rerio" xref: Reactome:REACT_90457 "Peptide transfer from P-site tRNA to the A-site tRNA, Canis familiaris" xref: Reactome:REACT_91228 "Peptide transfer from P-site tRNA to the A-site tRNA, Caenorhabditis elegans" xref: Reactome:REACT_95405 "Peptide transfer from P-site tRNA to the A-site tRNA, Plasmodium falciparum" xref: Reactome:REACT_98179 "Peptide transfer from P-site tRNA to the A-site tRNA, Xenopus tropicalis" is_a: GO:0016755 ! transferase activity, transferring amino-acyl groups [Term] id: GO:0000049 name: tRNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with transfer RNA." [GOC:ai] subset: gosubset_prok is_a: GO:0003723 ! RNA binding [Term] id: GO:0000050 name: urea cycle namespace: biological_process alt_id: GO:0006594 alt_id: GO:0006871 def: "The sequence of reactions by which arginine is synthesized from ornithine, then cleaved to yield urea and regenerate ornithine. The overall reaction equation is NH3 + CO2 + aspartate + 3 ATP + 2 H2O = urea + fumarate + 2 ADP + 2 phosphate + AMP + diphosphate." [GOC:pde, GOC:vw, ISBN:0198506732] synonym: "ornithine cycle" EXACT [] synonym: "urea biosynthesis" EXACT [] synonym: "urea biosynthetic process" EXACT [] xref: Reactome:REACT_100599 "Urea cycle, Oryza sativa" xref: Reactome:REACT_107747 "Urea cycle, Mus musculus" xref: Reactome:REACT_109525 "Urea cycle, Danio rerio" xref: Reactome:REACT_31787 "Urea cycle, Taeniopygia guttata" xref: Reactome:REACT_32463 "Urea cycle, Drosophila melanogaster" xref: Reactome:REACT_32971 "Urea cycle, Caenorhabditis elegans" xref: Reactome:REACT_33119 "Urea cycle, Bos taurus" xref: Reactome:REACT_78616 "Urea cycle, Plasmodium falciparum" xref: Reactome:REACT_80089 "Urea cycle, Canis familiaris" xref: Reactome:REACT_81058 "Urea cycle, Dictyostelium discoideum" xref: Reactome:REACT_82995 "Urea cycle, Mycobacterium tuberculosis" xref: Reactome:REACT_83831 "Urea cycle, Rattus norvegicus" xref: Reactome:REACT_84694 "Urea cycle, Saccharomyces cerevisiae" xref: Reactome:REACT_847 "Urea cycle, Homo sapiens" xref: Reactome:REACT_88394 "Urea cycle, Gallus gallus" xref: Reactome:REACT_90218 "Urea cycle, Escherichia coli" xref: Reactome:REACT_90565 "Urea cycle, Sus scrofa" xref: Reactome:REACT_92378 "Urea cycle, Xenopus tropicalis" xref: Reactome:REACT_95880 "Urea cycle, Staphylococcus aureus N315" xref: Reactome:REACT_97366 "Urea cycle, Arabidopsis thaliana" xref: Reactome:REACT_98985 "Urea cycle, Schizosaccharomyces pombe" xref: Wikipedia:Urea_cycle is_a: GO:0019627 ! urea metabolic process is_a: GO:0043604 ! amide biosynthetic process is_a: GO:0044711 ! single-organism biosynthetic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process [Term] id: GO:0000051 name: obsolete urea cycle intermediate metabolic process namespace: biological_process def: "OBSOLETE. The chemical reactions and pathways involving any of the intermediate compounds involved in the urea cycle, a cyclic metabolic pathway that converts waste nitrogen in the form of ammonium to urea." [GOC:jl, ISBN:0198506732] comment: This term was made obsolete because it is a grouping term that is not useful, but has caused true path violations. subset: gosubset_prok synonym: "urea cycle intermediate metabolic process" EXACT [] synonym: "urea cycle intermediate metabolism" EXACT [] is_obsolete: true [Term] id: GO:0000052 name: citrulline metabolic process namespace: biological_process def: "The chemical reactions and pathways involving citrulline, N5-carbamoyl-L-ornithine, an alpha amino acid not found in proteins." [ISBN:0198506732] subset: gosubset_prok synonym: "citrulline metabolism" EXACT [] is_a: GO:1901605 ! alpha-amino acid metabolic process [Term] id: GO:0000053 name: argininosuccinate metabolic process namespace: biological_process def: "The chemical reactions and pathways involving argininosuccinate, 2-(N(omega)-arginino)succinate, an intermediate in the ornithine-urea cycle, where it is synthesized from citrulline and aspartate." [ISBN:0198506732] synonym: "argininosuccinate metabolism" EXACT [] is_a: GO:0006575 ! cellular modified amino acid metabolic process is_a: GO:1901605 ! alpha-amino acid metabolic process [Term] id: GO:0000054 name: ribosomal subunit export from nucleus namespace: biological_process def: "The directed movement of a ribosomal subunit from the nucleus into the cytoplasm." [GOC:ai] subset: goslim_yeast synonym: "ribosomal subunit export from cell nucleus" EXACT [GOC:mah] synonym: "ribosomal subunit export out of nucleus" EXACT [GOC:mah] synonym: "ribosomal subunit transport from nucleus to cytoplasm" EXACT [GOC:mah] synonym: "ribosomal subunit-nucleus export" EXACT [GOC:mah] synonym: "ribosome export from nucleus" RELATED [GOC:mah, GOC:rb] is_a: GO:0033753 ! establishment of ribosome localization is_a: GO:0071428 ! rRNA-containing ribonucleoprotein complex export from nucleus relationship: part_of GO:0042254 ! ribosome biogenesis [Term] id: GO:0000055 name: ribosomal large subunit export from nucleus namespace: biological_process alt_id: GO:0000057 def: "The directed movement of a ribosomal large subunit from the nucleus into the cytoplasm." [GOC:mah] synonym: "50S ribosomal subunit export from nucleus" NARROW [GOC:mah] synonym: "60S ribosomal subunit export from nucleus" NARROW [GOC:mah] synonym: "ribosomal large subunit export from cell nucleus" EXACT [] synonym: "ribosomal large subunit export out of nucleus" EXACT [] synonym: "ribosomal large subunit transport from nucleus to cytoplasm" EXACT [] synonym: "ribosomal large subunit-nucleus export" EXACT [] is_a: GO:0000054 ! ribosomal subunit export from nucleus [Term] id: GO:0000056 name: ribosomal small subunit export from nucleus namespace: biological_process alt_id: GO:0000058 def: "The directed movement of a ribosomal small subunit from the nucleus into the cytoplasm." [GOC:mah] synonym: "30S ribosomal subunit export from nucleus" NARROW [GOC:mah] synonym: "40S ribosomal subunit export from nucleus" NARROW [GOC:mah] synonym: "ribosomal small subunit export from cell nucleus" EXACT [] synonym: "ribosomal small subunit export out of nucleus" EXACT [] synonym: "ribosomal small subunit transport from nucleus to cytoplasm" EXACT [] synonym: "ribosomal small subunit-nucleus export" EXACT [] is_a: GO:0000054 ! ribosomal subunit export from nucleus [Term] id: GO:0000059 name: protein import into nucleus, docking namespace: biological_process def: "A protein complex assembly process that contributes to protein import into the nucleus, and that results in the association of a cargo protein, a carrier protein such as an importin alpha/beta heterodimer, and a nucleoporin located at the periphery of the nuclear pore complex." [GOC:isa_complete, GOC:mah, PMID:14570049, PMID:7878057, PMID:9126736] synonym: "protein docking during protein import into nucleus" EXACT [] synonym: "protein docking during protein transport from cytoplasm to nucleus" EXACT [] synonym: "protein docking during protein-nucleus import" EXACT [] synonym: "protein transport from cytoplasm to nucleus, docking" EXACT [] synonym: "protein-nucleus import, docking" EXACT [] is_a: GO:0043623 ! cellular protein complex assembly relationship: part_of GO:0006606 ! protein import into nucleus [Term] id: GO:0000060 name: protein import into nucleus, translocation namespace: biological_process def: "A protein transport process that contributes to protein import into the nucleus, and that results in the vectorial transfer of a cargo-carrier protein complex through the nuclear pore complex from the cytoplasmic side to the nucleoplasmic side of the nuclear envelope." [GOC:curators, ISBN:0198506732, PMID:14570049, PMID:9126736] comment: Note that 'vectorial' is used in the definition in the mathematical and physical sense of pertaining to 'a quantity having direction as well as magnitude, especially as determining the position of one point in space relative to another. Note that 'translocation' is sometimes used in the literature to refer to the entire process of protein import into the nucleus, but in GO refers specifically to the step in which a cargo-carrier protein complex moves through the nuclear pore complex. synonym: "protein import into cell nucleus, translocation" EXACT [] synonym: "protein translocation during protein import into nucleus" EXACT [] synonym: "protein translocation during protein transport from cytoplasm to nucleus" EXACT [] synonym: "protein translocation during protein-nucleus import" EXACT [] synonym: "protein transport from cytoplasm to nucleus, translocation" EXACT [] synonym: "protein-nucleus import, translocation" EXACT [] is_a: GO:0006886 ! intracellular protein transport relationship: part_of GO:0006606 ! protein import into nucleus [Term] id: GO:0000061 name: protein import into nucleus, substrate release namespace: biological_process def: "A protein complex disassembly process that contributes to protein import into the nucleus, and that results in the dissociation of the cargo protein and the carrier (such as an importin alpha/beta heterodimer) from each other and from the nuclear pore complex." [GOC:mah, PMID:14570049, PMID:9126736, PMID:9687515] synonym: "protein import into cell nucleus, substrate release" EXACT [] synonym: "protein substrate release during protein import into nucleus" EXACT [] synonym: "protein substrate release during protein transport from cytoplasm to nucleus" EXACT [] synonym: "protein substrate release during protein-nucleus import" EXACT [] synonym: "protein transport from cytoplasm to nucleus, substrate release" EXACT [] synonym: "protein-nucleus import, substrate release" EXACT [] is_a: GO:0043624 ! cellular protein complex disassembly relationship: part_of GO:0006606 ! protein import into nucleus [Term] id: GO:0000062 name: fatty-acyl-CoA binding namespace: molecular_function def: "Interacting selectively and non-covalently with acyl-CoA, any derivative of coenzyme A in which the sulfhydryl group is in thiolester linkage with a fatty acyl group." [GOC:jl, ISBN:0198506732] subset: gosubset_prok synonym: "acyl-CoA or acyl binding" BROAD [] is_a: GO:0050662 ! coenzyme binding is_a: GO:1901681 ! sulfur compound binding [Term] id: GO:0000064 name: L-ornithine transmembrane transporter activity namespace: molecular_function def: "Enables the transfer of L-ornithine from one side of a membrane to the other. L-ornithine is 2,5-diaminopentanoic acid." [GOC:ai, GOC:mtg_transport, ISBN:0815340729] subset: gosubset_prok synonym: "histidine/arginine/lysine/ornithine porter activity" RELATED [] synonym: "L-ornithine transporter activity" BROAD [] xref: Reactome:REACT_100602 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Mus musculus" xref: Reactome:REACT_102399 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Xenopus tropicalis" xref: Reactome:REACT_103552 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Gallus gallus" xref: Reactome:REACT_103610 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Canis familiaris" xref: Reactome:REACT_104169 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Sus scrofa" xref: Reactome:REACT_109285 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Caenorhabditis elegans" xref: Reactome:REACT_115531 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Gallus gallus" xref: Reactome:REACT_151 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Homo sapiens" xref: Reactome:REACT_28177 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Drosophila melanogaster" xref: Reactome:REACT_30708 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Arabidopsis thaliana" xref: Reactome:REACT_78308 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Dictyostelium discoideum" xref: Reactome:REACT_84383 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Oryza sativa" xref: Reactome:REACT_88886 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Danio rerio" xref: Reactome:REACT_88959 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Rattus norvegicus" xref: Reactome:REACT_90007 "ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic), Taeniopygia guttata" is_a: GO:0015179 ! L-amino acid transmembrane transporter activity relationship: part_of GO:1903352 ! L-ornithine transmembrane transport [Term] id: GO:0000066 name: mitochondrial ornithine transport namespace: biological_process def: "The directed movement of ornithine, 2,5-diaminopentanoic acid, into, out of or within a mitochondrion." [GOC:ai] is_a: GO:0006839 ! mitochondrial transport is_a: GO:0015822 ! ornithine transport [Term] id: GO:0000067 name: obsolete DNA replication and chromosome cycle namespace: biological_process def: "OBSOLETE (was not defined before being made obsolete)." [GOC:ai] comment: This term was made obsolete because it has been superseded by more accurate terms to represent the biological processes occurring, and it is not clear that this term represents a useful entity. synonym: "DNA replication and chromosome cycle" EXACT [] is_obsolete: true consider: GO:0006260 consider: GO:0007059 consider: GO:0051276 [Term] id: GO:0000070 name: mitotic sister chromatid segregation namespace: biological_process alt_id: GO:0016359 def: "The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets." [GOC:ai, GOC:jl] subset: goslim_pombe synonym: "mitotic chromosome segregation" EXACT [] synonym: "mitotic sister-chromatid adhesion release" NARROW [] is_a: GO:0000819 ! sister chromatid segregation is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0098813 ! nuclear chromosome segregation intersection_of: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0007067 ! mitotic nuclear division [Term] id: GO:0000072 name: obsolete M phase specific microtubule process namespace: biological_process def: "OBSOLETE. A microtubule-based process that occurs only during M phase of the cell cycle." [GOC:mah] comment: This term was made obsolete because terms already exist for centrosome/spindle organization which would be more suitable for the existing annotations, and the phase could be captured as an annotation extension if necessary. synonym: "M phase specific microtubule process" EXACT [] synonym: "M-phase specific microtubule process" EXACT [] is_obsolete: true consider: GO:0007017 [Term] id: GO:0000073 name: spindle pole body separation namespace: biological_process alt_id: GO:0030475 def: "A largely uncharacterized process involving the release of duplicated spindle pole bodies (SPBs) and their migration away from each other within the nuclear membrane. Duplicated SPBs are connected by a bridge structure that may be severed in order to release the SPBs from one another. Following liberation, SPBs diffuse through the nuclear membrane until they are across from each other. SPB separation must take place in order for a bipolar mitotic spindle to assemble." [GOC:sgd_curators] is_a: GO:0022402 ! cell cycle process relationship: part_of GO:0051300 ! spindle pole body organization [Term] id: GO:0000075 name: cell cycle checkpoint namespace: biological_process alt_id: GO:0031576 alt_id: GO:0071779 def: "A cell cycle process that controls cell cycle progression by monitoring the integrity of specific cell cycle events. A cell cycle checkpoint begins with detection of deficiencies or defects and ends with signal transduction." [GOC:mtg_cell_cycle] comment: This term should not be used in direct manual annotation as it should always be possible to minimally designate mitotic or meiotic checkpoint, and usually to additionally specify the checkpoint (i.e mitotic spindle assembly checkpoint, mitotic DNA damage checkpoint etc). Note also that the effector processes are not part of the checkpoint but are positively regulated by the checkpoint signaling and should not be annotated here. subset: gocheck_do_not_manually_annotate synonym: "G1/S checkpoint" NARROW [] synonym: "G1/S transition checkpoint" NARROW [] synonym: "G2/M checkpoint" NARROW [] synonym: "G2/M transition checkpoint" NARROW [] xref: Reactome:REACT_100401 "Cell Cycle Checkpoints, Gallus gallus" xref: Reactome:REACT_102145 "Cell Cycle Checkpoints, Saccharomyces cerevisiae" xref: Reactome:REACT_102175 "Cell Cycle Checkpoints, Canis familiaris" xref: Reactome:REACT_106487 "Cell Cycle Checkpoints, Rattus norvegicus" xref: Reactome:REACT_109101 "Cell Cycle Checkpoints, Drosophila melanogaster" xref: Reactome:REACT_1538 "Cell Cycle Checkpoints, Homo sapiens" xref: Reactome:REACT_29957 "Cell Cycle Checkpoints, Bos taurus" xref: Reactome:REACT_31789 "Cell Cycle Checkpoints, Dictyostelium discoideum" xref: Reactome:REACT_33305 "Cell Cycle Checkpoints, Oryza sativa" xref: Reactome:REACT_79078 "Cell Cycle Checkpoints, Sus scrofa" xref: Reactome:REACT_84460 "Cell Cycle Checkpoints, Arabidopsis thaliana" xref: Reactome:REACT_89660 "Cell Cycle Checkpoints, Xenopus tropicalis" xref: Reactome:REACT_90285 "Cell Cycle Checkpoints, Mus musculus" xref: Reactome:REACT_90465 "Cell Cycle Checkpoints, Caenorhabditis elegans" xref: Reactome:REACT_92239 "Cell Cycle Checkpoints, Danio rerio" xref: Reactome:REACT_96499 "Cell Cycle Checkpoints, Taeniopygia guttata" xref: Reactome:REACT_99737 "Cell Cycle Checkpoints, Schizosaccharomyces pombe" xref: Wikipedia:Cell_cycle_checkpoint is_a: GO:0022402 ! cell cycle process [Term] id: GO:0000076 name: DNA replication checkpoint namespace: biological_process def: "A cell cycle checkpoint that prevents the initiation of nuclear division until DNA replication is complete, thereby ensuring that progeny inherit a full complement of the genome." [GOC:curators, GOC:rn, PMID:11728327, PMID:12537518] is_a: GO:0031570 ! DNA integrity checkpoint [Term] id: GO:0000077 name: DNA damage checkpoint namespace: biological_process def: "A cell cycle checkpoint that regulates progression through the cell cycle in response to DNA damage. A DNA damage checkpoint may blocks cell cycle progression (in G1, G2 or metaphase) or slow the rate at which S phase proceeds." [GOC:mtg_cell_cycle] synonym: "DNA damage response, signal transduction resulting in cell cycle arrest" NARROW [] xref: Wikipedia:DNA_damage_checkpoint xref: Wikipedia:Postreplication_checkpoint is_a: GO:0006974 ! cellular response to DNA damage stimulus is_a: GO:0031570 ! DNA integrity checkpoint [Term] id: GO:0000078 name: obsolete cytokinesis after mitosis checkpoint namespace: biological_process def: "OBSOLETE. A mitotic cell cycle checkpoint that detects whether chromosome segregation is complete and negatively regulates cytokinesis following mitosis." [GOC:mtg_cell_cycle] comment: The reason this term was made obsolete is that the two terms cytokinesis checkpoint (GO:0031565) and cytokinesis after mitosis (GO:0000078) were conflated in meaning. synonym: "cell morphogenesis checkpoint" EXACT [GOC:dph, GOC:vw] synonym: "cell shape checkpoint" EXACT [] is_obsolete: true consider: GO:0044878 consider: GO:0044879 [Term] id: GO:0000079 name: regulation of cyclin-dependent protein serine/threonine kinase activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity." [GOC:go_curators, GOC:pr] synonym: "regulation of CDK activity" EXACT [] synonym: "regulation of cyclin-dependent protein kinase activity" BROAD [] is_a: GO:0071900 ! regulation of protein serine/threonine kinase activity is_a: GO:1904029 ! regulation of cyclin-dependent protein kinase activity intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0004693 ! cyclin-dependent protein serine/threonine kinase activity relationship: regulates GO:0004693 ! cyclin-dependent protein serine/threonine kinase activity [Term] id: GO:0000080 name: mitotic G1 phase namespace: biological_process def: "The cell cycle 'gap' phase which is the interval between the completion of DNA segregation by mitosis and the beginning of DNA synthesis." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate synonym: "G1 phase of mitotic cell cycle" EXACT [] xref: Reactome:REACT_101162 "G1 Phase, Bos taurus" xref: Reactome:REACT_1590 "G1 Phase, Homo sapiens" xref: Reactome:REACT_29795 "G1 Phase, Taeniopygia guttata" xref: Reactome:REACT_34060 "G1 Phase, Canis familiaris" xref: Reactome:REACT_78665 "G1 Phase, Gallus gallus" xref: Reactome:REACT_78866 "G1 Phase, Sus scrofa" xref: Reactome:REACT_83686 "G1 Phase, Danio rerio" xref: Reactome:REACT_91654 "G1 Phase, Mus musculus" xref: Reactome:REACT_93384 "G1 Phase, Rattus norvegicus" xref: Reactome:REACT_93574 "G1 Phase, Xenopus tropicalis" is_a: GO:0051318 ! G1 phase relationship: part_of GO:0051329 ! mitotic interphase [Term] id: GO:0000082 name: G1/S transition of mitotic cell cycle namespace: biological_process def: "The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated." [GOC:mtg_cell_cycle] xref: Reactome:REACT_101799 "G1/S Transition, Taeniopygia guttata" xref: Reactome:REACT_102687 "G1/S Transition, Arabidopsis thaliana" xref: Reactome:REACT_104020 "G1/S Transition, Canis familiaris" xref: Reactome:REACT_104529 "G1/S Transition, Schizosaccharomyces pombe" xref: Reactome:REACT_104577 "G1/S Transition, Saccharomyces cerevisiae" xref: Reactome:REACT_106054 "G1/S Transition, Mus musculus" xref: Reactome:REACT_107492 "G1/S Transition, Dictyostelium discoideum" xref: Reactome:REACT_109784 "G1/S Transition, Oryza sativa" xref: Reactome:REACT_109821 "G1/S Transition, Danio rerio" xref: Reactome:REACT_110917 "G1/S Transition, Plasmodium falciparum" xref: Reactome:REACT_1783 "G1/S Transition, Homo sapiens" xref: Reactome:REACT_28713 "G1/S Transition, Xenopus tropicalis" xref: Reactome:REACT_45711 "G1/S Transition, Caenorhabditis elegans" xref: Reactome:REACT_84226 "G1/S Transition, Gallus gallus" xref: Reactome:REACT_85355 "G1/S Transition, Sus scrofa" xref: Reactome:REACT_87037 "G1/S Transition, Drosophila melanogaster" xref: Reactome:REACT_88046 "G1/S Transition, Bos taurus" xref: Reactome:REACT_95294 "G1/S Transition, Rattus norvegicus" is_a: GO:0044772 ! mitotic cell cycle phase transition is_a: GO:0044843 ! cell cycle G1/S phase transition [Term] id: GO:0000083 name: regulation of transcription involved in G1/S transition of mitotic cell cycle namespace: biological_process def: "Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle." [GOC:mtg_cell_cycle] xref: Reactome:REACT_683 "G1/S-Specific Transcription, Homo sapiens" is_a: GO:0006355 ! regulation of transcription, DNA-templated is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0006355 ! regulation of transcription, DNA-templated intersection_of: part_of GO:0000082 ! G1/S transition of mitotic cell cycle relationship: part_of GO:0000082 ! G1/S transition of mitotic cell cycle [Term] id: GO:0000084 name: mitotic S phase namespace: biological_process def: "The cell cycle phase, following G1, during which DNA synthesis takes place as part of a mitotic cell cycle." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate synonym: "S phase of mitotic cell cycle" EXACT [] synonym: "S-phase of mitotic cell cycle" EXACT [] xref: Reactome:REACT_105829 "S Phase, Caenorhabditis elegans" xref: Reactome:REACT_108550 "S Phase, Rattus norvegicus" xref: Reactome:REACT_110039 "S Phase, Schizosaccharomyces pombe" xref: Reactome:REACT_28988 "S Phase, Taeniopygia guttata" xref: Reactome:REACT_32013 "S Phase, Mycobacterium tuberculosis" xref: Reactome:REACT_34043 "S Phase, Oryza sativa" xref: Reactome:REACT_78838 "S Phase, Plasmodium falciparum" xref: Reactome:REACT_78845 "S Phase, Xenopus tropicalis" xref: Reactome:REACT_81914 "S Phase, Saccharomyces cerevisiae" xref: Reactome:REACT_82813 "S Phase, Arabidopsis thaliana" xref: Reactome:REACT_85811 "S Phase, Sus scrofa" xref: Reactome:REACT_89318 "S Phase, Drosophila melanogaster" xref: Reactome:REACT_899 "S Phase, Homo sapiens" xref: Reactome:REACT_92500 "S Phase, Mus musculus" xref: Reactome:REACT_92759 "S Phase, Canis familiaris" xref: Reactome:REACT_95174 "S Phase, Gallus gallus" xref: Reactome:REACT_96081 "S Phase, Dictyostelium discoideum" xref: Reactome:REACT_97603 "S Phase, Danio rerio" xref: Reactome:REACT_99645 "S Phase, Bos taurus" is_a: GO:0051320 ! S phase relationship: part_of GO:0051329 ! mitotic interphase [Term] id: GO:0000085 name: mitotic G2 phase namespace: biological_process def: "The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate synonym: "G2 phase of mitotic cell cycle" EXACT [] xref: Reactome:REACT_105223 "G2 Phase, Mus musculus" xref: Reactome:REACT_105307 "G2 Phase, Canis familiaris" xref: Reactome:REACT_106415 "G2 Phase, Xenopus tropicalis" xref: Reactome:REACT_106836 "G2 Phase, Bos taurus" xref: Reactome:REACT_1915 "G2 Phase, Homo sapiens" xref: Reactome:REACT_28975 "G2 Phase, Rattus norvegicus" xref: Reactome:REACT_85928 "G2 Phase, Sus scrofa" xref: Reactome:REACT_96332 "G2 Phase, Danio rerio" is_a: GO:0051319 ! G2 phase relationship: part_of GO:0051329 ! mitotic interphase [Term] id: GO:0000086 name: G2/M transition of mitotic cell cycle namespace: biological_process def: "The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex." [GOC:mtg_cell_cycle] synonym: "mitotic G2/M transition" EXACT [] xref: Reactome:REACT_100942 "G2/M Transition, Danio rerio" xref: Reactome:REACT_103766 "G2/M Transition, Schizosaccharomyces pombe" xref: Reactome:REACT_107882 "G2/M Transition, Sus scrofa" xref: Reactome:REACT_114616 "G2/M Transition, Arabidopsis thaliana" xref: Reactome:REACT_2203 "G2/M Transition, Homo sapiens" xref: Reactome:REACT_28929 "G2/M Transition, Xenopus tropicalis" xref: Reactome:REACT_30388 "G2/M Transition, Gallus gallus" xref: Reactome:REACT_34062 "G2/M Transition, Mus musculus" xref: Reactome:REACT_77778 "G2/M Transition, Taeniopygia guttata" xref: Reactome:REACT_83880 "G2/M Transition, Drosophila melanogaster" xref: Reactome:REACT_87036 "G2/M Transition, Saccharomyces cerevisiae" xref: Reactome:REACT_87230 "G2/M Transition, Canis familiaris" xref: Reactome:REACT_87807 "G2/M Transition, Dictyostelium discoideum" xref: Reactome:REACT_88018 "G2/M Transition, Caenorhabditis elegans" xref: Reactome:REACT_88369 "G2/M Transition, Rattus norvegicus" xref: Reactome:REACT_92702 "G2/M Transition, Bos taurus" is_a: GO:0044772 ! mitotic cell cycle phase transition is_a: GO:0044839 ! cell cycle G2/M phase transition intersection_of: GO:0044839 ! cell cycle G2/M phase transition intersection_of: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0000278 ! mitotic cell cycle [Term] id: GO:0000087 name: mitotic M phase namespace: biological_process def: "A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase and occurs as part of a mitotic cell cycle." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate synonym: "M phase of mitotic cell cycle" EXACT [] synonym: "M-phase of mitotic cell cycle" EXACT [] xref: Reactome:REACT_105412 "M Phase, Mus musculus" xref: Reactome:REACT_107095 "M Phase, Dictyostelium discoideum" xref: Reactome:REACT_109059 "M Phase, Saccharomyces cerevisiae" xref: Reactome:REACT_29488 "M Phase, Canis familiaris" xref: Reactome:REACT_33490 "M Phase, Caenorhabditis elegans" xref: Reactome:REACT_82055 "M Phase, Rattus norvegicus" xref: Reactome:REACT_87132 "M Phase, Bos taurus" xref: Reactome:REACT_88263 "M Phase, Xenopus tropicalis" xref: Reactome:REACT_910 "M Phase, Homo sapiens" xref: Reactome:REACT_92998 "M Phase, Danio rerio" xref: Reactome:REACT_93131 "M Phase, Schizosaccharomyces pombe" xref: Reactome:REACT_93566 "M Phase, Gallus gallus" xref: Reactome:REACT_93720 "M Phase, Drosophila melanogaster" xref: Reactome:REACT_94536 "M Phase, Taeniopygia guttata" is_a: GO:0000279 ! M phase is_a: GO:0098763 ! mitotic cell cycle phase intersection_of: GO:0000279 ! M phase intersection_of: happens_during GO:0000278 ! mitotic cell cycle relationship: happens_during GO:0000278 ! mitotic cell cycle [Term] id: GO:0000088 name: mitotic prophase namespace: biological_process def: "The cell cycle phase which is the first stage of M phase of mitosis and during which chromosomes condense and the two daughter centrioles and their asters migrate toward the poles of the cell." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate xref: Reactome:REACT_100605 "Mitotic Prophase, Saccharomyces cerevisiae" xref: Reactome:REACT_102122 "Mitotic Prophase, Mus musculus" xref: Reactome:REACT_105127 "Mitotic Prophase, Danio rerio" xref: Reactome:REACT_106058 "Mitotic Prophase, Drosophila melanogaster" xref: Reactome:REACT_28443 "Mitotic Prophase, Taeniopygia guttata" xref: Reactome:REACT_28607 "Mitotic Prophase, Rattus norvegicus" xref: Reactome:REACT_32677 "Mitotic Prophase, Xenopus tropicalis" xref: Reactome:REACT_765 "Mitotic Prophase, Homo sapiens" xref: Reactome:REACT_79474 "Mitotic Prophase, Caenorhabditis elegans" xref: Reactome:REACT_80300 "Mitotic Prophase, Gallus gallus" xref: Reactome:REACT_83888 "Mitotic Prophase, Dictyostelium discoideum" xref: Reactome:REACT_90347 "Mitotic Prophase, Canis familiaris" xref: Reactome:REACT_90481 "Mitotic Prophase, Schizosaccharomyces pombe" is_a: GO:0051324 ! prophase relationship: part_of GO:0000087 ! mitotic M phase [Term] id: GO:0000089 name: mitotic metaphase namespace: biological_process def: "The cell cycle phase, following prophase, during which chromosomes become aligned on the equatorial plate of the cell as part of a mitotic cell cycle." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate xref: Reactome:REACT_434 "Mitotic Metaphase, Homo sapiens" is_a: GO:0051323 ! metaphase relationship: part_of GO:0000087 ! mitotic M phase [Term] id: GO:0000090 name: mitotic anaphase namespace: biological_process def: "The cell cycle phase during which chromosomes separate and migrate towards the poles of the spindle the as part of a mitotic cell cycle." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate xref: Reactome:REACT_1275 "Mitotic Anaphase, Homo sapiens" is_a: GO:0051322 ! anaphase relationship: part_of GO:0000087 ! mitotic M phase [Term] id: GO:0000091 name: mitotic anaphase A namespace: biological_process def: "The cell cycle phase during which the kinetochore microtubules shorten as chromosomes move toward the spindle poles as part of mitosis." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate is_a: GO:0000090 ! mitotic anaphase [Term] id: GO:0000092 name: mitotic anaphase B namespace: biological_process def: "The cell cycle phase during which the polar microtubules elongate and the two poles of the spindle move farther apart as part of mitosis." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate is_a: GO:0000090 ! mitotic anaphase [Term] id: GO:0000093 name: mitotic telophase namespace: biological_process def: "The cell cycle phase which follows anaphase during M phase of mitosis and during which the chromosomes arrive at the poles of the cell and the division of the cytoplasm starts." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate is_a: GO:0051326 ! telophase relationship: part_of GO:0000087 ! mitotic M phase [Term] id: GO:0000094 name: obsolete septin assembly and septum formation namespace: biological_process def: "OBSOLETE (was not defined before being made obsolete)." [GOC:go_curators] comment: This term was made obsolete because it was not defined and the string name implied two separate processes. synonym: "septin assembly and septum formation" EXACT [] is_obsolete: true consider: GO:0000917 consider: GO:0000918 consider: GO:0000921 [Term] id: GO:0000095 name: S-adenosyl-L-methionine transmembrane transporter activity namespace: molecular_function alt_id: GO:0015177 def: "Enables the transfer of S-adenosylmethionine from one side of a membrane to the other. S-adenosylmethionine is S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism." [GOC:ai] synonym: "S-adenosyl methionine permease activity" EXACT [] synonym: "S-adenosyl methionine transporter activity" EXACT [] synonym: "S-adenosylmethionine permease activity" EXACT [] synonym: "S-adenosylmethionine transmembrane transporter activity" EXACT [] synonym: "S-adenosylmethionine transporter activity" BROAD [] synonym: "SAM transmembrane transporter activity" EXACT [] is_a: GO:0051185 ! coenzyme transporter activity is_a: GO:0072349 ! modified amino acid transmembrane transporter activity is_a: GO:1901682 ! sulfur compound transmembrane transporter activity relationship: part_of GO:1901962 ! S-adenosyl-L-methionine transmembrane transport [Term] id: GO:0000096 name: sulfur amino acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving amino acids containing sulfur, comprising cysteine, homocysteine, methionine and selenocysteine." [GOC:ai] subset: gosubset_prok synonym: "sulfur amino acid metabolism" EXACT [] synonym: "sulphur amino acid metabolic process" EXACT [] synonym: "sulphur amino acid metabolism" EXACT [] xref: Reactome:REACT_115639 "Sulfur amino acid metabolism, Homo sapiens" xref: Reactome:REACT_118084 "Sulfur amino acid metabolism, Rattus norvegicus" xref: Reactome:REACT_118094 "Sulfur amino acid metabolism, Bos taurus" xref: Reactome:REACT_118099 "Sulfur amino acid metabolism, Escherichia coli" xref: Reactome:REACT_118166 "Sulfur amino acid metabolism, Taeniopygia guttata" xref: Reactome:REACT_118184 "Sulfur amino acid metabolism, Canis familiaris" xref: Reactome:REACT_118203 "Sulfur amino acid metabolism, Sus scrofa" xref: Reactome:REACT_118227 "Sulfur amino acid metabolism, Mycobacterium tuberculosis" xref: Reactome:REACT_118256 "Sulfur amino acid metabolism, Staphylococcus aureus N315" xref: Reactome:REACT_118291 "Sulfur amino acid metabolism, Caenorhabditis elegans" xref: Reactome:REACT_118309 "Sulfur amino acid metabolism, Gallus gallus" xref: Reactome:REACT_118314 "Sulfur amino acid metabolism, Arabidopsis thaliana" xref: Reactome:REACT_118323 "Sulfur amino acid metabolism, Xenopus tropicalis" xref: Reactome:REACT_118328 "Sulfur amino acid metabolism, Drosophila melanogaster" xref: Reactome:REACT_118349 "Sulfur amino acid metabolism, Oryza sativa" xref: Reactome:REACT_118370 "Sulfur amino acid metabolism, Mus musculus" xref: Reactome:REACT_118388 "Sulfur amino acid metabolism, Saccharomyces cerevisiae" xref: Reactome:REACT_118463 "Sulfur amino acid metabolism, Schizosaccharomyces pombe" xref: Reactome:REACT_118518 "Sulfur amino acid metabolism, Dictyostelium discoideum" xref: Reactome:REACT_118541 "Sulfur amino acid metabolism, Danio rerio" xref: Reactome:REACT_27187 "Sulfur amino acid metabolism, Mycobacterium tuberculosis" is_a: GO:0006082 ! organic acid metabolic process is_a: GO:0006790 ! sulfur compound metabolic process is_a: GO:1901564 ! organonitrogen compound metabolic process [Term] id: GO:0000097 name: sulfur amino acid biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of amino acids containing sulfur, comprising cysteine, methionine and selenocysteine." [GOC:ai] subset: gosubset_prok synonym: "sulfur amino acid anabolism" EXACT [] synonym: "sulfur amino acid biosynthesis" EXACT [] synonym: "sulfur amino acid formation" EXACT [] synonym: "sulfur amino acid synthesis" EXACT [] synonym: "sulphur amino acid biosynthesis" EXACT [] synonym: "sulphur amino acid biosynthetic process" EXACT [] is_a: GO:0000096 ! sulfur amino acid metabolic process is_a: GO:0016053 ! organic acid biosynthetic process is_a: GO:0044272 ! sulfur compound biosynthetic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process [Term] id: GO:0000098 name: sulfur amino acid catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of amino acids containing sulfur, comprising cysteine, methionine and selenocysteine." [GOC:ai] subset: gosubset_prok synonym: "sulfur amino acid breakdown" EXACT [] synonym: "sulfur amino acid catabolism" EXACT [] synonym: "sulfur amino acid degradation" EXACT [] synonym: "sulphur amino acid catabolic process" EXACT [] synonym: "sulphur amino acid catabolism" EXACT [] xref: Reactome:REACT_115654 "Degradation of cysteine and homocysteine, Homo sapiens" is_a: GO:0000096 ! sulfur amino acid metabolic process is_a: GO:0016054 ! organic acid catabolic process is_a: GO:0044273 ! sulfur compound catabolic process is_a: GO:1901565 ! organonitrogen compound catabolic process [Term] id: GO:0000099 name: sulfur amino acid transmembrane transporter activity namespace: molecular_function def: "Enables the transfer of sulfur amino acids from one side of a membrane to the other. Sulphur amino acids contain sulfur in the form of cystine, methionine or their derivatives." [GOC:ai, GOC:mtg_transport, ISBN:0815340729] subset: gosubset_prok synonym: "sulfur amino acid transporter activity" BROAD [] synonym: "sulphur amino acid transmembrane transporter activity" EXACT [] synonym: "sulphur amino acid transporter activity" BROAD [] is_a: GO:0015171 ! amino acid transmembrane transporter activity is_a: GO:1901682 ! sulfur compound transmembrane transporter activity [Term] id: GO:0000100 name: S-methylmethionine transmembrane transporter activity namespace: molecular_function alt_id: GO:0015178 def: "Catalysis of the transfer of S-methylmethionine from one side of a membrane to the other." [GOC:ai] subset: gosubset_prok synonym: "S-methylmethionine permease activity" EXACT [] synonym: "S-methylmethionine transporter activity" BROAD [] is_a: GO:0000099 ! sulfur amino acid transmembrane transporter activity is_a: GO:0072349 ! modified amino acid transmembrane transporter activity relationship: part_of GO:0015806 ! S-methylmethionine transport [Term] id: GO:0000101 name: sulfur amino acid transport namespace: biological_process def: "The directed movement of amino acids containing sulfur (cystine, methionine and their derivatives) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: gosubset_prok synonym: "sulphur amino acid transport" EXACT [] is_a: GO:0006865 ! amino acid transport is_a: GO:0072348 ! sulfur compound transport [Term] id: GO:0000102 name: L-methionine secondary active transmembrane transporter activity namespace: molecular_function def: "Catalysis of the transfer of L-methionine from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy. Chemiosmotic sources of energy include uniport, symport or antiport." [GOC:mtg_transport] synonym: "L-methionine porter activity" RELATED [] is_a: GO:0005294 ! neutral L-amino acid secondary active transmembrane transporter activity is_a: GO:0015191 ! L-methionine transmembrane transporter activity is_a: GO:1901680 ! sulfur-containing amino acid secondary active transmembrane transporter activity [Term] id: GO:0000103 name: sulfate assimilation namespace: biological_process alt_id: GO:0019378 def: "The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds." [GOC:jl] subset: gosubset_prok synonym: "sulfate assimilation, phosphoadenylyl sulfate reduction by an oxidoreductase, acting on sulfur group of donors, NAD or NADP as acceptor" NARROW [] synonym: "sulphate assimilation" EXACT [] synonym: "sulphate assimilation, phosphoadenylyl sulphate reduction by an oxidoreductase, acting on sulphur group of donors, NAD or NADP as acceptor" NARROW [] xref: Reactome:REACT_27155 "Sulfate assimilation, Mycobacterium tuberculosis" is_a: GO:0006790 ! sulfur compound metabolic process [Term] id: GO:0000104 name: succinate dehydrogenase activity namespace: molecular_function alt_id: GO:0019739 def: "Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor." [EC:1.3.99.1, GOC:kd] subset: gosubset_prok synonym: "fumarate dehydrogenase activity" EXACT [EC:1.3.99.1] synonym: "fumarate reductase activity" EXACT [EC:1.3.99.1] synonym: "fumaric hydrogenase activity" EXACT [EC:1.3.99.1] synonym: "succinate oxidoreductase activity" EXACT [EC:1.3.99.1] synonym: "succinate:(acceptor) oxidoreductase activity" EXACT [EC:1.3.99.1] synonym: "succinate:acceptor oxidoreductase activity" EXACT [EC:1.3.99.1] synonym: "succinic acid dehydrogenase activity" EXACT [EC:1.3.99.1] synonym: "succinic dehydrogenase activity" BROAD [EC:1.3.99.1] synonym: "succinodehydrogenase activity" EXACT [EC:1.3.99.1] synonym: "succinyl dehydrogenase activity" EXACT [EC:1.3.99.1] xref: EC:1.3.99.1 xref: MetaCyc:SUCC-FUM-OXRED-RXN xref: RHEA:16360 is_a: GO:0016627 ! oxidoreductase activity, acting on the CH-CH group of donors [Term] id: GO:0000105 name: histidine biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of histidine, 2-amino-3-(1H-imidazol-4-yl)propanoic acid." [GOC:go_curators] subset: gosubset_prok synonym: "histidine anabolism" EXACT [] synonym: "histidine biosynthesis" EXACT [] synonym: "histidine formation" EXACT [] synonym: "histidine synthesis" EXACT [] xref: MetaCyc:HISTSYN-PWY is_a: GO:0006547 ! histidine metabolic process is_a: GO:0008652 ! cellular amino acid biosynthetic process [Term] id: GO:0000107 name: imidazoleglycerol-phosphate synthase activity namespace: molecular_function def: "Catalysis of the reaction: phosphoribulosylformimino-AICAR-P + L-glutamine = D-erythro-imidazole-glycerol-phosphate + aminoimidazole carboxamide ribonucleotide + L-glutamate + 2 H(+)." [MetaCyc:GLUTAMIDOTRANS-RXN] subset: gosubset_prok synonym: "glutamine amidotransferase:cyclase activity" BROAD [] synonym: "imidazole glycerol phosphate synthase activity" EXACT [] synonym: "imidazole-glycerol-phosphate synthase activity" RELATED [] synonym: "imidazoleglycerol phosphate synthase activity" EXACT [] xref: EC:2.4.2.- xref: MetaCyc:GLUTAMIDOTRANS-RXN is_a: GO:0016763 ! transferase activity, transferring pentosyl groups [Term] id: GO:0000108 name: obsolete repairosome namespace: cellular_component def: "OBSOLETE. A stable complex of proteins that carry out the DNA damage recognition and incision reactions characteristic of nucleotide excision repair (NER), such as DNA damage recognition, DNA helix unwinding, and endonucleolytic cleavage at sites flanking damaged DNA; includes TFIIH subunits and additional polypeptides; may form in the absence of DNA damage." [PMID:10681587, PMID:9852079] comment: This term was made obsolete because 'repairosome' has fallen out of use in the literature, and the large complex described in the definition has not been confirmed to exist. The term has also confused annotators. synonym: "repairosome" EXACT [] is_obsolete: true replaced_by: GO:0000109 [Term] id: GO:0000109 name: nucleotide-excision repair complex namespace: cellular_component def: "Any complex formed of proteins that act in nucleotide-excision repair." [PMID:10915862] comment: Note that process information is included in the term and definition for the purpose of describing and distinguishing the complex. subset: goslim_pir synonym: "UvrB-UvrC complex" NARROW [PMID:12145219] synonym: "UvrBC complex" NARROW [GOC:bm, PMID:12145219] is_a: GO:0044428 ! nuclear part is_a: GO:1990391 ! DNA repair complex [Term] id: GO:0000110 name: nucleotide-excision repair factor 1 complex namespace: cellular_component def: "One of several protein complexes involved in nucleotide-excision repair; possesses DNA damage recognition and endodeoxynuclease activities. In S. cerevisiae, it is composed of Rad1p, Rad10p, and Rad14p; in human the subunits are ERCC4/XPF, ERCC1 and XPA, respectively." [PMID:10915862] comment: Note that process and function information are included in the term and definition for the purpose of describing and distinguishing the complex. synonym: "NEF1 complex" EXACT [] synonym: "XPA-ERCC1-ERCC4 complex" EXACT [PMID:8197175] is_a: GO:0000109 ! nucleotide-excision repair complex [Term] id: GO:0000111 name: nucleotide-excision repair factor 2 complex namespace: cellular_component def: "One of several protein complexes involved in nucleotide-excision repair; possesses damaged DNA binding activity. In S. cerevisiae, it is composed of Rad4p and Rad23p." [PMID:10915862] comment: Note that process and function information are included in the term and definition for the purpose of describing and distinguishing the complex. synonym: "NEF2 complex" EXACT [] is_a: GO:0000109 ! nucleotide-excision repair complex [Term] id: GO:0000112 name: nucleotide-excision repair factor 3 complex namespace: cellular_component def: "One of several protein complexes involved in nucleotide-excision repair; possesses endodeoxynuclease and DNA helicase activities. In S. cerevisiae, it is composed of Rad2p and the core TFIIH-Ssl2p complex (core TFIIH is composed of Rad3p, Tfb1p, Tfb2p, Ssl1p, Tfb4p and Tfb5p. Note that Ssl2p is also called Rad25p)." [GOC:ew, PMID:10915862, PMID:14500720, PMID:7813015] comment: Note that process and function information are included in the term and definition for the purpose of describing and distinguishing the complex. synonym: "NEF3 complex" EXACT [] is_a: GO:0000109 ! nucleotide-excision repair complex relationship: has_part GO:0000439 ! core TFIIH complex [Term] id: GO:0000113 name: nucleotide-excision repair factor 4 complex namespace: cellular_component def: "One of several protein complexes involved in nucleotide-excision repair; possesses DNA damage recognition and DNA-dependent ATPase activities. In S. cerevisiae, it is composed of Rad7p and Rad16p." [PMID:10915862] comment: Note that process and function information are included in the term and definition for the purpose of describing and distinguishing the complex. synonym: "NEF4 complex" EXACT [] is_a: GO:0000109 ! nucleotide-excision repair complex [Term] id: GO:0000114 name: obsolete regulation of transcription involved in G1 phase of mitotic cell cycle namespace: biological_process def: "OBSOLETE. Any process that regulates transcription such that the target genes are transcribed as part of the G1 phase of the mitotic cell cycle." [GOC:dph, GOC:mah, GOC:tb] comment: This term was made obsolete because it is unclear exactly what it means. It could mean either 'regulation of transcription during phase X' or 'regulation of transition between phase X and phase Y'. synonym: "G1-specific transcription in mitotic cell cycle" RELATED [] synonym: "regulation of transcription from RNA polymerase II promoter during G1 phase of cell cycle" EXACT [] synonym: "regulation of transcription involved in G1 phase of mitotic cell cycle" EXACT [] is_obsolete: true consider: GO:0000083 [Term] id: GO:0000115 name: obsolete regulation of transcription involved in S phase of mitotic cell cycle namespace: biological_process def: "OBSOLETE. A cell cycle process that regulates transcription such that the target genes are transcribed as part of the S phase of the mitotic cell cycle." [GOC:dph, GOC:mah, GOC:tb] comment: This term was made obsolete because it is unclear exactly what it means. It could mean either 'regulation of transcription during phase X' or 'regulation of transition between phase X and phase Y'. synonym: "regulation of transcription from RNA polymerase II promoter during S-phase of mitotic cell cycle" RELATED [] synonym: "regulation of transcription involved in S phase of mitotic cell cycle" EXACT [] synonym: "regulation of transcription involved in S-phase of mitotic cell cycle" EXACT [] synonym: "S-phase-specific transcription in mitotic cell cycle" RELATED [] synonym: "S-specific transcription in mitotic cell cycle" EXACT [] is_obsolete: true [Term] id: GO:0000116 name: obsolete regulation of transcription involved in G2-phase of mitotic cell cycle namespace: biological_process def: "OBSOLETE. Any process that regulates transcription such that the target genes are transcribed as part of the G2 phase of the mitotic cell cycle." [GOC:dph, GOC:mah, GOC:tb] comment: This term was made obsolete because it is unclear exactly what it means. It could mean either 'regulation of transcription during phase X' or 'regulation of transition between phase X and phase Y'. synonym: "G2-specific transcription in mitotic cell cycle" RELATED [] synonym: "regulation of transcription from RNA polymerase II during G2-phase of mitotic cell cycle" RELATED [] synonym: "regulation of transcription involved in G2-phase of mitotic cell cycle" EXACT [] is_obsolete: true consider: GO:0000117 [Term] id: GO:0000117 name: regulation of transcription involved in G2/M transition of mitotic cell cycle namespace: biological_process def: "Any process that regulates transcription such that the target genes are transcribed as part of the G2/M transition of the mitotic cell cycle." [GOC:mtg_cell_cycle] synonym: "G2/M-specific transcription in mitotic cell cycle" RELATED [] synonym: "regulation of transcription from RNA polymerase II promoter during G2/M transition of mitotic cell cycle" RELATED [] is_a: GO:0006355 ! regulation of transcription, DNA-templated is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0006355 ! regulation of transcription, DNA-templated intersection_of: part_of GO:0000086 ! G2/M transition of mitotic cell cycle relationship: part_of GO:0000086 ! G2/M transition of mitotic cell cycle [Term] id: GO:0000118 name: histone deacetylase complex namespace: cellular_component def: "A protein complex that possesses histone deacetylase activity." [GOC:mah] comment: Note that this term represents a location, not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function of this complex is represented by the molecular function term 'histone deacetylase activity ; GO:0004407'. synonym: "HDAC complex" EXACT [] is_a: GO:0044451 ! nucleoplasm part is_a: GO:1902494 ! catalytic complex [Term] id: GO:0000120 name: RNA polymerase I transcription factor complex namespace: cellular_component def: "A transcription factor complex that acts at promoters of genes transcribed by RNA polymerase I." [GOC:mah] is_a: GO:0044452 ! nucleolar part is_a: GO:0044798 ! nuclear transcription factor complex [Term] id: GO:0000121 name: glycerol-1-phosphatase activity namespace: molecular_function def: "Catalysis of the reaction: glycerol-1-phosphate + H2O = glycerol + phosphate." [EC:3.1.3.21] synonym: "alpha-glycerol phosphatase activity" EXACT [EC:3.1.3.21] synonym: "alpha-glycerophosphatase activity" EXACT [EC:3.1.3.21] synonym: "glycerol 3-phosphatase activity" EXACT [EC:3.1.3.21] synonym: "glycerol 3-phosphate phosphohydrolase activity" EXACT [EC:3.1.3.21] synonym: "glycerol-1-phosphate phosphohydrolase activity" EXACT [EC:3.1.3.21] synonym: "glycerol-3-phosphate phosphatase activity" EXACT [EC:3.1.3.21] xref: EC:3.1.3.21 xref: MetaCyc:GLYCEROL-1-PHOSPHATASE-RXN xref: RHEA:11479 is_a: GO:0016791 ! phosphatase activity [Term] id: GO:0000122 name: negative regulation of transcription from RNA polymerase II promoter namespace: biological_process alt_id: GO:0010553 alt_id: GO:0045816 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:go_curators, GOC:txnOH] synonym: "down regulation of global transcription from RNA polymerase II promoter" RELATED [] synonym: "down regulation of transcription from RNA polymerase II promoter" EXACT [] synonym: "down-regulation of global transcription from RNA polymerase II promoter" RELATED [] synonym: "down-regulation of transcription from RNA polymerase II promoter" EXACT [] synonym: "downregulation of global transcription from RNA polymerase II promoter" RELATED [] synonym: "downregulation of transcription from RNA polymerase II promoter" EXACT [] synonym: "inhibition of global transcription from RNA polymerase II promoter" RELATED [] synonym: "inhibition of transcription from RNA polymerase II promoter" EXACT [] synonym: "negative regulation of gene-specific transcription from RNA polymerase II promoter" RELATED [] synonym: "negative regulation of global transcription from Pol II promoter" RELATED [] synonym: "negative regulation of transcription from Pol II promoter" EXACT [] synonym: "negative regulation of transcription from RNA polymerase II promoter, global" RELATED [] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0045892 ! negative regulation of transcription, DNA-templated intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter relationship: negatively_regulates GO:0006366 ! transcription from RNA polymerase II promoter [Term] id: GO:0000123 name: histone acetyltransferase complex namespace: cellular_component def: "A protein complex that possesses histone acetyltransferase activity." [GOC:mah] comment: Note that this term represents a location, not a function; the activity possessed by this complex is mentioned in the definition for the purpose of describing and distinguishing the complex. The function of this complex is represented by the molecular function term 'histone acetyltransferase activity ; GO:0004402'. synonym: "histone acetylase complex" EXACT [] is_a: GO:0031248 ! protein acetyltransferase complex is_a: GO:0044451 ! nucleoplasm part [Term] id: GO:0000124 name: SAGA complex namespace: cellular_component def: "A SAGA-type histone acetyltransferase complex that contains Spt8 (in budding yeast) or a homolog thereof; additional polypeptides include Spt group, consisting of Spt7, Spt3, and Spt20/Ada5, which interact with the TATA-binding protein (TBP); the Ada group, consisting of Ada1, Ada2, Ada3, Ada4/Gcn5, and Ada5/Spt20, which is functionally linked to the nucleosomal HAT activity; Tra1, an ATM/PI-3 kinase-related protein that targets DNA-bound activators for recruitment to promoters; the TBP-associated factor (TAF) proteins, consisting of Taf5, Taf6, Taf9, Taf10, and Taf12, which mediate nucleosomal HAT activity and are thought to help recruit the basal transcription machinery; the ubiquitin specifc protease Ubp-8." [PMID:10637607, PMID:17337012] {comment="PMID:19056896", comment="PMID:20838651"} synonym: "Spt-Ada-Gcn5-acetyltransferase complex" EXACT [] is_a: GO:0070461 ! SAGA-type complex is_a: GO:1905368 ! peptidase complex relationship: has_part GO:0071819 ! DUBm complex [Term] id: GO:0000125 name: PCAF complex namespace: cellular_component def: "A large multiprotein complex that possesses histone acetyltransferase activity and is involved in regulation of transcription. The composition is similar to that of the SAGA complex, but includes fewer Spt and Ada proteins, and more TAFs." [PMID:10637607] comment: See also the cellular component term 'SAGA complex ; GO:0000124'. synonym: "PCAF histone acetylase-associated complex" EXACT [] synonym: "SPT3-TAF9-PCAF acetylase complex" EXACT [GOC:rl, PMID:18838386] is_a: GO:0070461 ! SAGA-type complex [Term] id: GO:0000126 name: transcription factor TFIIIB complex namespace: cellular_component def: "A transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIB contains the TATA-binding protein (TBP) and two Pol III-specific proteins, B'' and BRF." [GOC:mah, PMID:11433012] is_a: GO:0090576 ! RNA polymerase III transcription factor complex [Term] id: GO:0000127 name: transcription factor TFIIIC complex namespace: cellular_component def: "A heterotrimeric transcription factor complex that is involved in regulating transcription from RNA polymerase III (Pol III) promoters. TFIIIC contains three conserved subunits that associate with the proximal Pol III promoter element, and additional subunits that associate with sequence elements downstream of the promoter and are more diverged among species. It also functions as a boundary element to partition genome content into distinct domains outside Pol III promoter regions." [GOC:mah, GOC:vw, PMID:11433012, PMID:16751097] is_a: GO:0090576 ! RNA polymerase III transcription factor complex [Term] id: GO:0000128 name: flocculation namespace: biological_process def: "The reversible, non-sexual aggregation of single-celled organisms in suspension to form aggregates of many cells known as flocs." [GOC:jl, GOC:vw, PMID:21114594, PMID:8740415] comment: The word floc derives from the Latin word floccus, which means a tuft of wool. subset: goslim_pir subset: gosubset_prok xref: Wikipedia:Flocculation is_a: GO:0098630 ! aggregation of unicellular organisms [Term] id: GO:0000131 name: incipient cellular bud site namespace: cellular_component def: "The portion of the budding yeast plasma membrane where a daughter cell will emerge. The yeast marks this spot with bud-site selection proteins before bud emergence occurs. Actin is polarized to this spot just prior to and during bud emergence." [GOC:clt] is_a: GO:0044424 ! intracellular part [Term] id: GO:0000132 name: establishment of mitotic spindle orientation namespace: biological_process alt_id: GO:0030607 alt_id: GO:0030609 def: "A cell cycle process that sets the alignment of mitotic spindle relative to other cellular structures." [GOC:ems] synonym: "establishment of spindle orientation during mitosis" RELATED [GOC:dph, GOC:tb] synonym: "establishment of spindle orientation involved in mitotic cell cycle" EXACT [GOC:dph, GOC:tb] synonym: "mitotic spindle orientation" EXACT [] synonym: "orienting of mitotic spindle" EXACT [] is_a: GO:0040001 ! establishment of mitotic spindle localization is_a: GO:0051294 ! establishment of spindle orientation intersection_of: GO:0051294 ! establishment of spindle orientation intersection_of: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0000278 ! mitotic cell cycle [Term] id: GO:0000133 name: polarisome namespace: cellular_component def: "Protein complex that plays a role in determining cell polarity by directing the localized assembly of actin filaments at polarization sites; in Saccharomyces the polarisome includes Bni1p, Spa2p, Pea2p, and Bud6p." [PMID:14734532, PMID:14998522, PMID:9632790] subset: goslim_pir is_a: GO:0043234 ! protein complex is_a: GO:0044448 ! cell cortex part relationship: part_of GO:0030427 ! site of polarized growth [Term] id: GO:0000136 name: alpha-1,6-mannosyltransferase complex namespace: cellular_component def: "A large, multiprotein complex with alpha-(1->6)-mannosyltransferase activity, located in the cis Golgi membrane; adds mannan to N-linked glycans on proteins." [GOC:mcc, PMID:10037752, PMID:11095735, PMID:18083825] is_a: GO:0031501 ! mannosyltransferase complex is_a: GO:0044431 ! Golgi apparatus part is_a: GO:0098796 ! membrane protein complex relationship: part_of GO:0000137 ! Golgi cis cisterna relationship: part_of GO:0030173 ! integral component of Golgi membrane [Term] id: GO:0000137 name: Golgi cis cisterna namespace: cellular_component def: "The Golgi cisterna closest to the endoplasmic reticulum; the first processing compartment through which proteins pass after export from the ER." [ISBN:0815316194] is_a: GO:0031985 ! Golgi cisterna [Term] id: GO:0000138 name: Golgi trans cisterna namespace: cellular_component def: "The Golgi cisterna farthest from the endoplasmic reticulum; the final processing compartment through which proteins pass before exiting the Golgi apparatus; the compartment in which N-linked protein glycosylation is completed." [ISBN:0815316194] synonym: "late Golgi" RELATED [GOC:mah] is_a: GO:0031985 ! Golgi cisterna [Term] id: GO:0000139 name: Golgi membrane namespace: cellular_component def: "The lipid bilayer surrounding any of the compartments of the Golgi apparatus." [GOC:mah] is_a: GO:0044431 ! Golgi apparatus part is_a: GO:0098588 ! bounding membrane of organelle [Term] id: GO:0000140 name: acylglycerone-phosphate reductase activity namespace: molecular_function def: "Catalysis of the reaction: 1-palmitoylglycerol-3-phosphate + NADP+ = palmitoylglycerone phosphate + NADPH + H(+)." [EC:1.1.1.101] synonym: "1-acyldihydroxyacetone-phosphate reductase activity" EXACT [] synonym: "1-palmitoylglycerol-3-phosphate:NADP+ oxidoreductase activity" EXACT [EC:1.1.1.101] synonym: "acyldihydroxyacetone phosphate reductase activity" EXACT [EC:1.1.1.101] synonym: "palmitoyl dihydroxyacetone phosphate reductase activity" EXACT [EC:1.1.1.101] synonym: "palmitoyl-dihydroxyacetone-phosphate reductase activity" EXACT [EC:1.1.1.101] synonym: "palmitoyldihydroxyacetone-phosphate reductase activity" EXACT [EC:1.1.1.101] xref: EC:1.1.1.101 xref: MetaCyc:ACYLGLYCERONE-PHOSPHATE-REDUCTASE-RXN xref: Reactome:REACT_759 "O-hexadecylglycerone phosphate + NADPH + H+ => 1-hexadecyl glycerol-3-phosphate + NADP+, Homo sapiens" xref: RHEA:17344 is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Term] id: GO:0000142 name: cellular bud neck contractile ring namespace: cellular_component def: "A contractile ring, i.e. a cytoskeletal structure composed of actin filaments and myosin, that forms beneath the plasma membrane at the mother-bud neck in mitotic cells that divide by budding in preparation for completing cytokinesis. An example of this structure is found in Saccharomyces cerevisiae." [GOC:krc, PMID:16009555] synonym: "neck ring" EXACT [] is_a: GO:0005826 ! actomyosin contractile ring intersection_of: GO:0005826 ! actomyosin contractile ring intersection_of: part_of GO:0005935 ! cellular bud neck relationship: part_of GO:0005935 ! cellular bud neck [Term] id: GO:0000144 name: cellular bud neck septin ring namespace: cellular_component def: "A ring-shaped structure that forms at the site of cytokinesis in the bud neck of a budding cell; composed of members of the conserved family of filament forming proteins called septins as well as septin-associated proteins. In S. cerevisiae, this structure forms at the time of bud emergence and the septins show a high rate of exchange." [GOC:krc, PMID:16009555] is_a: GO:0000399 ! cellular bud neck septin structure is_a: GO:0005940 ! septin ring is_a: GO:0032161 ! cleavage apparatus septin structure intersection_of: GO:0005940 ! septin ring intersection_of: part_of GO:0005935 ! cellular bud neck relationship: part_of GO:0005935 ! cellular bud neck [Term] id: GO:0000145 name: exocyst namespace: cellular_component def: "A protein complex peripherally associated with the plasma membrane that determines where vesicles dock and fuse. At least eight complex components are conserved between yeast and mammals." [PMID:15292201, PMID:27243008, PMID:9700152] synonym: "Sec6/8 complex" EXACT [] xref: Wikipedia:Exocyst is_a: GO:0044448 ! cell cortex part is_a: GO:0099023 ! tethring complex [Term] id: GO:0000146 name: microfilament motor activity namespace: molecular_function def: "Catalysis of movement along a microfilament, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP)." [GOC:mah, ISBN:0815316194] synonym: "actin filament motor activity" EXACT [GOC:dph] synonym: "actin-filament motor activity" EXACT [] synonym: "muscle motor activity" NARROW [] synonym: "myosin ATPase activity" RELATED [] xref: Reactome:REACT_15541 "Traversal of the cortical actin network and docking at plasma membrane, Homo sapiens" xref: Reactome:REACT_20539 "Traversal of the cortical actin network., Mus musculus" is_a: GO:0003774 ! motor activity [Term] id: GO:0000147 name: actin cortical patch assembly namespace: biological_process def: "Assembly of an actin cortical patch, a discrete actin-containing structure found at the plasma membrane of fungal cells." [GOC:mah] is_a: GO:0022607 ! cellular component assembly is_a: GO:0030866 ! cortical actin cytoskeleton organization is_a: GO:0044396 ! actin cortical patch organization [Term] id: GO:0000148 name: 1,3-beta-D-glucan synthase complex namespace: cellular_component def: "A protein complex that catalyzes the transfer of a glucose group from UDP-glucose to a (1->3)-beta-D-glucan chain." [EC:2.4.1.34] synonym: "(1->3)-beta-glucan synthase complex" EXACT [GOC:tb] synonym: "1,3-beta-glucan synthase complex" EXACT [GOC:tb] is_a: GO:0098797 ! plasma membrane protein complex is_a: GO:1990234 ! transferase complex [Term] id: GO:0000149 name: SNARE binding namespace: molecular_function def: "Interacting selectively and non-covalently with a SNARE (soluble N-ethylmaleimide-sensitive factor attached protein receptor) protein." [PMID:12642621] subset: goslim_chembl synonym: "SNAP receptor binding" EXACT [] xref: Reactome:REACT_100180 "Acetylcholine synaptic vesicle docking and priming, Rattus norvegicus" xref: Reactome:REACT_101078 "Noradrenalin synaptic vesicle docking and priming, Canis familiaris" xref: Reactome:REACT_103740 "Acetylcholine synaptic vesicle docking and priming, Canis familiaris" xref: Reactome:REACT_105540 "Vamp7 associated Lysosome to Plasma membrane transport, Mus musculus" xref: Reactome:REACT_106347 "release of L-Glutamate at the synapse, Canis familiaris" xref: Reactome:REACT_107235 "Vamp2 associated secretory vesicle to plasma membrane transport, Dictyostelium discoideum" xref: Reactome:REACT_107965 "Noradrenalin synaptic vesicle docking and priming, Mus musculus" xref: Reactome:REACT_109894 "Vamp7 associated Lysosome to Plasma membrane transport, Dictyostelium discoideum" xref: Reactome:REACT_110250 "Vamp2 associated secretory vesicle to plasma membrane transport, Canis familiaris" xref: Reactome:REACT_110371 "Release of noradrenaline at the synapse, Rattus norvegicus" xref: Reactome:REACT_110396 "Vamp7 associated Lysosome to Plasma membrane transport, Xenopus tropicalis" xref: Reactome:REACT_112169 "Acetylcholine synaptic vesicle docking and priming, Caenorhabditis elegans" xref: Reactome:REACT_112728 "Release of noradrenaline at the synapse, Caenorhabditis elegans" xref: Reactome:REACT_113606 "Glutamate synaptic vesicle docking and priming, Caenorhabditis elegans" xref: Reactome:REACT_113753 "Exocytosis of Insulin, Danio rerio" xref: Reactome:REACT_114225 "Noradrenalin synaptic vesicle docking and priming, Gallus gallus" xref: Reactome:REACT_114547 "Noradrenalin synaptic vesicle docking and priming, Caenorhabditis elegans" xref: Reactome:REACT_115054 "release of L-Glutamate at the synapse, Xenopus tropicalis" xref: Reactome:REACT_115130 "Acetylcholine synaptic vesicle docking and priming, Gallus gallus" xref: Reactome:REACT_115353 "Release of acetylcholine at the synapse, Xenopus tropicalis" xref: Reactome:REACT_12411 "release of L-Glutamate at the synapse, Homo sapiens" xref: Reactome:REACT_12617 "Glutamate synaptic vesicle docking and priming, Homo sapiens" xref: Reactome:REACT_14778 "Vamp7 associated Lysosome to Plasma membrane transport, Homo sapiens" xref: Reactome:REACT_14821 "Vamp8 associated secretory vesicle to plasma membrane transport, Homo sapiens" xref: Reactome:REACT_14822 "Vamp2 associated secretory vesicle to plasma membrane transport, Homo sapiens" xref: Reactome:REACT_15326 "Exocytosis of Insulin, Homo sapiens" xref: Reactome:REACT_15338 "Serotonin loaded synaptic vesicle docking and priming, Homo sapiens" xref: Reactome:REACT_15404 "Release of acetylcholine at the synapse, Homo sapiens" xref: Reactome:REACT_15411 "Noradrenalin synaptic vesicle docking and priming, Homo sapiens" xref: Reactome:REACT_15448 "Release of noradrenaline at the synapse, Homo sapiens" xref: Reactome:REACT_15483 "Acetylcholine synaptic vesicle docking and priming, Homo sapiens" xref: Reactome:REACT_15503 "Release of docked serotonin loaded synaptic vesicle, Homo sapiens" xref: Reactome:REACT_15517 "Dopamine synaptic vesicle docking and priming, Homo sapiens" xref: Reactome:REACT_15533 "Release of docked dopamine loaded synaptic vesicle, Homo sapiens" xref: Reactome:REACT_15541 "Traversal of the cortical actin network and docking at plasma membrane, Homo sapiens" xref: Reactome:REACT_23813 "Release of GABA at the synapse, Homo sapiens" xref: Reactome:REACT_23973 "GABA loaded synaptic vesicle Docking and Priming, Homo sapiens" xref: Reactome:REACT_29535 "Acetylcholine synaptic vesicle docking and priming, Danio rerio" xref: Reactome:REACT_31215 "Exocytosis of Insulin, Rattus norvegicus" xref: Reactome:REACT_31588 "Vamp2 associated secretory vesicle to plasma membrane transport, Danio rerio" xref: Reactome:REACT_34035 "Vamp2 associated secretory vesicle to plasma membrane transport, Mus musculus" xref: Reactome:REACT_77361 "Vamp2 associated secretory vesicle to plasma membrane transport, Sus scrofa" xref: Reactome:REACT_77506 "Glutamate synaptic vesicle docking and priming, Danio rerio" xref: Reactome:REACT_77785 "Vamp7 associated Lysosome to Plasma membrane transport, Danio rerio" xref: Reactome:REACT_77831 "release of L-Glutamate at the synapse, Mus musculus" xref: Reactome:REACT_79299 "Glutamate synaptic vesicle docking and priming, Mus musculus" xref: Reactome:REACT_80371 "Vamp2 associated secretory vesicle to plasma membrane transport, Bos taurus" xref: Reactome:REACT_82023 "Acetylcholine synaptic vesicle docking and priming, Mus musculus" xref: Reactome:REACT_82703 "Vamp7 associated Lysosome to Plasma membrane transport, Canis familiaris" xref: Reactome:REACT_83226 "Glutamate synaptic vesicle docking and priming, Rattus norvegicus" xref: Reactome:REACT_84308 "Release of noradrenaline at the synapse, Canis familiaris" xref: Reactome:REACT_84628 "Exocytosis of Insulin, Xenopus tropicalis" xref: Reactome:REACT_87193 "Glutamate synaptic vesicle docking and priming, Canis familiaris" xref: Reactome:REACT_87411 "Vamp8 associated secretory vesicle to plasma membrane transport, Canis familiaris" xref: Reactome:REACT_87768 "Vamp2 associated secretory vesicle to plasma membrane transport, Xenopus tropicalis" xref: Reactome:REACT_90536 "Vamp7 associated Lysosome to Plasma membrane transport, Arabidopsis thaliana" xref: Reactome:REACT_92466 "Vamp8 associated secretory vesicle to plasma membrane transport, Bos taurus" xref: Reactome:REACT_93575 "Release of acetylcholine at the synapse, Rattus norvegicus" xref: Reactome:REACT_93655 "Release of acetylcholine at the synapse, Canis familiaris" xref: Reactome:REACT_93705 "Noradrenalin synaptic vesicle docking and priming, Rattus norvegicus" xref: Reactome:REACT_94126 "Vamp8 associated secretory vesicle to plasma membrane transport, Danio rerio" xref: Reactome:REACT_94434 "Exocytosis of Insulin, Bos taurus" xref: Reactome:REACT_95323 "Vamp7 associated Lysosome to Plasma membrane transport, Oryza sativa" xref: Reactome:REACT_96543 "Glutamate synaptic vesicle docking and priming, Xenopus tropicalis" xref: Reactome:REACT_96609 "release of L-Glutamate at the synapse, Rattus norvegicus" xref: Reactome:REACT_96753 "Acetylcholine synaptic vesicle docking and priming, Xenopus tropicalis" xref: Reactome:REACT_96842 "Vamp8 associated secretory vesicle to plasma membrane transport, Mus musculus" xref: Reactome:REACT_97101 "Exocytosis of Insulin, Canis familiaris" xref: Reactome:REACT_98480 "Noradrenalin synaptic vesicle docking and priming, Xenopus tropicalis" xref: Reactome:REACT_98819 "Noradrenalin synaptic vesicle docking and priming, Danio rerio" xref: Reactome:REACT_99501 "Release of noradrenaline at the synapse, Mus musculus" is_a: GO:0005515 ! protein binding [Term] id: GO:0000150 name: recombinase activity namespace: molecular_function def: "Catalysis of the identification and base-pairing of homologous sequences between single-stranded DNA and double-stranded DNA." [GOC:elh] comment: Note that this term represents activities that do not break or form phosphodiester bonds, and is therefore not a parent of 'site-specific recombinase activity ; GO:0009009'. subset: goslim_metagenomics subset: gosubset_prok synonym: "strand transferase" NARROW [] xref: Reactome:REACT_27300 "Formation of Meiotic Heteroduplex, Homo sapiens" is_a: GO:0003824 ! catalytic activity relationship: part_of GO:0006310 ! DNA recombination [Term] id: GO:0000151 name: ubiquitin ligase complex namespace: cellular_component def: "A protein complex that includes a ubiquitin-protein ligase and enables ubiquitin protein ligase activity. The complex also contains other proteins that may confer substrate specificity on the complex." [GOC:jh2, PMID:9529603] subset: goslim_pir is_a: GO:0044424 ! intracellular part is_a: GO:1990234 ! transferase complex [Term] id: GO:0000152 name: nuclear ubiquitin ligase complex namespace: cellular_component def: "A ubiquitin ligase complex found in the nucleus." [GOC:mah] is_a: GO:0000151 ! ubiquitin ligase complex is_a: GO:0044428 ! nuclear part intersection_of: GO:0000151 ! ubiquitin ligase complex intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000153 name: cytoplasmic ubiquitin ligase complex namespace: cellular_component def: "A ubiquitin ligase complex found in the cytoplasm." [GOC:mah] is_a: GO:0000151 ! ubiquitin ligase complex is_a: GO:0044444 ! cytoplasmic part intersection_of: GO:0000151 ! ubiquitin ligase complex intersection_of: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0000154 name: rRNA modification namespace: biological_process alt_id: GO:0016548 def: "The covalent alteration of one or more nucleotides within an rRNA molecule to produce an rRNA molecule with a sequence that differs from that coded genetically." [GOC:curators] comment: The term 'RNA editing' (GO:0016547) was merged into 'RNA modification' (GO:0009451) on the basis of statements in the preface of Modification and Editing of RNA (ISBN:1555811337) that there is no clear distinction between modification and editing. Parallel changes were made for substrate (e.g. tRNA, rRNA, etc.) specific child terms of 'RNA editing'. subset: gosubset_prok synonym: "rRNA editing" NARROW [GOC:hjd] is_a: GO:0006364 ! rRNA processing is_a: GO:0009451 ! RNA modification [Term] id: GO:0000155 name: phosphorelay sensor kinase activity namespace: molecular_function def: "Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response." [GOC:bf, GOC:mcc, PMID:10966457, PMID:20223701, PMID:9191038] subset: gosubset_prok synonym: "two-component sensor activity" NARROW [] synonym: "two-component sensor molecule" NARROW [] synonym: "two-component system sensor activity" NARROW [] xref: EC:2.7.3.- is_a: GO:0004673 ! protein histidine kinase activity is_a: GO:0038023 ! signaling receptor activity relationship: part_of GO:0000160 ! phosphorelay signal transduction system relationship: part_of GO:0023014 ! signal transduction by protein phosphorylation [Term] id: GO:0000156 name: phosphorelay response regulator activity namespace: molecular_function def: "Responds to a phosphorelay sensor to initiate a change in cell state or activity. The activity of the response regulator is regulated by transfer of a phosphate from a histidine residue in the sensor, to an aspartate residue in the response regulator. Many but not all response regulators act as transcriptional regulators to elicit a response." [GOC:bf, PMID:10966457, PMID:11842140] subset: gosubset_prok synonym: "two-component response regulator activity" NARROW [] is_a: GO:0004871 ! signal transducer activity relationship: part_of GO:0000160 ! phosphorelay signal transduction system relationship: part_of GO:0035556 ! intracellular signal transduction [Term] id: GO:0000159 name: protein phosphatase type 2A complex namespace: cellular_component def: "A protein complex that has protein serine/threonine phosphatase activity that is polycation-stimulated (PCS), being directly stimulated by protamine, polylysine, or histone H1; it constitutes a subclass of several enzymes activated by different histones and polylysine, and consists of catalytic, scaffolding, and regulatory subunits. The catalytic and scaffolding subunits form the core enzyme, and the holoenzyme also includes the regulatory subunit." [GOC:mah, ISBN:0198547684, PMID:17245430] synonym: "protein phosphatase 2 complex" RELATED [GOC:dph, GOC:rl] is_a: GO:0008287 ! protein serine/threonine phosphatase complex is_a: GO:0044424 ! intracellular part [Term] id: GO:0000160 name: phosphorelay signal transduction system namespace: biological_process def: "A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins." [PMID:9191038] subset: goslim_metagenomics subset: gosubset_prok synonym: "histidyl-aspartyl phosphorelay" EXACT [] synonym: "phosphorelay signal transduction system" NARROW [] is_a: GO:0035556 ! intracellular signal transduction [Term] id: GO:0000161 name: MAPK cascade involved in osmosensory signaling pathway namespace: biological_process def: "A MAPK cascade involved in signal transduction in response to change in osmotic conditions." [PMID:9561267] synonym: "High Osmolarity Glycerol (HOG) MAPK pathway" NARROW [PMID:20880736] synonym: "Hog1 MAPK pathway" NARROW [PMID:20880736] synonym: "MAPKKK cascade during osmolarity sensing" EXACT [] synonym: "MAPKKK cascade involved in osmosensory signaling pathway" EXACT [GOC:signaling] synonym: "MAPKKK cascade involved in osmosensory signalling pathway" EXACT [GOC:mah] synonym: "osmolarity sensing, MAPKKK cascade" EXACT [] is_a: GO:0000165 ! MAPK cascade intersection_of: GO:0000165 ! MAPK cascade intersection_of: part_of GO:0007231 ! osmosensory signaling pathway relationship: part_of GO:0007231 ! osmosensory signaling pathway [Term] id: GO:0000162 name: tryptophan biosynthetic process namespace: biological_process alt_id: GO:0009096 def: "The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate." [GOC:mah, ISBN:0471331309, MetaCyc:TRPSYN-PWY] subset: gosubset_prok synonym: "aromatic amino acid family biosynthetic process, anthranilate pathway" EXACT [] synonym: "tryptophan anabolism" EXACT [] synonym: "tryptophan biosynthesis" EXACT [] synonym: "tryptophan formation" EXACT [] synonym: "tryptophan synthesis" EXACT [] xref: MetaCyc:TRPSYN-PWY is_a: GO:0006568 ! tryptophan metabolic process is_a: GO:0009073 ! aromatic amino acid family biosynthetic process is_a: GO:0046219 ! indolalkylamine biosynthetic process is_a: GO:1901607 ! alpha-amino acid biosynthetic process [Term] id: GO:0000164 name: protein phosphatase type 1 complex namespace: cellular_component def: "A protein complex that possesses magnesium-dependent protein serine/threonine phosphatase (AMD phosphatase) activity, and consists of a catalytic subunit and one or more regulatory subunits that dictates the phosphatase's substrate specificity, function, and activity." [GOC:mah, GOC:ssd] is_a: GO:0008287 ! protein serine/threonine phosphatase complex is_a: GO:0044444 ! cytoplasmic part [Term] id: GO:0000165 name: MAPK cascade namespace: biological_process def: "An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell." [GOC:bf, GOC:mtg_signaling_feb11, PMID:20811974, PMID:9561267] comment: MAPK cascades lie downstream of many cell surface receptors and cooperate in transmitting various extracellular signals to the nucleus. One way by which the specificity of each cascade is regulated is through the existence of several distinct components in each tier of the different cascades. The cascades are typically named according to the component in the MAPK tier. synonym: "ERK/MAPK cascade" NARROW [] synonym: "MAP kinase cascade" EXACT [] synonym: "MAP kinase kinase kinase cascade" EXACT [] synonym: "MAPK signal transduction" EXACT [GOC:signaling] synonym: "MAPK signaling" RELATED [] synonym: "MAPK signalling" RELATED [] synonym: "MAPKKK cascade" EXACT [GOC:curators] synonym: "MAPKKK cascade during sporulation" NARROW [] synonym: "mitogen-activated protein kinase cascade" EXACT [GOC:bf] xref: Reactome:REACT_101634 "RAF/MAP kinase cascade, Bos taurus" xref: Reactome:REACT_107261 "RAF/MAP kinase cascade, Saccharomyces cerevisiae" xref: Reactome:REACT_107863 "RAF/MAP kinase cascade, Canis familiaris" xref: Reactome:REACT_108330 "RAF/MAP kinase cascade, Xenopus tropicalis" xref: Reactome:REACT_112235 "RAF/MAP kinase cascade, Dictyostelium discoideum" xref: Reactome:REACT_112942 "RAF/MAP kinase cascade, Arabidopsis thaliana" xref: Reactome:REACT_113285 "RAF/MAP kinase cascade, Oryza sativa" xref: Reactome:REACT_634 "RAF/MAP kinase cascade, Homo sapiens" xref: Reactome:REACT_79658 "RAF/MAP kinase cascade, Schizosaccharomyces pombe" xref: Reactome:REACT_85806 "RAF/MAP kinase cascade, Drosophila melanogaster" xref: Reactome:REACT_87028 "RAF/MAP kinase cascade, Danio rerio" xref: Reactome:REACT_87232 "RAF/MAP kinase cascade, Mus musculus" xref: Reactome:REACT_87855 "RAF/MAP kinase cascade, Rattus norvegicus" xref: Reactome:REACT_92078 "RAF/MAP kinase cascade, Sus scrofa" xref: Reactome:REACT_92987 "RAF/MAP kinase cascade, Caenorhabditis elegans" xref: Reactome:REACT_94585 "RAF/MAP kinase cascade, Taeniopygia guttata" xref: Reactome:REACT_94805 "RAF/MAP kinase cascade, Gallus gallus" xref: Wikipedia:MAPK_cascade xref: Wikipedia:Mitogen-activated_protein_kinase is_a: GO:0023014 ! signal transduction by protein phosphorylation is_a: GO:0035556 ! intracellular signal transduction [Term] id: GO:0000166 name: nucleotide binding namespace: molecular_function def: "Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose." [GOC:mah, ISBN:0198547684] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: gosubset_prok is_a: GO:0036094 ! small molecule binding is_a: GO:1901265 ! nucleoside phosphate binding [Term] id: GO:0000167 name: activation of MAPKKK activity involved in osmosensory signaling pathway namespace: biological_process def: "Any process that initiates the activity of the inactive enzyme MAP kinase kinase kinase during osmolarity sensing." [PMID:9561267] synonym: "activation of MAP kinase kinase kinase activity during osmolarity sensing" EXACT [] synonym: "activation of MAPKKK activity during osmolarity sensing" EXACT [] synonym: "activation of MAPKKK activity involved in osmosensory signalling pathway" EXACT [GOC:mah] synonym: "osmolarity sensing, activation of MAP kinase kinase kinase activity" EXACT [] synonym: "osmolarity sensing, activation of MAPKKK activity" EXACT [] is_a: GO:0000185 ! activation of MAPKKK activity is_a: GO:0047484 ! regulation of response to osmotic stress is_a: GO:0080135 ! regulation of cellular response to stress intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0038081 ! MAP kinase kinase kinase activity involved in osmosensory signaling pathway relationship: positively_regulates GO:0038081 ! MAP kinase kinase kinase activity involved in osmosensory signaling pathway [Term] id: GO:0000168 name: activation of MAPKK activity involved in osmosensory signaling pathway namespace: biological_process alt_id: GO:0007233 def: "Any process that initiates the activity of the inactive enzyme MAP kinase kinase during osmolarity sensing." [PMID:9561267] synonym: "activation of MAP kinase kinase activity during osmolarity sensing" EXACT [] synonym: "activation of MAPKK activity during osmolarity sensing" EXACT [] synonym: "activation of MAPKK activity involved in osmosensory signalling pathway" EXACT [GOC:mah] synonym: "activation of Pbs2 kinase" NARROW [] synonym: "osmolarity sensing, activation of MAP kinase kinase activity" EXACT [] synonym: "osmolarity sensing, activation of MAPKK activity" EXACT [] is_a: GO:0000186 ! activation of MAPKK activity is_a: GO:0047484 ! regulation of response to osmotic stress is_a: GO:0080135 ! regulation of cellular response to stress intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0038080 ! MAP kinase kinase activity involved in osmosensory signaling pathway relationship: positively_regulates GO:0038080 ! MAP kinase kinase activity involved in osmosensory signaling pathway [Term] id: GO:0000169 name: activation of MAPK activity involved in osmosensory signaling pathway namespace: biological_process def: "Any process that initiates the activity of the inactive enzyme MAP kinase activity during osmolarity sensing." [PMID:9561267] synonym: "activation of MAPK activity during osmolarity sensing" EXACT [] synonym: "activation of MAPK activity involved in osmosensory signalling pathway" EXACT [GOC:mah] synonym: "osmolarity sensing, activation of MAPK activity" EXACT [] is_a: GO:0000187 ! activation of MAPK activity is_a: GO:0047484 ! regulation of response to osmotic stress is_a: GO:0080135 ! regulation of cellular response to stress intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0038079 ! MAP kinase activity involved in osmosensory signaling pathway relationship: positively_regulates GO:0038079 ! MAP kinase activity involved in osmosensory signaling pathway [Term] id: GO:0000170 name: sphingosine hydroxylase activity namespace: molecular_function def: "Catalysis of the hydroxylation of sphingolipid long chain bases." [PMID:9556590] xref: Reactome:REACT_100351 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Danio rerio" xref: Reactome:REACT_103503 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Gallus gallus" xref: Reactome:REACT_104963 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Canis familiaris" xref: Reactome:REACT_115687 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Gallus gallus" xref: Reactome:REACT_19258 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Homo sapiens" xref: Reactome:REACT_29940 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Oryza sativa" xref: Reactome:REACT_31871 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Drosophila melanogaster" xref: Reactome:REACT_80095 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Bos taurus" xref: Reactome:REACT_82371 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Xenopus tropicalis" xref: Reactome:REACT_85471 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Dictyostelium discoideum" xref: Reactome:REACT_85651 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Sus scrofa" xref: Reactome:REACT_86222 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Arabidopsis thaliana" xref: Reactome:REACT_91283 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Schizosaccharomyces pombe" xref: Reactome:REACT_92284 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Rattus norvegicus" xref: Reactome:REACT_96037 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Taeniopygia guttata" xref: Reactome:REACT_97092 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Caenorhabditis elegans" xref: Reactome:REACT_99475 "dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O, Mus musculus" is_a: GO:0016491 ! oxidoreductase activity [Term] id: GO:0000171 name: ribonuclease MRP activity namespace: molecular_function def: "Catalysis of the site-specific cleavage of RNA by a catalytic RNA-mediated mechanism; substrates include the A3 site in the ITS1 of pre-rRNA." [PMID:17881380] synonym: "RNase MRP" EXACT [] xref: Wikipedia:RNase_MRP is_a: GO:0004540 ! ribonuclease activity [Term] id: GO:0000172 name: ribonuclease MRP complex namespace: cellular_component def: "A ribonucleoprotein complex that contains an RNA molecule of the snoRNA family, and cleaves the rRNA precursor as part of rRNA transcript processing. It also has other roles: In S. cerevisiae it is involved in cell cycle-regulated degradation of daughter cell-specific mRNAs, while in mammalian cells it also enters the mitochondria and processes RNAs to create RNA primers for DNA replication." [GOC:sgd_curators, PMID:10690410, PMID:14729943, PMID:7510714] synonym: "ribonuclease mitochondrial RNA processing complex" EXACT [] synonym: "RNase MRP complex" EXACT [] is_a: GO:0005732 ! small nucleolar ribonucleoprotein complex [Term] id: GO:0000173 name: inactivation of MAPK activity involved in osmosensory signaling pathway namespace: biological_process def: "Any process that terminates the activity of the active enzyme MAP kinase during osmolarity sensing." [PMID:9561267] synonym: "inactivation of MAPK activity during osmolarity sensing" EXACT [] synonym: "inactivation of MAPK activity involved in osmosensory signalling pathway" EXACT [GOC:mah] synonym: "osmolarity sensing, inactivation of MAPK" EXACT [] synonym: "osmolarity sensing, termination of MAPK activity" EXACT [] synonym: "termination of MAPK activity during osmolarity sensing" EXACT [] is_a: GO:0000188 ! inactivation of MAPK activity is_a: GO:0047484 ! regulation of response to osmotic stress is_a: GO:0080135 ! regulation of cellular response to stress intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007231 ! osmosensory signaling pathway relationship: negatively_regulates GO:0007231 ! osmosensory signaling pathway relationship: negatively_regulates GO:0038079 ! MAP kinase activity involved in osmosensory signaling pathway [Term] id: GO:0000174 name: obsolete inactivation of MAPK (mating sensu Saccharomyces) namespace: biological_process def: "OBSOLETE. Downregulation of MAP kinase activity in the context of transduction of mating pheromone signal, as described for Saccharomyces." [PMID:9561267] comment: This term was made obsolete because it is a gene product specific term. synonym: "inactivation of MAPK (mating sensu Saccharomyces)" EXACT [] is_obsolete: true replaced_by: GO:0000750 [Term] id: GO:0000175 name: 3'-5'-exoribonuclease activity namespace: molecular_function def: "Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule." [GOC:mah, ISBN:0198547684] subset: gosubset_prok synonym: "3'-5' exoribonuclease activity" EXACT [] xref: EC:3.1.13.- xref: Reactome:REACT_102966 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Schizosaccharomyces pombe" xref: Reactome:REACT_108214 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Sus scrofa" xref: Reactome:REACT_20588 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Homo sapiens" xref: Reactome:REACT_33991 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Dictyostelium discoideum" xref: Reactome:REACT_34078 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Danio rerio" xref: Reactome:REACT_78363 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Bos taurus" xref: Reactome:REACT_82118 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Rattus norvegicus" xref: Reactome:REACT_88115 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Arabidopsis thaliana" xref: Reactome:REACT_89880 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Oryza sativa" xref: Reactome:REACT_92153 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Caenorhabditis elegans" xref: Reactome:REACT_93499 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Drosophila melanogaster" xref: Reactome:REACT_95913 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Canis familiaris" xref: Reactome:REACT_95921 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Mus musculus" xref: Reactome:REACT_96267 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Taeniopygia guttata" xref: Reactome:REACT_99422 "3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex, Xenopus tropicalis" is_a: GO:0008408 ! 3'-5' exonuclease activity is_a: GO:0016896 ! exoribonuclease activity, producing 5'-phosphomonoesters [Term] id: GO:0000176 name: nuclear exosome (RNase complex) namespace: cellular_component def: "A ribonuclease complex that has 3-prime to 5-prime processive and distributive hydrolytic exoribonuclease activity and endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured." [PMID:17174896, PMID:20531386, PMID:26726035] synonym: "eukaryotic exosome multienzyme ribonuclease complex" EXACT [] synonym: "nuclear exosome (ribonuclease complex)" EXACT [] synonym: "nuclear exosome multienzyme ribonuclease complex" EXACT [] is_a: GO:0000178 ! exosome (RNase complex) is_a: GO:0044428 ! nuclear part intersection_of: GO:0000178 ! exosome (RNase complex) intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0005634 ! nucleus relationship: part_of GO:0031981 ! nuclear lumen [Term] id: GO:0000177 name: cytoplasmic exosome (RNase complex) namespace: cellular_component def: "A ribonuclease complex that has 3-prime to 5-prime processive hydrolytic exoribonuclease activity producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured." [PMID:17174896, PMID:20531386, PMID:26726035] synonym: "cytoplasmic exosome (ribonuclease complex)" EXACT [] synonym: "cytoplasmic exosome multienzyme ribonuclease complex" EXACT [] synonym: "prokaryotic exosome multienzyme ribonuclease complex" EXACT [] is_a: GO:0000178 ! exosome (RNase complex) is_a: GO:0044444 ! cytoplasmic part intersection_of: GO:0000178 ! exosome (RNase complex) intersection_of: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0000178 name: exosome (RNase complex) namespace: cellular_component def: "A ribonuclease complex that has 3-prime to 5-prime exoribonuclease activity and possibly endoribonuclease activity, producing 5-prime-phosphomonoesters. Participates in a multitude of cellular RNA processing and degradation events preventing nuclear export and/or translation of aberrant RNAs. Restricted to processing linear and circular single-stranded RNAs (ssRNA) only. RNAs with complex secondary structures may have to be unwound or pre-processed by co-factors prior to entering the complex, esp if the 3-prime end is structured." [PMID:17174896, PMID:20531386, PMID:26726035] comment: Note that this term should not be confused with 'exosome' used in the context of vesicles released from multivesicular bodies. subset: goslim_pir synonym: "exosome (ribonucleasease complex)" EXACT [] synonym: "exosome multienzyme ribonuclease complex" EXACT [] is_a: GO:0044424 ! intracellular part is_a: GO:1905354 ! exoribonuclease complex [Term] id: GO:0000179 name: rRNA (adenine-N6,N6-)-dimethyltransferase activity namespace: molecular_function alt_id: GO:0043790 def: "Catalysis of the dimethylation two adjacent A residues in the loop closing the 3'-terminal stem of the 18S rRNA, using S-adenosyl-L-methionine as a methyl donor." [ISBN:1555811337, PMID:10690410] subset: gosubset_prok synonym: "18S rRNA dimethylase activity" EXACT [] synonym: "dimethyladenosine transferase activity" EXACT [IMG:02532] synonym: "S-adenosylmethionine-6-N', N'-adenosyl(rRNA) dimethyltransferase activity" EXACT [IMG:02532] xref: EC:2.1.1.- is_a: GO:0008170 ! N-methyltransferase activity is_a: GO:0016433 ! rRNA (adenine) methyltransferase activity [Term] id: GO:0000180 name: obsolete cytosolic large ribosomal subunit namespace: cellular_component def: "OBSOLETE (was not defined before being made obsolete)." [GOC:ai] comment: This term was made obsolete because more specific children exist. synonym: "cytosolic large ribosomal subunit" EXACT [] is_obsolete: true consider: GO:0022625 [Term] id: GO:0000181 name: obsolete cytosolic small ribosomal subunit namespace: cellular_component def: "OBSOLETE (was not defined before being made obsolete)." [GOC:ai] comment: This term was made obsolete because more specific children exist. synonym: "cytosolic small ribosomal subunit" EXACT [] is_obsolete: true consider: GO:0022627 [Term] id: GO:0000182 name: rDNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with DNA sequences encoding ribosomal RNA." [GOC:mah] synonym: "ribosomal DNA binding" EXACT [] is_a: GO:1990837 ! sequence-specific double-stranded DNA binding [Term] id: GO:0000183 name: chromatin silencing at rDNA namespace: biological_process def: "Repression of transcription of ribosomal DNA by altering the structure of chromatin." [PMID:10219245] synonym: "chromatin silencing at ribosomal DNA" EXACT [] synonym: "heterochromatic silencing at rDNA" EXACT [] synonym: "rDNA chromatin silencing" EXACT [GOC:mah] is_a: GO:0006342 ! chromatin silencing [Term] id: GO:0000184 name: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay namespace: biological_process def: "The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins." [GOC:krc, GOC:ma, PMID:10025395] synonym: "mRNA breakdown, nonsense-mediated decay" EXACT [] synonym: "mRNA catabolic process, nonsense-mediated" EXACT [] synonym: "mRNA catabolism, nonsense-mediated" EXACT [] synonym: "mRNA degradation, nonsense-mediated decay" EXACT [] synonym: "nonsense-mediated mRNA decay" EXACT [] synonym: "nuclear mRNA catabolic process, nonsense-mediated decay" EXACT [] xref: Reactome:REACT_75886 "Nonsense-Mediated Decay, Homo sapiens" xref: Wikipedia:Nonsense-mediated_decay xref: Wikipedia:Nonsense-mediated_mRNA_decay is_a: GO:0000956 ! nuclear-transcribed mRNA catabolic process [Term] id: GO:0000185 name: activation of MAPKKK activity namespace: biological_process def: "Any process that initiates the activity of the inactive enzyme MAP kinase kinase kinase (MAPKKK)." [PMID:9561267] synonym: "activation of MAP kinase kinase kinase" EXACT [] synonym: "activation of MAP3K activity" EXACT [GOC:bf] synonym: "activation of MAPKKK activity during sporulation" NARROW [] synonym: "positive regulation of MAP kinase kinase kinase activity" BROAD [] synonym: "positive regulation of MAPKKK activity" BROAD [] is_a: GO:0032147 ! activation of protein kinase activity is_a: GO:0043405 ! regulation of MAP kinase activity is_a: GO:0043410 ! positive regulation of MAPK cascade is_a: GO:0071902 ! positive regulation of protein serine/threonine kinase activity relationship: positively_regulates GO:0004709 ! MAP kinase kinase kinase activity [Term] id: GO:0000186 name: activation of MAPKK activity namespace: biological_process alt_id: GO:0007255 def: "The initiation of the activity of the inactive enzyme MAP kinase kinase (MAPKK)." [PMID:9561267] synonym: "activation of MAP kinase kinase activity" EXACT [] synonym: "activation of MAP/ERK kinase kinase" EXACT [] synonym: "activation of MAP2K activity" EXACT [GOC:bf] synonym: "activation of MAPKK activity during sporulation" NARROW [] synonym: "positive regulation of MAPKK activity" BROAD [] xref: Reactome:REACT_101798 "Prolonged ERK activation events, Mus musculus" xref: Reactome:REACT_102728 "Prolonged ERK activation events, Schizosaccharomyces pombe" xref: Reactome:REACT_103900 "Prolonged ERK activation events, Gallus gallus" xref: Reactome:REACT_104177 "MEK activation, Danio rerio" xref: Reactome:REACT_104271 "Prolonged ERK activation events, Canis familiaris" xref: Reactome:REACT_110634 "MEK activation, Canis familiaris" xref: Reactome:REACT_113771 "Prolonged ERK activation events, Arabidopsis thaliana" xref: Reactome:REACT_114228 "Prolonged ERK activation events, Dictyostelium discoideum" xref: Reactome:REACT_114817 "Prolonged ERK activation events, Oryza sativa" xref: Reactome:REACT_12005 "Prolonged ERK activation events, Homo sapiens" xref: Reactome:REACT_33773 "Prolonged ERK activation events, Caenorhabditis elegans" xref: Reactome:REACT_81505 "MEK activation, Gallus gallus" xref: Reactome:REACT_81553 "Prolonged ERK activation events, Xenopus tropicalis" xref: Reactome:REACT_82861 "MEK activation, Xenopus tropicalis" xref: Reactome:REACT_86719 "Prolonged ERK activation events, Rattus norvegicus" xref: Reactome:REACT_86891 "Prolonged ERK activation events, Bos taurus" xref: Reactome:REACT_87045 "Prolonged ERK activation events, Taeniopygia guttata" xref: Reactome:REACT_89175 "Prolonged ERK activation events, Danio rerio" xref: Reactome:REACT_89555 "MEK activation, Bos taurus" xref: Reactome:REACT_91625 "Prolonged ERK activation events, Drosophila melanogaster" xref: Reactome:REACT_94138 "Prolonged ERK activation events, Sus scrofa" xref: Reactome:REACT_94626 "MEK activation, Mus musculus" xref: Reactome:REACT_95763 "MEK activation, Taeniopygia guttata" xref: Reactome:REACT_962 "MEK activation, Homo sapiens" xref: Reactome:REACT_97271 "Prolonged ERK activation events, Saccharomyces cerevisiae" xref: Reactome:REACT_98727 "MEK activation, Rattus norvegicus" is_a: GO:0032147 ! activation of protein kinase activity is_a: GO:0043405 ! regulation of MAP kinase activity is_a: GO:0043410 ! positive regulation of MAPK cascade relationship: positively_regulates GO:0004708 ! MAP kinase kinase activity [Term] id: GO:0000187 name: activation of MAPK activity namespace: biological_process def: "The initiation of the activity of the inactive enzyme MAP kinase (MAPK)." [PMID:9561267] synonym: "activation of MAP kinase" EXACT [] synonym: "activation of MAPK activity during sporulation" NARROW [] synonym: "MAPK activation" EXACT [] xref: Reactome:REACT_100881 "activated TAK1 mediates p38 MAPK activation, Canis familiaris" xref: Reactome:REACT_101870 "ERK activation, Caenorhabditis elegans" xref: Reactome:REACT_101978 "ERK activation, Drosophila melanogaster" xref: Reactome:REACT_102664 "activated TAK1 mediates p38 MAPK activation, Caenorhabditis elegans" xref: Reactome:REACT_102813 "activated TAK1 mediates p38 MAPK activation, Arabidopsis thaliana" xref: Reactome:REACT_103235 "ERK activation, Sus scrofa" xref: Reactome:REACT_103251 "activated TAK1 mediates p38 MAPK activation, Dictyostelium discoideum" xref: Reactome:REACT_106101 "ERK activation, Bos taurus" xref: Reactome:REACT_112664 "ERK activation, Oryza sativa" xref: Reactome:REACT_113767 "ERK activation, Dictyostelium discoideum" xref: Reactome:REACT_114778 "ERK activation, Arabidopsis thaliana" xref: Reactome:REACT_1482 "ERK activation, Homo sapiens" xref: Reactome:REACT_21399 "activated TAK1 mediates p38 MAPK activation, Homo sapiens" xref: Reactome:REACT_25355 "MAPK activation in TLR cascade, Gallus gallus" xref: Reactome:REACT_25370 "Activated TAK1 mediates p38 MAP kinase phosphorylation, Gallus gallus" xref: Reactome:REACT_28684 "ERK activation, Gallus gallus" xref: Reactome:REACT_29727 "activated TAK1 mediates p38 MAPK activation, Xenopus tropicalis" xref: Reactome:REACT_30502 "ERK activation, Saccharomyces cerevisiae" xref: Reactome:REACT_32301 "activated TAK1 mediates p38 MAPK activation, Rattus norvegicus" xref: Reactome:REACT_34590 "ERK activation, Rattus norvegicus" xref: Reactome:REACT_77440 "activated TAK1 mediates p38 MAPK activation, Mus musculus" xref: Reactome:REACT_77987 "ERK activation, Taeniopygia guttata" xref: Reactome:REACT_78017 "activated TAK1 mediates p38 MAPK activation, Bos taurus" xref: Reactome:REACT_83894 "activated TAK1 mediates p38 MAPK activation, Sus scrofa" xref: Reactome:REACT_84937 "ERK activation, Schizosaccharomyces pombe" xref: Reactome:REACT_86273 "activated TAK1 mediates p38 MAPK activation, Taeniopygia guttata" xref: Reactome:REACT_86655 "activated TAK1 mediates p38 MAPK activation, Danio rerio" xref: Reactome:REACT_87442 "activated TAK1 mediates p38 MAPK activation, Drosophila melanogaster" xref: Reactome:REACT_88492 "ERK activation, Canis familiaris" xref: Reactome:REACT_88606 "ERK activation, Mus musculus" xref: Reactome:REACT_91962 "activated TAK1 mediates p38 MAPK activation, Oryza sativa" xref: Reactome:REACT_93371 "activated TAK1 mediates p38 MAPK activation, Gallus gallus" xref: Reactome:REACT_98123 "ERK activation, Xenopus tropicalis" xref: Reactome:REACT_99633 "ERK activation, Danio rerio" is_a: GO:0032147 ! activation of protein kinase activity is_a: GO:0043406 ! positive regulation of MAP kinase activity [Term] id: GO:0000188 name: inactivation of MAPK activity namespace: biological_process def: "Any process that terminates the activity of the active enzyme MAP kinase." [PMID:9561267] synonym: "inactivation of MAPK during sporulation" NARROW [] synonym: "termination of MAPK activity" EXACT [] is_a: GO:0043407 ! negative regulation of MAP kinase activity [Term] id: GO:0000189 name: MAPK import into nucleus namespace: biological_process def: "The directed movement of a MAP kinase to the nucleus upon activation." [PMID:9561267] comment: Note that 'translocation' is sometimes used in the literature to refer to the entire process of protein import into the nucleus, but in GO refers specifically to the step in which a cargo-carrier protein complex moves through the nuclear pore complex. synonym: "nuclear translocation of MAPK" NARROW [GOC:mah] xref: Reactome:REACT_103042 "Nuclear translocation of phospho-ERK-1 dimer, Schizosaccharomyces pombe" xref: Reactome:REACT_105886 "Nuclear translocation of phospho-ERK-2 dimer, Gallus gallus" xref: Reactome:REACT_106064 "Nuclear translocation of phospho-ERK-2 dimer, Mus musculus" xref: Reactome:REACT_107045 "Nuclear translocation of phospho-ERK-1 dimer, Canis familiaris" xref: Reactome:REACT_110766 "Nuclear translocation of phospho-ERK-1 dimer, Danio rerio" xref: Reactome:REACT_113196 "Nuclear translocation of phospho-ERK-1 dimer, Oryza sativa" xref: Reactome:REACT_114932 "Nuclear translocation of phospho-ERK-1 dimer, Dictyostelium discoideum" xref: Reactome:REACT_115101 "Nuclear translocation of phospho-ERK-1 dimer, Arabidopsis thaliana" xref: Reactome:REACT_1866 "Nuclear translocation of phospho-ERK-1 dimer, Homo sapiens" xref: Reactome:REACT_29004 "Nuclear translocation of phospho-ERK-1 dimer, Caenorhabditis elegans" xref: Reactome:REACT_32259 "Nuclear translocation of phospho-ERK-1 dimer, Saccharomyces cerevisiae" xref: Reactome:REACT_33595 "Nuclear translocation of phospho-ERK-1 dimer, Mus musculus" xref: Reactome:REACT_487 "Nuclear translocation of phospho-ERK-2 dimer, Homo sapiens" xref: Reactome:REACT_510 "Nuclear translocation of phospho-ERK-2 dimer, Rattus norvegicus" xref: Reactome:REACT_78269 "Nuclear translocation of phospho-ERK-2 dimer, Danio rerio" xref: Reactome:REACT_79422 "Nuclear translocation of phospho-ERK-2 dimer, Bos taurus" xref: Reactome:REACT_81446 "Nuclear translocation of phospho-ERK-2 dimer, Taeniopygia guttata" xref: Reactome:REACT_87335 "Nuclear translocation of phospho-ERK-2 dimer, Xenopus tropicalis" xref: Reactome:REACT_89933 "Nuclear translocation of phospho-ERK-1 dimer, Drosophila melanogaster" xref: Reactome:REACT_94910 "Nuclear translocation of phospho-ERK-1 dimer, Bos taurus" xref: Reactome:REACT_95119 "Nuclear translocation of phospho-ERK-2 dimer, Sus scrofa" xref: Reactome:REACT_97762 "Nuclear translocation of phospho-ERK-2 dimer, Canis familiaris" is_a: GO:0006606 ! protein import into nucleus relationship: part_of GO:0000165 ! MAPK cascade [Term] id: GO:0000190 name: obsolete MAPKKK cascade (pseudohyphal growth) namespace: biological_process def: "OBSOLETE. MAPKKK cascade involved in transduction of signal promoting pseudohyphal or invasive growth." [PMID:9561267] comment: This term was made obsolete because it is a gene product specific term. synonym: "MAPKKK cascade (pseudohyphal growth)" EXACT [] is_obsolete: true [Term] id: GO:0000191 name: obsolete activation of MAPKKK (pseudohyphal growth) namespace: biological_process def: "OBSOLETE. Upregulation of MAPKKK activity in the context of regulating pseudohyphal or invasive growth." [PMID:9561267] comment: This term was made obsolete because it is a gene product specific term. synonym: "activation of MAPKKK (pseudohyphal growth)" EXACT [] is_obsolete: true [Term] id: GO:0000192 name: obsolete activation of MAPKK (pseudohyphal growth) namespace: biological_process def: "OBSOLETE. Upregulation of a MAP kinase kinase in the context of regulating pseudohyphal or invasive growth." [PMID:9561267] comment: This term was made obsolete because it is a gene product specific term. synonym: "activation of MAPKK (pseudohyphal growth)" EXACT [] is_obsolete: true [Term] id: GO:0000193 name: obsolete activation of MAPK (pseudohyphal growth) namespace: biological_process def: "OBSOLETE. Upregulation of MAP kinase activity in the context of regulating pseudohyphal or invasive growth." [PMID:9561267] comment: This term was made obsolete because it is a gene product specific term. synonym: "activation of MAPK (pseudohyphal growth)" EXACT [] is_obsolete: true [Term] id: GO:0000194 name: obsolete inactivation of MAPK (pseudohyphal growth) namespace: biological_process def: "OBSOLETE. Downregulation of MAP kinase activity in the context of regulating pseudohyphal or invasive growth." [PMID:9561267] comment: This term was made obsolete because it is a gene product specific term. synonym: "inactivation of MAPK (pseudohyphal growth)" EXACT [] is_obsolete: true [Term] id: GO:0000195 name: obsolete nuclear translocation of MAPK (pseudohyphal growth) namespace: biological_process def: "OBSOLETE. Movement of a MAP kinase to the nucleus in the context of regulating pseudohyphal or invasive growth." [PMID:9561267] comment: This term was made obsolete because it is a gene product specific term. synonym: "nuclear translocation of MAPK (pseudohyphal growth)" EXACT [] is_obsolete: true [Term] id: GO:0000196 name: MAPK cascade involved in cell wall organization or biogenesis namespace: biological_process def: "A MAPK cascade that contributes to cell wall organization or biogenesis." [PMID:9561267] synonym: "cell integrity MAPK pathway" EXACT [GOC:vw, PMID:23934882] synonym: "cell wall biogenesis, MAPKKK cascade" EXACT [] synonym: "MAPK cascade involved in cell wall biogenesis" NARROW [GOC:vw] synonym: "MAPKKK cascade involved in cell wall biogenesis" EXACT [GOC:signaling] synonym: "Mpk1 cascade" NARROW [PMID:10523653] synonym: "Pmk1 MAPK cell integrity signaling" NARROW [PMID:20032302] synonym: "Pmk1 mitogen-activated protein kinase (MAPK) cell integrity pathway" NARROW [PMID:23934882] synonym: "PMK1-MAPK signal transduction pathway" NARROW [PMID:23454094] synonym: "Slt2 cascade" NARROW [PMID:10523653] is_a: GO:0000165 ! MAPK cascade intersection_of: GO:0000165 ! MAPK cascade intersection_of: part_of GO:0071554 ! cell wall organization or biogenesis relationship: part_of GO:0071554 ! cell wall organization or biogenesis [Term] id: GO:0000197 name: activation of MAPKKK activity involved in cell wall organization or biogenesis namespace: biological_process def: "Any process that initiates the activity of the inactive enzyme MAP kinase kinase kinase in the context of cell wall organization or biogenesis." [PMID:9561267] synonym: "activation of MAP kinase kinase kinase activity during cell wall biogenesis" EXACT [] synonym: "activation of MAPKKK activity involved in cell wall biogenesis" RELATED [] synonym: "activation of MAPKKK activity involved in cell wall integrity" EXACT [GOC:dgf] synonym: "cell wall biogenesis, activation of MAP kinase kinase kinase activity" EXACT [] synonym: "cell wall biogenesis, activation of MAPKKK activity" EXACT [] is_a: GO:0000185 ! activation of MAPKKK activity is_a: GO:1903139 ! positive regulation of MAPK cascade involved in cell wall organization or biogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0038070 ! MAP kinase kinase kinase activity involved in cell wall organization or biogenesis relationship: positively_regulates GO:0038070 ! MAP kinase kinase kinase activity involved in cell wall organization or biogenesis [Term] id: GO:0000198 name: activation of MAPKK activity involved in cell wall organization or biogenesis namespace: biological_process def: "Any process that initiates the activity of the inactive enzyme MAP kinase kinase in the context of cell wall organization or biogenesis." [PMID:9561267] synonym: "activation of MAP kinase kinase activity during cell wall biogenesis" EXACT [] synonym: "activation of MAPKK activity involved in cell wall biogenesis" RELATED [] synonym: "activation of MAPKK activity involved in cell wall integrity" EXACT [GOC:dgf] synonym: "cell wall biogenesis, activation of MAP kinase kinase activity" EXACT [] synonym: "cell wall biogenesis, activation of MAPKK activity" EXACT [] is_a: GO:0000186 ! activation of MAPKK activity is_a: GO:1903139 ! positive regulation of MAPK cascade involved in cell wall organization or biogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0038068 ! MAP kinase kinase activity involved in cell wall organization or biogenesis relationship: positively_regulates GO:0038068 ! MAP kinase kinase activity involved in cell wall organization or biogenesis [Term] id: GO:0000199 name: activation of MAPK activity involved in cell wall organization or biogenesis namespace: biological_process def: "Any process that initiates the activity of the inactive enzyme MAP kinase in the context of cell wall biogenesis, the assembly and arrangement of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells." [PMID:9561267] synonym: "activation of MAPK activity involved in cell wall biogenesis" NARROW [] synonym: "activation of MAPK activity involved in cell wall integrity" EXACT [GOC:dgf] synonym: "cell wall biogenesis, activation of MAPK activity" EXACT [] is_a: GO:0000187 ! activation of MAPK activity is_a: GO:1903139 ! positive regulation of MAPK cascade involved in cell wall organization or biogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0038067 ! MAP kinase activity involved in cell wall organization or biogenesis relationship: positively_regulates GO:0038067 ! MAP kinase activity involved in cell wall organization or biogenesis [Term] id: GO:0000200 name: inactivation of MAPK activity involved in cell wall organization or biogenesis namespace: biological_process def: "Any process that terminates the activity of the active enzyme MAP kinase in the context of cell wall organization or biogenesis." [PMID:9561267] synonym: "cell wall biogenesis, inactivation of MAPK activity" EXACT [] synonym: "cell wall biogenesis, termination of MAPK activity" EXACT [] synonym: "inactivation of MAPK activity involved in cell wall integrity" EXACT [GOC:dgf] synonym: "inactivation of MAPK activity involved in cell wall organization or biogenesis" RELATED [] synonym: "termination of MAPK activity during cell wall biogenesis" EXACT [] is_a: GO:0000188 ! inactivation of MAPK activity is_a: GO:1903138 ! negative regulation of MAPK cascade involved in cell wall organization or biogenesis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0038067 ! MAP kinase activity involved in cell wall organization or biogenesis relationship: negatively_regulates GO:0038067 ! MAP kinase activity involved in cell wall organization or biogenesis [Term] id: GO:0000201 name: MAPK import into nucleus involved in cell wall organization or biogenesis namespace: biological_process def: "The directed movement of a MAP kinase to the nucleus that occurs in the context of cell wall organization or biogenesis." [PMID:9561267] synonym: "cell wall biogenesis, MAPK import into nucleus" EXACT [GOC:mah] synonym: "cell wall biogenesis, nuclear translocation of MAPK" NARROW [GOC:mah] synonym: "MAPK import into nucleus involved in cell wall biogenesis" NARROW [GOC:vw] synonym: "MAPK import into nucleus involved in cell wall integrity" EXACT [GOC:dgf, GOC:mah] synonym: "nuclear translocation of MAPK involved in cell wall biogenesis" NARROW [GOC:mah] synonym: "nuclear translocation of MAPK involved in cell wall integrity" NARROW [GOC:dgf, GOC:mah] is_a: GO:0000189 ! MAPK import into nucleus intersection_of: GO:0000189 ! MAPK import into nucleus intersection_of: part_of GO:0042546 ! cell wall biogenesis relationship: part_of GO:0000196 ! MAPK cascade involved in cell wall organization or biogenesis relationship: part_of GO:0042546 ! cell wall biogenesis [Term] id: GO:0000202 name: obsolete MAPKKK cascade during sporulation (sensu Saccharomyces) namespace: biological_process def: "OBSOLETE. MAPKKK cascade involved in transduction of signal promoting sporulation. As in, but not restricted to, the taxon Saccharomyces (Saccharomyces, ncbi_taxonomy_id:4930)." [PMID:9561267] comment: This term was made obsolete because it is a gene product specific term. synonym: "MAPKKK cascade during sporulation (sensu Saccharomyces)" EXACT [] is_obsolete: true [Term] id: GO:0000203 name: obsolete activation of MAPKKK during sporulation (sensu Saccharomyces) namespace: biological_process def: "OBSOLETE. Upregulation of MAPKKK activity in the context of sporulation. As in, but not restricted to, the taxon Saccharomyces (Saccharomyces, ncbi_taxonomy_id:4930)." [PMID:9561267] comment: This term was made obsolete because it is a gene product specific term. synonym: "activation of MAPKKK during sporulation (sensu Saccharomyces)" EXACT [] is_obsolete: true [Term] id: GO:0000204 name: obsolete activation of MAPKK during sporulation (sensu Saccharomyces) namespace: biological_process def: "OBSOLETE. Upregulation of a MAP kinase kinase in the context of sporulation. As in, but not restricted to, the taxon Saccharomyces (Saccharomyces, ncbi_taxonomy_id:4930)." [PMID:9561267] comment: This term was made obsolete because it is a gene product specific term. synonym: "activation of MAPKK during sporulation (sensu Saccharomyces)" EXACT [] is_obsolete: true [Term] id: GO:0000205 name: obsolete activation of MAPK during sporulation (sensu Saccharomyces) namespace: biological_process def: "OBSOLETE. Upregulation of MAP kinase activity in the context of sporulation. As in, but not restricted to, the taxon Saccharomyces (Saccharomyces, ncbi_taxonomy_id:4930)." [PMID:9561267] comment: This term was made obsolete because it is a gene product specific term. synonym: "activation of MAPK during sporulation (sensu Saccharomyces)" EXACT [] is_obsolete: true [Term] id: GO:0000206 name: obsolete inactivation of MAPK during sporulation (sensu Saccharomyces) namespace: biological_process def: "OBSOLETE. Downregulation of MAP kinase activity in the context of sporulation. As in, but not restricted to, the taxon Saccharomyces (Saccharomyces, ncbi_taxonomy_id:4930)." [PMID:9561267] comment: This term was made obsolete because it is a gene product specific term. synonym: "inactivation of MAPK during sporulation (sensu Saccharomyces)" EXACT [] is_obsolete: true [Term] id: GO:0000207 name: obsolete nuclear translocation of MAPK during sporulation (sensu Saccharomyces) namespace: biological_process def: "OBSOLETE. Movement of a MAP kinase to the nucleus in the context of sporulation. As in, but not restricted to, the taxon Saccharomyces (Saccharomyces, ncbi_taxonomy_id:4930)." [PMID:9561267] comment: This term was made obsolete because it is a gene product specific term. synonym: "nuclear translocation of MAPK during sporulation (sensu Saccharomyces)" EXACT [] is_obsolete: true [Term] id: GO:0000208 name: MAPK import into nucleus involved in osmosensory signaling pathway namespace: biological_process def: "The directed movement of a MAP kinase to the nucleus during osmolarity sensing." [PMID:9561267] synonym: "MAPK import into nucleus during osmolarity sensing" EXACT [GOC:mah] synonym: "MAPK import into nucleus involved in osmosensory signalling pathway" EXACT [GOC:mah] synonym: "nuclear translocation of MAPK during osmolarity sensing" EXACT [] synonym: "nuclear translocation of MAPK involved in osmosensory signaling pathway" NARROW [GOC:mah] synonym: "nuclear translocation of MAPK involved in osmosensory signalling pathway" NARROW [GOC:mah] synonym: "osmolarity sensing, MAPK import into nucleus" EXACT [GOC:mah] synonym: "osmolarity sensing, nuclear translocation of MAPK" NARROW [GOC:mah] is_a: GO:0000189 ! MAPK import into nucleus intersection_of: GO:0000189 ! MAPK import into nucleus intersection_of: part_of GO:0007231 ! osmosensory signaling pathway relationship: part_of GO:0000161 ! MAPK cascade involved in osmosensory signaling pathway relationship: part_of GO:0007231 ! osmosensory signaling pathway [Term] id: GO:0000209 name: protein polyubiquitination namespace: biological_process def: "Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain." [ISBN:0815316194] synonym: "polyubiquitin" RELATED [] synonym: "protein polyubiquitinylation" EXACT [] synonym: "protein polyubiquitylation" EXACT [] xref: Reactome:REACT_75842 "Antigen processing: Ubiquitination & Proteasome degradation, Homo sapiens" is_a: GO:0016567 ! protein ubiquitination [Term] id: GO:0000210 name: NAD+ diphosphatase activity namespace: molecular_function def: "Catalysis of the reaction: NAD+ + H2O = AMP + NMN." [EC:3.6.1.22] subset: gosubset_prok synonym: "NAD diphosphatase activity" EXACT [] synonym: "NAD pyrophosphatase activity" EXACT [] synonym: "NAD(+) pyrophosphatase activity" EXACT [EC:3.6.1.22] synonym: "NAD+ phosphohydrolase activity" EXACT [EC:3.6.1.22] synonym: "NAD+ pyrophosphatase activity" EXACT [EC:3.6.1.22] synonym: "NADH pyrophosphatase activity" BROAD [EC:3.6.1.22] synonym: "NADP pyrophosphatase activity" BROAD [EC:3.6.1.22] synonym: "nicotinamide adenine dinucleotide pyrophosphatase activity" EXACT [EC:3.6.1.22] xref: EC:3.6.1.22 xref: MetaCyc:NADPYROPHOSPHAT-RXN xref: RHEA:11803 is_a: GO:0004551 ! nucleotide diphosphatase activity [Term] id: GO:0000211 name: obsolete protein degradation tagging activity namespace: molecular_function def: "OBSOLETE. Covalent addition of polyubiquitin to another protein, targeting the tagged protein for destruction." [GOC:cl, ISBN:0815316194] comment: This term was made obsolete because it represents a biological process and a molecular function. synonym: "protein degradation tagging activity" EXACT [] is_obsolete: true consider: GO:0005515 consider: GO:0019941 consider: GO:0042787 [Term] id: GO:0000212 name: meiotic spindle organization namespace: biological_process alt_id: GO:0043147 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a meiotic cell cycle." [GOC:go_curators, GOC:mah] synonym: "meiotic spindle organisation" EXACT [GOC:curators] synonym: "meiotic spindle organization and biogenesis" RELATED [GOC:mah] synonym: "meiotic spindle stabilization" RELATED [] synonym: "spindle organization during meiosis" EXACT [GOC:mah] is_a: GO:1903046 ! meiotic cell cycle process relationship: part_of GO:0051321 ! meiotic cell cycle [Term] id: GO:0000213 name: tRNA-intron endonuclease activity namespace: molecular_function def: "Catalysis of the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron." [EC:3.1.27.9] synonym: "splicing endonuclease activity" EXACT [EC:3.1.27.9] synonym: "transfer ribonucleate intron endoribonuclease activity" EXACT [EC:3.1.27.9] synonym: "transfer splicing endonuclease activity" EXACT [EC:3.1.27.9] synonym: "tRNA splicing endonuclease activity" EXACT [EC:3.1.27.9] synonym: "tRNA-intron endoribonuclease activity" EXACT [] synonym: "tRNA-splicing endonuclease activity" EXACT [EC:3.1.27.9] synonym: "tRNATRPintron endonuclease activity" EXACT [EC:3.1.27.9] xref: EC:3.1.27.9 xref: MetaCyc:3.1.27.9-RXN is_a: GO:0004549 ! tRNA-specific ribonuclease activity is_a: GO:0016892 ! endoribonuclease activity, producing 3'-phosphomonoesters [Term] id: GO:0000214 name: tRNA-intron endonuclease complex namespace: cellular_component def: "A protein complex that catalyzes the endonucleolytic cleavage of pre-tRNA, producing 5'-hydroxyl and 2',3'-cyclic phosphate termini, and specifically removing the intron." [EC:3.1.27.9] synonym: "SEN complex" EXACT [GOC:se, PMID:22391451] synonym: "tRNA splicing endonuclease complex" EXACT [GOC:se, PMID:22391451] is_a: GO:0044428 ! nuclear part is_a: GO:1902555 ! endoribonuclease complex is_a: GO:1905348 ! endonuclease complex [Term] id: GO:0000215 name: tRNA 2'-phosphotransferase activity namespace: molecular_function def: "Catalysis of the reaction: 2'-phospho-[ligated tRNA] + NAD+ = mature tRNA + ADP ribose 1'',2''-phosphate + nicotinamide + H2O. This reaction is the transfer of the splice junction 2-phosphate from ligated tRNA to NAD+ to produce ADP-ribose 1'-2' cyclic phosphate." [EC:2.7.1.160, PMID:9148937] subset: goslim_chembl synonym: "2'-phospho-[ligated tRNA]:NAD+ phosphotransferase activity" EXACT [EC:2.7.1.160] synonym: "2'-phospho-tRNA:NAD+ phosphotransferase activity" EXACT [EC:2.7.1.160] synonym: "Tpt1" RELATED [EC:2.7.1.160] synonym: "Tpt1p" RELATED [EC:2.7.1.160] synonym: "yeast 2'-phosphotransferase activity" NARROW [EC:2.7.1.160] xref: EC:2.7.1.160 xref: MetaCyc:2.7.1.160-RXN is_a: GO:0008665 ! 2'-phosphotransferase activity is_a: GO:0016773 ! phosphotransferase activity, alcohol group as acceptor [Term] id: GO:0000216 name: obsolete M/G1 transition of mitotic cell cycle namespace: biological_process def: "OBSOLETE. Progression from M phase to G1 phase of the mitotic cell cycle." [GOC:mah, GOC:mtg_cell_cycle] comment: This term was made obsolete because it does not refer to a real biological process. synonym: "M/G1 transition of mitotic cell cycle" EXACT [] xref: Reactome:REACT_103126 "M/G1 Transition, Sus scrofa" xref: Reactome:REACT_103368 "M/G1 Transition, Taeniopygia guttata" xref: Reactome:REACT_105126 "M/G1 Transition, Caenorhabditis elegans" xref: Reactome:REACT_108209 "M/G1 Transition, Schizosaccharomyces pombe" xref: Reactome:REACT_108301 "M/G1 Transition, Saccharomyces cerevisiae" xref: Reactome:REACT_109437 "M/G1 Transition, Rattus norvegicus" xref: Reactome:REACT_110954 "M/G1 Transition, Dictyostelium discoideum" xref: Reactome:REACT_1725 "M/G1 Transition, Homo sapiens" xref: Reactome:REACT_32146 "M/G1 Transition, Arabidopsis thaliana" xref: Reactome:REACT_32196 "M/G1 Transition, Plasmodium falciparum" xref: Reactome:REACT_77227 "M/G1 Transition, Danio rerio" xref: Reactome:REACT_77394 "M/G1 Transition, Mus musculus" xref: Reactome:REACT_78459 "M/G1 Transition, Gallus gallus" xref: Reactome:REACT_79481 "M/G1 Transition, Drosophila melanogaster" xref: Reactome:REACT_83776 "M/G1 Transition, Oryza sativa" xref: Reactome:REACT_86397 "M/G1 Transition, Canis familiaris" xref: Reactome:REACT_89032 "M/G1 Transition, Xenopus tropicalis" xref: Reactome:REACT_94915 "M/G1 Transition, Bos taurus" is_obsolete: true [Term] id: GO:0000217 name: DNA secondary structure binding namespace: molecular_function def: "Interacting selectively and non-covalently with DNA containing secondary structure elements such as four-way junctions, bubbles, loops, Y-form DNA, or double-strand/single-strand junctions." [GOC:krc] is_a: GO:0043566 ! structure-specific DNA binding [Term] id: GO:0000219 name: obsolete vacuolar hydrogen-transporting ATPase namespace: cellular_component def: "OBSOLETE (was not defined before being made obsolete)." [GOC:go_curators] comment: This term was made obsolete because more specific terms were created. synonym: "V-ATPase" EXACT [] synonym: "vacuolar hydrogen-transporting ATPase" EXACT [] is_obsolete: true consider: GO:0016469 [Term] id: GO:0000220 name: vacuolar proton-transporting V-type ATPase, V0 domain namespace: cellular_component def: "The V0 domain of a proton-transporting V-type ATPase found in the vacuolar membrane." [GOC:mah, PMID:16449553] comment: Note that this domain often consists of five subunits, although in some mammalian tissues it may have an additional subunit. synonym: "vacuolar hydrogen ion-transporting ATPase V0 domain" EXACT [] is_a: GO:0033179 ! proton-transporting V-type ATPase, V0 domain is_a: GO:0044437 ! vacuolar part intersection_of: GO:0033179 ! proton-transporting V-type ATPase, V0 domain intersection_of: part_of GO:0005773 ! vacuole relationship: part_of GO:0005773 ! vacuole relationship: part_of GO:0016471 ! vacuolar proton-transporting V-type ATPase complex [Term] id: GO:0000221 name: vacuolar proton-transporting V-type ATPase, V1 domain namespace: cellular_component def: "The V1 domain of a proton-transporting V-type ATPase found in the vacuolar membrane." [GOC:mah, PMID:16449553] comment: Note that this domain generally consists of eight subunits. synonym: "vacuolar hydrogen ion-transporting ATPase V1 domain" EXACT [] is_a: GO:0033180 ! proton-transporting V-type ATPase, V1 domain is_a: GO:0044437 ! vacuolar part intersection_of: GO:0033180 ! proton-transporting V-type ATPase, V1 domain intersection_of: part_of GO:0005773 ! vacuole relationship: part_of GO:0005773 ! vacuole relationship: part_of GO:0016471 ! vacuolar proton-transporting V-type ATPase complex [Term] id: GO:0000222 name: plasma membrane proton-transporting V-type ATPase, V0 domain namespace: cellular_component def: "The V0 domain of a proton-transporting V-type ATPase found in the plasma membrane." [GOC:mah] synonym: "plasma membrane hydrogen ion-transporting ATPase V0 domain" EXACT [] is_a: GO:0033179 ! proton-transporting V-type ATPase, V0 domain is_a: GO:0098797 ! plasma membrane protein complex intersection_of: GO:0033179 ! proton-transporting V-type ATPase, V0 domain intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005887 ! integral component of plasma membrane relationship: part_of GO:0033181 ! plasma membrane proton-transporting V-type ATPase complex [Term] id: GO:0000223 name: plasma membrane proton-transporting V-type ATPase, V1 domain namespace: cellular_component def: "The V1 domain of a proton-transporting V-type ATPase found in the plasma membrane." [GOC:mah] synonym: "plasma membrane hydrogen ion-transporting ATPase V1 domain" EXACT [] is_a: GO:0033180 ! proton-transporting V-type ATPase, V1 domain is_a: GO:0098797 ! plasma membrane protein complex intersection_of: GO:0033180 ! proton-transporting V-type ATPase, V1 domain intersection_of: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005886 ! plasma membrane relationship: part_of GO:0005887 ! integral component of plasma membrane relationship: part_of GO:0033181 ! plasma membrane proton-transporting V-type ATPase complex [Term] id: GO:0000224 name: peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity namespace: molecular_function def: "Catalysis of the reaction: 4-N-(N-acetyl-D-glucosaminyl)-protein + H2O = N-acetyl-beta-D-glucosaminylamine + peptide L-aspartate. This reaction is the hydrolysis of an N4-(acetyl-beta-D-glucosaminyl)asparagine residue in which the N-acetyl-D-glucosamine residue may be further glycosylated, to yield a (substituted) N-acetyl-beta-D-glucosaminylamine and the peptide containing an aspartic residue." [EC:3.5.1.52] subset: gosubset_prok synonym: "glycopeptidase activity" BROAD [EC:3.5.1.52] synonym: "glycopeptide N-glycosidase activity" BROAD [EC:3.5.1.52] synonym: "jack-bean glycopeptidase" NARROW [EC:3.5.1.52] synonym: "N-glycanase activity" RELATED [EC:3.5.1.52] synonym: "N-linked-glycopeptide-(N-acetyl-beta-D-glucosaminyl)-L-asparagine amidohydrolase activity" EXACT [EC:3.5.1.52] synonym: "N-oligosaccharide glycopeptidase activity" RELATED [EC:3.5.1.52] synonym: "peptide:N-glycanase" RELATED [] synonym: "PNGase" EXACT [] synonym: "PNGase A" RELATED [EC:3.5.1.52] synonym: "PNGase F" RELATED [EC:3.5.1.52] xref: EC:3.5.1.52 xref: MetaCyc:3.5.1.52-RXN is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides [Term] id: GO:0000225 name: N-acetylglucosaminylphosphatidylinositol deacetylase activity namespace: molecular_function def: "Catalysis of the reaction: N-acetyl-D-glucosaminylphosphatidylinositol + H2O = D-glucosaminylphosphatidylinositol + acetate. This reaction is the second step of the biosynthesis of glycosylphosphatidylinositol (GPI), used to anchor various eukaryotic proteins to the cell-surface membrane." [EC:3.5.1.89] comment: Note that this function was formerly EC:3.1.1.69. synonym: "6-(N-acetyl-alpha-D-glucosaminyl)-1-phosphatidyl-1D-myo-inositol acetylhydrolase activity" EXACT [EC:3.5.1.89] synonym: "acetylglucosaminylphosphatidylinositol deacetylase activity" EXACT [EC:3.5.1.89] synonym: "GlcNAc-PI de-N-acetylase activity" EXACT [EC:3.5.1.89] synonym: "GlcNAc-PI deacetylase activity" EXACT [EC:3.5.1.89] synonym: "N-acetyl-D-glucosaminylphosphatidylinositol acetylhydrolase activity" EXACT [EC:3.5.1.89] synonym: "N-acetylglucosaminylphosphatidylinositol de-N-acetylase activity" EXACT [EC:3.5.1.89] xref: EC:3.5.1.89 xref: MetaCyc:3.1.1.69-RXN xref: Reactome:REACT_100003 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Gallus gallus" xref: Reactome:REACT_103061 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Taeniopygia guttata" xref: Reactome:REACT_107021 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Caenorhabditis elegans" xref: Reactome:REACT_111009 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Dictyostelium discoideum" xref: Reactome:REACT_114989 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Arabidopsis thaliana" xref: Reactome:REACT_29732 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Schizosaccharomyces pombe" xref: Reactome:REACT_32276 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Saccharomyces cerevisiae" xref: Reactome:REACT_33502 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Bos taurus" xref: Reactome:REACT_33809 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Drosophila melanogaster" xref: Reactome:REACT_77843 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Danio rerio" xref: Reactome:REACT_779 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Homo sapiens" xref: Reactome:REACT_82306 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Oryza sativa" xref: Reactome:REACT_82765 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Mus musculus" xref: Reactome:REACT_88022 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Plasmodium falciparum" xref: Reactome:REACT_88604 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Canis familiaris" xref: Reactome:REACT_91074 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Rattus norvegicus" xref: Reactome:REACT_98776 "N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate, Sus scrofa" xref: RHEA:11663 is_a: GO:0016811 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides is_a: GO:0019213 ! deacetylase activity [Term] id: GO:0000226 name: microtubule cytoskeleton organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins." [GOC:mah] subset: goslim_pombe synonym: "microtubule cytoskeleton organisation" EXACT [GOC:mah] synonym: "microtubule cytoskeleton organization and biogenesis" RELATED [GOC:mah] synonym: "microtubule dynamics" EXACT [GOC:dph, GOC:tb] is_a: GO:0007010 ! cytoskeleton organization is_a: GO:0007017 ! microtubule-based process is_a: GO:1902589 ! single-organism organelle organization [Term] id: GO:0000227 name: oxaloacetate secondary active transmembrane transporter activity namespace: molecular_function def: "Catalysis of the transfer of oxaloacetate from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy. Chemiosmotic sources of energy include uniport, symport or antiport." [GOC:mtg_transport] synonym: "oxaloacetate carrier activity" RELATED [] is_a: GO:0015131 ! oxaloacetate transmembrane transporter activity is_a: GO:0015291 ! secondary active transmembrane transporter activity [Term] id: GO:0000228 name: nuclear chromosome namespace: cellular_component def: "A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact." [GOC:dph, GOC:mah] subset: goslim_chembl subset: goslim_generic synonym: "nuclear interphase chromosome" NARROW [] is_a: GO:0005694 ! chromosome is_a: GO:0044428 ! nuclear part intersection_of: GO:0005694 ! chromosome intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0005634 ! nucleus relationship: part_of GO:0031981 ! nuclear lumen [Term] id: GO:0000229 name: cytoplasmic chromosome namespace: cellular_component def: "A chromosome found in the cytoplasm." [GOC:mah] subset: goslim_chembl subset: goslim_generic subset: gosubset_prok synonym: "cytoplasmic interphase chromosome" NARROW [] is_a: GO:0005694 ! chromosome is_a: GO:0044444 ! cytoplasmic part intersection_of: GO:0005694 ! chromosome intersection_of: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0000230 name: obsolete nuclear mitotic chromosome namespace: cellular_component def: "OBSOLETE. A chromosome found in the nucleus during mitosis." [GOC:mah] comment: This term was made obsolete because it is based on a temporal division of the cell cycle. synonym: "nuclear mitotic chromosome" EXACT [] is_obsolete: true consider: GO:0000794 [Term] id: GO:0000231 name: obsolete cytoplasmic mitotic chromosome namespace: cellular_component def: "OBSOLETE. A chromosome found in the cytoplasm during mitosis." [GOC:mah] comment: This term was made obsolete because it is based on a temporal division of the cell cycle. synonym: "cytoplasmic mitotic chromosome" EXACT [] is_obsolete: true consider: GO:0000793 [Term] id: GO:0000232 name: obsolete nuclear interphase chromosome namespace: cellular_component def: "OBSOLETE. A chromosome found in the nucleus during interphase." [GOC:mah] comment: This term was made obsolete because it is based on a temporal division of the cell cycle. synonym: "nuclear interphase chromosome" EXACT [] is_obsolete: true consider: GO:0000228 [Term] id: GO:0000233 name: obsolete cytoplasmic interphase chromosome namespace: cellular_component def: "OBSOLETE. A chromosome found in the cytoplasm during interphase." [GOC:mah] comment: This term was made obsolete because it is based on a temporal division of the cell cycle. synonym: "cytoplasmic interphase chromosome" EXACT [] is_obsolete: true consider: GO:0000229 [Term] id: GO:0000234 name: phosphoethanolamine N-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + ethanolamine phosphate = S-adenosyl-L-homocysteine + N-methylethanolamine phosphate." [EC:2.1.1.103] synonym: "phosphoethanolamine methyltransferase activity" EXACT [EC:2.1.1.103] synonym: "S-adenosyl-L-methionine:ethanolamine-phosphate N-methyltransferase activity" EXACT [EC:2.1.1.103] xref: EC:2.1.1.103 xref: KEGG:R02037 xref: MetaCyc:2.1.1.103-RXN xref: RHEA:20368 is_a: GO:0008170 ! N-methyltransferase activity is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity [Term] id: GO:0000235 name: astral microtubule namespace: cellular_component def: "Any of the spindle microtubules that radiate in all directions from the spindle poles and are thought to contribute to the forces that separate the poles and position them in relation to the rest of the cell." [ISBN:0815316194] is_a: GO:0005876 ! spindle microtubule is_a: GO:0005881 ! cytoplasmic microtubule intersection_of: GO:0005876 ! spindle microtubule intersection_of: part_of GO:0005818 ! aster relationship: part_of GO:0005818 ! aster [Term] id: GO:0000236 name: mitotic prometaphase namespace: biological_process def: "The cell cycle phase in higher eukaryotes which follows mitotic prophase and during which the nuclear envelope is disrupted and breaks into membrane vesicles, and the spindle microtubules enter the nuclear region. Kinetochores mature on each centromere and attach to some of the spindle microtubules. Kinetochore microtubules begin the process of aligning chromosomes in one plane halfway between the poles." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate xref: Reactome:REACT_102823 "Mitotic Prometaphase, Mus musculus" xref: Reactome:REACT_104270 "Mitotic Prometaphase, Bos taurus" xref: Reactome:REACT_105082 "Mitotic Prometaphase, Dictyostelium discoideum" xref: Reactome:REACT_114704 "Mitotic Prometaphase, Schizosaccharomyces pombe" xref: Reactome:REACT_118069 "Mitotic Prometaphase, Gallus gallus" xref: Reactome:REACT_118526 "Mitotic Prometaphase, Saccharomyces cerevisiae" xref: Reactome:REACT_118539 "Mitotic Prometaphase, Taeniopygia guttata" xref: Reactome:REACT_31336 "Mitotic Prometaphase, Danio rerio" xref: Reactome:REACT_31385 "Mitotic Prometaphase, Caenorhabditis elegans" xref: Reactome:REACT_682 "Mitotic Prometaphase, Homo sapiens" xref: Reactome:REACT_79351 "Mitotic Prometaphase, Rattus norvegicus" xref: Reactome:REACT_83126 "Mitotic Prometaphase, Drosophila melanogaster" xref: Reactome:REACT_98905 "Mitotic Prometaphase, Xenopus tropicalis" xref: Reactome:REACT_99376 "Mitotic Prometaphase, Canis familiaris" is_a: GO:0098763 ! mitotic cell cycle phase relationship: happens_during GO:0000278 ! mitotic cell cycle [Term] id: GO:0000237 name: leptotene namespace: biological_process def: "The cell cycle phase which is the first stage of prophase I in meiosis, and during which the chromosomes first become visible." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate xref: Wikipedia:Leptotene xref: Wikipedia:Meiosis#Leptotene is_a: GO:0098764 ! meiosis I cell cycle phase relationship: part_of GO:0007128 ! meiotic prophase I [Term] id: GO:0000238 name: zygotene namespace: biological_process def: "The cell cycle phase which follows leptotene during prophase I of meiosis, and during which each chromosome pairs with its homolog; the two become aligned and crossing over may occur." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate xref: Wikipedia:Meiosis#Zygotene xref: Wikipedia:Zygotene is_a: GO:0098764 ! meiosis I cell cycle phase relationship: part_of GO:0007128 ! meiotic prophase I [Term] id: GO:0000239 name: pachytene namespace: biological_process def: "The cell cycle phase which follows zygotene during prophase I of meiosis, and during which crossing over occurs between a chromatid in one partner and another chromatid in the homologous chromosome." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate xref: Wikipedia:Meiosis#Pachytene xref: Wikipedia:Pachytene is_a: GO:0098764 ! meiosis I cell cycle phase relationship: part_of GO:0007128 ! meiotic prophase I [Term] id: GO:0000240 name: diplotene namespace: biological_process def: "The cell cycle phase which follows pachytene during prophase I of meiosis, during which the homologous chromosomes begin to separate and the synaptonemal complex dissolves." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate xref: Wikipedia:Diplotene xref: Wikipedia:Meiosis#Diplotene is_a: GO:0098764 ! meiosis I cell cycle phase relationship: part_of GO:0007128 ! meiotic prophase I [Term] id: GO:0000241 name: diakinesis namespace: biological_process def: "The cell cycle phase which follows diplotene during prophase I of meiosis, the separation of homologous chromosomes is complete and crossing over has occurred." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate xref: Wikipedia:Diakinesis xref: Wikipedia:Meiosis#Diakinesis is_a: GO:0098764 ! meiosis I cell cycle phase relationship: part_of GO:0007128 ! meiotic prophase I [Term] id: GO:0000242 name: pericentriolar material namespace: cellular_component def: "A network of small fibers that surrounds the centrioles in cells; contains the microtubule nucleating activity of the centrosome." [GOC:clt, ISBN:0815316194] is_a: GO:0044450 ! microtubule organizing center part relationship: part_of GO:0005813 ! centrosome [Term] id: GO:0000243 name: commitment complex namespace: cellular_component def: "A spliceosomal complex that is formed by association of the U1 snRNP with the 5' splice site of an unspliced intron in an RNA transcript." [GOC:krc, ISBN:0879695897, PMID:9150140] synonym: "mammalian spliceosomal complex E" NARROW [GOC:krc, GOC:mah, ISBN:0879695897, ISBN:0879697393] synonym: "mammalian spliceosomal E complex" NARROW [GOC:mah] synonym: "yeast spliceosomal complex CC" NARROW [GOC:krc, GOC:mah, ISBN:0879695897, ISBN:0879697393] is_a: GO:0005684 ! U2-type spliceosomal complex relationship: has_part GO:0005685 ! U1 snRNP [Term] id: GO:0000244 name: spliceosomal tri-snRNP complex assembly namespace: biological_process alt_id: GO:0000351 alt_id: GO:0000355 def: "The formation of a tri-snRNP complex containing U4 and U6 (or U4atac and U6atac) snRNAs and U5 snRNAs and associated proteins. This includes reannealing of U4 and U6 (or U4atac and U6atac) snRNAs released from previous rounds of splicing to reform the U4/U6 snRNP (or U4atac/U6atac snRNP) as well as the subsequent association of the U5 snRNP with the U4/U6 snRNP (or U4atac/U6atac snRNP) to form a tri-snRNP that is ready to reassemble into another spliceosome complex." [ISBN:0879695897, PMID:9452384] synonym: "assembly of spliceosomal tri-snRNP" EXACT [] synonym: "assembly of spliceosomal tri-snRNP U4/U6.U5" NARROW [] synonym: "assembly of spliceosomal tri-snRNP U4atac/U6atac.U5" NARROW [] synonym: "snRNP recycling" BROAD [] synonym: "spliceosomal tri-snRNP assembly" EXACT [] synonym: "spliceosomal tri-snRNP U4/U6.U5 assembly" NARROW [] synonym: "spliceosomal tri-snRNP U4atac/U6atac.U5 assembly" NARROW [] is_a: GO:0000387 ! spliceosomal snRNP assembly [Term] id: GO:0000245 name: spliceosomal complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a spliceosomal complex, a ribonucleoprotein apparatus that catalyzes nuclear mRNA splicing via transesterification reactions." [PMID:9476892] synonym: "spliceosome assembly" BROAD [] is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0000246 name: delta24(24-1) sterol reductase activity namespace: molecular_function def: "Catalysis of the reaction: ergosterol + NADP(+) = ergosta-5,7,22,24(24(1))-tetraen-3beta-ol + H(+) + NADPH." [EC:1.3.1.71, RHEA:18504] subset: gosubset_prok synonym: "C-24(28) sterol reductase activity" EXACT [EC:1.3.1.71] synonym: "D24(24-1)-sterol reductase activity" EXACT [] synonym: "delta24(241)-sterol reductase activity" EXACT [EC:1.3.1.71] synonym: "ergosterol:NADP+ delta24(241)-oxidoreductase activity" EXACT [EC:1.3.1.71] synonym: "sterol Delta(24(28))-methylene reductase activity" EXACT [EC:1.3.1.71] synonym: "sterol Delta(24(28))-reductase activity" EXACT [EC:1.3.1.71] synonym: "sterol delta-24(28) methylene reductase activity" EXACT [] synonym: "sterol delta-24(28) reductase activity" EXACT [] synonym: "sterol delta24(28)-methylene reductase activity" EXACT [EC:1.3.1.71] synonym: "sterol delta24(28)-reductase activity" EXACT [EC:1.3.1.71] xref: EC:1.3.1.71 xref: KEGG:R05641 xref: MetaCyc:1.3.1.71-RXN xref: RHEA:18504 is_a: GO:0016628 ! oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor [Term] id: GO:0000247 name: C-8 sterol isomerase activity namespace: molecular_function def: "Catalysis of the reaction which results in unsaturation at C-7 in the B ring of sterols." [MetaCyc:RXN3O-203, PMID:8988026] synonym: "delta-8-delta-7 sterol isomerase activity" EXACT [] xref: EC:5.3.3.- is_a: GO:0016863 ! intramolecular oxidoreductase activity, transposing C=C bonds [Term] id: GO:0000248 name: C-5 sterol desaturase activity namespace: molecular_function def: "Catalysis of the reaction: 5,7,24(28)-ergostatrienol + O2 + NADPH = 5,7,22,24(28)-ergostatetraenol + 2 H2O + NADP+." [MetaCyc:RXN3O-227] synonym: "sterol-C5-desaturase activity" EXACT [] xref: Reactome:REACT_10092 "Cholesta-7,24-dien-3beta-ol is desaturated to form cholesta-5,7,24-trien-3beta-ol, Homo sapiens" xref: Reactome:REACT_106801 "Cholesta-7,24-dien-3beta-ol is desaturated to form cholesta-5,7,24-trien-3beta-ol, Taeniopygia guttata" xref: Reactome:REACT_108498 "Cholesta-7,24-dien-3beta-ol is desaturated to form cholesta-5,7,24-trien-3beta-ol, Rattus norvegicus" xref: Reactome:REACT_110659 "Cholesta-7,24-dien-3beta-ol is desaturated to form cholesta-5,7,24-trien-3beta-ol, Bos taurus" xref: Reactome:REACT_34122 "Cholesta-7,24-dien-3beta-ol is desaturated to form cholesta-5,7,24-trien-3beta-ol, Danio rerio" xref: Reactome:REACT_34697 "Cholesta-7,24-dien-3beta-ol is desaturated to form cholesta-5,7,24-trien-3beta-ol, Saccharomyces cerevisiae" xref: Reactome:REACT_79598 "Cholesta-7,24-dien-3beta-ol is desaturated to form cholesta-5,7,24-trien-3beta-ol, Mus musculus" xref: Reactome:REACT_84206 "Cholesta-7,24-dien-3beta-ol is desaturated to form cholesta-5,7,24-trien-3beta-ol, Oryza sativa" xref: Reactome:REACT_85577 "Cholesta-7,24-dien-3beta-ol is desaturated to form cholesta-5,7,24-trien-3beta-ol, Sus scrofa" xref: Reactome:REACT_86700 "Cholesta-7,24-dien-3beta-ol is desaturated to form cholesta-5,7,24-trien-3beta-ol, Canis familiaris" xref: Reactome:REACT_98513 "Cholesta-7,24-dien-3beta-ol is desaturated to form cholesta-5,7,24-trien-3beta-ol, Schizosaccharomyces pombe" is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water is_a: GO:0070704 ! sterol desaturase activity [Term] id: GO:0000249 name: C-22 sterol desaturase activity namespace: molecular_function def: "Catalysis of the formation of the C-22(23) double bond in the sterol side chain. An example reaction: 5,7,24(28)-ergostatrienol + O2 + NADPH = 5,7,22,24(28)-ergostatetraenol + 2 H2O + NADP+." [MetaCyc:RXN3O-227] is_a: GO:0016717 ! oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water is_a: GO:0070704 ! sterol desaturase activity [Term] id: GO:0000250 name: lanosterol synthase activity namespace: molecular_function def: "Catalysis of the reaction: (S)-2,3-epoxysqualene = lanosterol. This is a cyclization reaction that forms the sterol nucleus." [EC:5.4.99.7, RHEA:14624] subset: gosubset_prok synonym: "(S)-2,3-epoxysqualene mutase (cyclizing, lanosterol-forming)" EXACT [EC:5.4.99.7] synonym: "2,3-epoxysqualene lanosterol cyclase activity" EXACT [EC:5.4.99.7] synonym: "2,3-epoxysqualene--lanosterol cyclase activity" EXACT [EC:5.4.99.7] synonym: "2,3-epoxysqualene-lanosterol cyclase activity" EXACT [] synonym: "2,3-oxidosqualene sterol cyclase activity" BROAD [EC:5.4.99.7] synonym: "2,3-oxidosqualene-lanosterol cyclase activity" EXACT [EC:5.4.99.7] synonym: "lanosterol 2,3-oxidosqualene cyclase activity" EXACT [EC:5.4.99.7] synonym: "OSC" EXACT [] synonym: "oxidosqualene--lanosterol cyclase activity" EXACT [EC:5.4.99.7] synonym: "oxidosqualene-lanosterol cyclase activity" EXACT [] synonym: "oxidosqualene:lanosterol cyclase activity" EXACT [PMID:18033581] synonym: "squalene 2,3-epoxide:lanosterol cyclase activity" EXACT [EC:5.4.99.7] synonym: "squalene epoxidase-cyclase activity" BROAD [EC:5.4.99.7] synonym: "squalene-2,3-oxide-lanosterol cyclase activity" EXACT [EC:5.4.99.7] xref: EC:5.4.99.7 xref: KEGG:R03199 xref: MetaCyc:LANOSTEROL-SYNTHASE-RXN xref: Reactome:REACT_106250 "Squalene 2,3-epoxide cyclizes, forming lanosterol, Danio rerio" xref: Reactome:REACT_112890 "Squalene 2,3-epoxide cyclizes, forming lanosterol, Oryza sativa" xref: Reactome:REACT_114747 "Squalene 2,3-epoxide cyclizes, forming lanosterol, Arabidopsis thaliana" xref: Reactome:REACT_29522 "Squalene 2,3-epoxide cyclizes, forming lanosterol, Schizosaccharomyces pombe" xref: Reactome:REACT_33379 "Squalene 2,3-epoxide cyclizes, forming lanosterol, Xenopus tropicalis" xref: Reactome:REACT_78122 "Squalene 2,3-epoxide cyclizes, forming lanosterol, Taeniopygia guttata" xref: Reactome:REACT_84749 "Squalene 2,3-epoxide cyclizes, forming lanosterol, Bos taurus" xref: Reactome:REACT_86645 "Squalene 2,3-epoxide cyclizes, forming lanosterol, Saccharomyces cerevisiae" xref: Reactome:REACT_88346 "Squalene 2,3-epoxide cyclizes, forming lanosterol, Rattus norvegicus" xref: Reactome:REACT_89548 "Squalene 2,3-epoxide cyclizes, forming lanosterol, Gallus gallus" xref: Reactome:REACT_92166 "Squalene 2,3-epoxide cyclizes, forming lanosterol, Dictyostelium discoideum" xref: Reactome:REACT_93681 "Squalene 2,3-epoxide cyclizes, forming lanosterol, Canis familiaris" xref: Reactome:REACT_9391 "Squalene 2,3-epoxide cyclizes, forming lanosterol, Homo sapiens" xref: Reactome:REACT_96289 "Squalene 2,3-epoxide cyclizes, forming lanosterol, Mus musculus" xref: RHEA:14624 is_a: GO:0031559 ! oxidosqualene cyclase activity [Term] id: GO:0000252 name: C-3 sterol dehydrogenase (C-4 sterol decarboxylase) activity namespace: molecular_function def: "Catalysis of the reaction: 3-beta-hydroxy-4-beta-methyl-5-alpha-cholesta-8,24-dien-4-alpha-carboxylate + NAD(P)+ = 4-alpha-methyl-5-alpha-cholesta-8,24-dien-3-one + CO2 + NAD(P)H." [EC:1.1.1.170, PMID:9811880] comment: Note that zymosterol is cholesta-8,24-dien-3-ol. synonym: "3beta-hydroxy-4alpha-methylcholestenecarboxylate 3-dehydrogenase (decarboxylating)" RELATED [EC:1.1.1.170] synonym: "3beta-hydroxy-4beta-methyl-5alpha-cholest-7-ene-4alpha-carboxylate:NAD(P)+ 3-oxidoreductase (decarboxylating)" EXACT [] synonym: "3beta-hydroxy-4beta-methylcholestenecarboxylate 3-dehydrogenase (decarboxylating)" RELATED [] synonym: "3beta-hydroxy-4beta-methylcholestenoate dehydrogenase activity" RELATED [] synonym: "C-3 sterol dehydrogenase (C-4 decarboxylase) activity" RELATED [] synonym: "C-3 sterol dehydrogenase activity" RELATED [] synonym: "sterol 4alpha-carboxylic decarboxylase activity" RELATED [] synonym: "sterol-4-carboxylate 3-dehydrogenase (decarboxylating) activity" RELATED [] synonym: "sterol-4alpha-carboxylate 3-dehydrogenase (decarboxylating)" RELATED [] xref: EC:1.1.1.- xref: Reactome:REACT_10053 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Homo sapiens" xref: Reactome:REACT_103278 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Sus scrofa" xref: Reactome:REACT_103729 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Bos taurus" xref: Reactome:REACT_105643 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Gallus gallus" xref: Reactome:REACT_106602 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Bos taurus" xref: Reactome:REACT_107465 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Canis familiaris" xref: Reactome:REACT_108692 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Mus musculus" xref: Reactome:REACT_108789 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Rattus norvegicus" xref: Reactome:REACT_109155 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Danio rerio" xref: Reactome:REACT_112688 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Mycobacterium tuberculosis" xref: Reactome:REACT_112771 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Escherichia coli" xref: Reactome:REACT_112854 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Schizosaccharomyces pombe" xref: Reactome:REACT_112960 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Saccharomyces cerevisiae" xref: Reactome:REACT_112995 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Schizosaccharomyces pombe" xref: Reactome:REACT_113072 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Oryza sativa" xref: Reactome:REACT_113373 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Dictyostelium discoideum" xref: Reactome:REACT_113553 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Saccharomyces cerevisiae" xref: Reactome:REACT_114106 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Oryza sativa" xref: Reactome:REACT_114356 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Dictyostelium discoideum" xref: Reactome:REACT_115015 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Arabidopsis thaliana" xref: Reactome:REACT_115441 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Arabidopsis thaliana" xref: Reactome:REACT_30127 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Rattus norvegicus" xref: Reactome:REACT_31080 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Taeniopygia guttata" xref: Reactome:REACT_32363 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Sus scrofa" xref: Reactome:REACT_33091 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Canis familiaris" xref: Reactome:REACT_77107 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Gallus gallus" xref: Reactome:REACT_82876 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Xenopus tropicalis" xref: Reactome:REACT_85383 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Mus musculus" xref: Reactome:REACT_89091 "4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one, Xenopus tropicalis" xref: Reactome:REACT_91545 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Danio rerio" xref: Reactome:REACT_91980 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Taeniopygia guttata" xref: Reactome:REACT_9949 "4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone), Homo sapiens" is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Term] id: GO:0000253 name: 3-keto sterol reductase activity namespace: molecular_function alt_id: GO:0050576 def: "Catalysis of the reaction: a 3-beta-hydroxyl sterol + NADP+ = a 3-keto sterol + NADPH + H(+)." [EC:1.1.1.270, GOC:mah, MetaCyc:1.1.1.270-RXN, MetaCyc:RXN3O-4110, MetaCyc:RXN66-19, MetaCyc:RXN66-24, MetaCyc:RXN66-314, MetaCyc:RXN66-319, PMID:9811880] comment: Note that zymosterol is cholesta-8,24-dien-3-ol. synonym: "3-keto-steroid reductase activity" EXACT [] synonym: "3-KSR activity" EXACT [EC:1.1.1.270] synonym: "3beta-hydroxy-steroid:NADP+ 3-oxidoreductase" RELATED [EC:1.1.1.270] xref: EC:1.1.1.270 xref: MetaCyc:1.1.1.270-RXN xref: MetaCyc:RXN3O-4110 xref: MetaCyc:RXN66-19 xref: MetaCyc:RXN66-24 xref: MetaCyc:RXN66-314 xref: MetaCyc:RXN66-319 xref: Reactome:REACT_10036 "4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol, Homo sapiens" xref: Reactome:REACT_10079 "Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol), Homo sapiens" xref: Reactome:REACT_101014 "Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol), Schizosaccharomyces pombe" xref: Reactome:REACT_102533 "4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol, Xenopus tropicalis" xref: Reactome:REACT_103243 "4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol, Canis familiaris" xref: Reactome:REACT_103645 "4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol, Gallus gallus" xref: Reactome:REACT_106908 "Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol), Saccharomyces cerevisiae" xref: Reactome:REACT_107179 "4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol, Taeniopygia guttata" xref: Reactome:REACT_108259 "Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol), Canis familiaris" xref: Reactome:REACT_31386 "4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol, Danio rerio" xref: Reactome:REACT_69122 "4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol, Sus scrofa" xref: Reactome:REACT_78849 "4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol, Mus musculus" xref: Reactome:REACT_79755 "4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol, Rattus norvegicus" xref: Reactome:REACT_82599 "4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol, Schizosaccharomyces pombe" xref: Reactome:REACT_82943 "Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol), Sus scrofa" xref: Reactome:REACT_84146 "Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol), Gallus gallus" xref: Reactome:REACT_88684 "Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol), Bos taurus" xref: Reactome:REACT_91551 "Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol), Mus musculus" xref: Reactome:REACT_92714 "Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol), Rattus norvegicus" xref: Reactome:REACT_95205 "Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol), Taeniopygia guttata" xref: Reactome:REACT_96469 "4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol, Bos taurus" xref: Reactome:REACT_96959 "Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol), Danio rerio" xref: Reactome:REACT_96973 "Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol), Xenopus tropicalis" xref: Reactome:REACT_97126 "4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol, Saccharomyces cerevisiae" xref: RHEA:18412 is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Term] id: GO:0000254 name: C-4 methylsterol oxidase activity namespace: molecular_function def: "Catalysis of the reaction: 4,4-dimethyl-5-alpha-cholesta-8,24-dien-3-beta-ol + NAD(P)H + H(+) + O2 = 4-beta-hydroxymethyl-4-alpha-methyl-5-alpha-cholesta-8,24-dien-3-beta-ol + NAD(P)+ + H2O." [EC:1.14.13.72, PMID:9811880] comment: Note that zymosterol is cholesta-8,24-dien-3-ol. synonym: "4,4-dimethyl-5alpha-cholest-7-en-3beta-ol,hydrogen-donor:oxygen oxidoreductase (hydroxylating)" EXACT [EC:1.14.13.72] synonym: "4,4-dimethyl-5alpha-cholest-7-en-3beta-ol,NAD(P)H:oxygen oxidoreductase (hydroxylating)" EXACT [EC:1.14.13.72] synonym: "4-methylsterol oxidase activity" EXACT [] synonym: "methylsterol hydroxylase activity" RELATED [] synonym: "methylsterol monooxygenase activity" RELATED [] xref: EC:1.14.13.72 xref: MetaCyc:1.14.13.72-RXN xref: Reactome:REACT_10059 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Homo sapiens" xref: Reactome:REACT_10070 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Homo sapiens" xref: Reactome:REACT_104089 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Danio rerio" xref: Reactome:REACT_104631 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Oryza sativa" xref: Reactome:REACT_105610 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Taeniopygia guttata" xref: Reactome:REACT_105653 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Bos taurus" xref: Reactome:REACT_107576 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Dictyostelium discoideum" xref: Reactome:REACT_112865 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Xenopus tropicalis" xref: Reactome:REACT_115505 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Xenopus tropicalis" xref: Reactome:REACT_28712 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Mus musculus" xref: Reactome:REACT_29355 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Sus scrofa" xref: Reactome:REACT_31445 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Mus musculus" xref: Reactome:REACT_32207 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Sus scrofa" xref: Reactome:REACT_32840 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Saccharomyces cerevisiae" xref: Reactome:REACT_76969 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Oryza sativa" xref: Reactome:REACT_79112 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Schizosaccharomyces pombe" xref: Reactome:REACT_83222 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Gallus gallus" xref: Reactome:REACT_84661 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Schizosaccharomyces pombe" xref: Reactome:REACT_84707 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Arabidopsis thaliana" xref: Reactome:REACT_85609 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Taeniopygia guttata" xref: Reactome:REACT_86519 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Canis familiaris" xref: Reactome:REACT_88988 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Canis familiaris" xref: Reactome:REACT_89551 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Saccharomyces cerevisiae" xref: Reactome:REACT_94158 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Gallus gallus" xref: Reactome:REACT_95387 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Danio rerio" xref: Reactome:REACT_95721 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Dictyostelium discoideum" xref: Reactome:REACT_96643 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Rattus norvegicus" xref: Reactome:REACT_97328 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Bos taurus" xref: Reactome:REACT_99679 "4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, Rattus norvegicus" xref: Reactome:REACT_99766 "4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol, Arabidopsis thaliana" is_a: GO:0016709 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen [Term] id: GO:0000255 name: allantoin metabolic process namespace: biological_process def: "The chemical reactions and pathways involving allantoin, (2,5-dioxo-4-imidazolidinyl)urea, an intermediate or end product of purine catabolism." [GOC:mah, ISBN:0198547684] subset: gosubset_prok synonym: "allantoin metabolism" EXACT [] is_a: GO:0043603 ! cellular amide metabolic process is_a: GO:0046483 ! heterocycle metabolic process is_a: GO:1901360 ! organic cyclic compound metabolic process is_a: GO:1901564 ! organonitrogen compound metabolic process [Term] id: GO:0000256 name: allantoin catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of allantoin, (2,5-dioxo-4-imidazolidinyl)urea." [GOC:mah, ISBN:0198547684] subset: gosubset_prok synonym: "allantoin breakdown" EXACT [] synonym: "allantoin catabolism" EXACT [] synonym: "allantoin degradation" EXACT [] is_a: GO:0000255 ! allantoin metabolic process is_a: GO:0043605 ! cellular amide catabolic process is_a: GO:0046700 ! heterocycle catabolic process is_a: GO:1901361 ! organic cyclic compound catabolic process is_a: GO:1901565 ! organonitrogen compound catabolic process [Term] id: GO:0000257 name: nitrilase activity namespace: molecular_function def: "Catalysis of the reaction: a nitrile + H2O = a carboxylate + NH3. Acts on a wide range of aromatic nitriles including (indole-3-yl)-acetonitrile and some aliphatic nitriles, and on the corresponding acid amides." [EC:3.5.5.1, GOC:kd] subset: gosubset_prok synonym: "acetonitrilase activity" EXACT [EC:3.5.5.1] synonym: "benzonitrilase activity" EXACT [EC:3.5.5.1] synonym: "nitrile aminohydrolase activity" EXACT [EC:3.5.5.1] xref: EC:3.5.5.1 xref: KEGG:R00540 xref: MetaCyc:3.5.5.1-RXN xref: RHEA:21727 xref: UM-BBD_enzymeID:e0283 is_a: GO:0016815 ! hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in nitriles [Term] id: GO:0000258 name: obsolete isoleucine/valine:sodium symporter activity namespace: molecular_function def: "OBSOLETE. Catalysis of the reaction: (isoleucine or valine)(out) + Na+(out) = (isoleucine or valine)(in) + Na+(in)." [TC:2.A.26.1.1] comment: This term was made obsolete because it represents a multifunctional gene product. synonym: "isoleucine/valine:sodium symporter activity" EXACT [] is_obsolete: true consider: GO:0005283 consider: GO:0005304 consider: GO:0015188 [Term] id: GO:0000259 name: obsolete intracellular nucleoside transmembrane transporter activity namespace: molecular_function def: "OBSOLETE. Enables the directed movement of a nucleoside, a nucleobase linked to either beta-D-ribofuranose (ribonucleoside) or 2-deoxy-beta-D-ribofuranose (a deoxyribonucleotide) within a cell." [GOC:ai] comment: This term was made obsolete because it contains component and function information. synonym: "intracellular nucleoside transmembrane transporter activity" EXACT [] is_obsolete: true consider: GO:0005337 consider: GO:0005622 [Term] id: GO:0000260 name: obsolete hydrogen-translocating V-type ATPase activity namespace: molecular_function def: "OBSOLETE. Catalysis of the reaction: ATP + H2O + H(+)(in) = ADP + phosphate + H+(out). Found in vacuoles of eukaryotes and in bacteria." [TC:3.A.2.2.1, TC:3.A.2.2.3] comment: This term was made obsolete because it represents a gene product. synonym: "hydrogen-translocating V-type ATPase activity" EXACT [] is_obsolete: true replaced_by: GO:0046961 [Term] id: GO:0000261 name: obsolete sodium-translocating V-type ATPase activity namespace: molecular_function def: "OBSOLETE. Catalysis of the reaction: ATP + H2O + Na+(in) = ADP + phosphate + Na+(out). Found in vacuoles of eukaryotes and in bacteria." [TC:3.A.2.2.2] comment: This term was made obsolete because it represents a gene product. synonym: "sodium-translocating V-type ATPase activity" EXACT [] is_obsolete: true replaced_by: GO:0046962 [Term] id: GO:0000262 name: mitochondrial chromosome namespace: cellular_component def: "A chromosome found in the mitochondrion of a eukaryotic cell." [GOC:mah] synonym: "mitochondrial DNA" NARROW [] synonym: "mitochondrial genome" RELATED [] synonym: "mtDNA" NARROW [] xref: NIF_Subcellular:sao1186327184 is_a: GO:0000229 ! cytoplasmic chromosome is_a: GO:0044429 ! mitochondrial part intersection_of: GO:0005694 ! chromosome intersection_of: part_of GO:0005739 ! mitochondrion relationship: part_of GO:0005739 ! mitochondrion relationship: part_of GO:0042645 ! mitochondrial nucleoid [Term] id: GO:0000263 name: obsolete heterotrimeric G-protein GTPase, alpha-subunit namespace: molecular_function def: "OBSOLETE. Subunit of a heterotrimeric G-protein GTPase that contains the guanine nucleotide binding site and possesses GTPase activity." [GOC:mah, ISBN:0198547684] comment: This term was made obsolete because it does not represent a molecular function. synonym: "heterotrimeric G-protein GTPase, alpha-subunit" EXACT [] is_obsolete: true consider: GO:0003924 consider: GO:0005834 [Term] id: GO:0000264 name: obsolete heterotrimeric G-protein GTPase, beta-subunit namespace: molecular_function def: "OBSOLETE. Subunit of a heterotrimeric G-protein GTPase; associates tightly with the gamma subunit." [GOC:mah, ISBN:0198547684] comment: This term was made obsolete because it does not represent a molecular function. synonym: "heterotrimeric G-protein GTPase, beta-subunit" EXACT [] is_obsolete: true consider: GO:0003924 consider: GO:0005834 [Term] id: GO:0000265 name: obsolete heterotrimeric G-protein GTPase, gamma-subunit namespace: molecular_function def: "OBSOLETE. Smallest subunit of a heterotrimeric G-protein GTPase; associates tightly with the beta subunit." [GOC:mah, ISBN:0198547684] comment: This term was made obsolete because it does not represent a molecular function. synonym: "heterotrimeric G-protein GTPase, gamma-subunit" EXACT [] is_obsolete: true consider: GO:0003924 consider: GO:0005834 [Term] id: GO:0000266 name: mitochondrial fission namespace: biological_process def: "The division of a mitochondrion within a cell to form two or more separate mitochondrial compartments." [PMID:11038192] synonym: "mitochondrial division" EXACT [] synonym: "mitochondrial proliferation" RELATED [] is_a: GO:0007005 ! mitochondrion organization is_a: GO:0048285 ! organelle fission [Term] id: GO:0000267 name: obsolete cell fraction namespace: cellular_component def: "OBSOLETE: A generic term for parts of cells prepared by disruptive biochemical techniques." [GOC:ma] comment: This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component. subset: goslim_pir subset: gosubset_prok synonym: "cell fraction" EXACT [] is_obsolete: true consider: GO:0005575 [Term] id: GO:0000268 name: peroxisome targeting sequence binding namespace: molecular_function alt_id: GO:0005051 def: "Interacting selectively and non-covalently with a peroxisomal targeting sequence, any of several sequences of amino acids within a protein that can act as a signal for the localization of the protein into the peroxisome." [GOC:mah, ISBN:0879693568] synonym: "peroxisome targeting signal receptor" NARROW [] synonym: "PTS binding" EXACT [] synonym: "PTS receptor" NARROW [] is_a: GO:0005048 ! signal sequence binding [Term] id: GO:0000269 name: toxin export channel activity namespace: molecular_function def: "Enables the energy independent passage of toxins, sized less than 1000 Da, across a membrane towards the outside of the cell. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria." [GOC:mtg_transport] is_a: GO:0015288 ! porin activity is_a: GO:0019534 ! toxin transporter activity [Term] id: GO:0000270 name: peptidoglycan metabolic process namespace: biological_process alt_id: GO:0009284 def: "The chemical reactions and pathways involving peptidoglycans, any of a class of glycoconjugates found only in bacterial cell walls and consisting of strands of glycosaminoglycan cross-linked by oligopeptides to form a huge and rigid network." [http://www.dsmz.de/species/murein.htm, ISBN:0198506732] subset: gosubset_prok synonym: "murein metabolic process" EXACT [] synonym: "murein metabolism" EXACT [] synonym: "peptidoglycan metabolism" EXACT [] is_a: GO:0030203 ! glycosaminoglycan metabolic process [Term] id: GO:0000271 name: polysaccharide biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [CHEBI:18154, GOC:go_curators] subset: gosubset_prok synonym: "glycan biosynthesis" EXACT [] synonym: "glycan biosynthetic process" EXACT [] synonym: "polysaccharide anabolism" EXACT [] synonym: "polysaccharide biosynthesis" EXACT [] synonym: "polysaccharide formation" EXACT [] synonym: "polysaccharide synthesis" EXACT [] is_a: GO:0005976 ! polysaccharide metabolic process is_a: GO:0009059 ! macromolecule biosynthetic process is_a: GO:0016051 ! carbohydrate biosynthetic process [Term] id: GO:0000272 name: polysaccharide catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [CHEBI:18154, GOC:go_curators] subset: gosubset_prok synonym: "polysaccharide breakdown" EXACT [] synonym: "polysaccharide catabolism" EXACT [] synonym: "polysaccharide degradation" EXACT [] is_a: GO:0005976 ! polysaccharide metabolic process is_a: GO:0009057 ! macromolecule catabolic process is_a: GO:0016052 ! carbohydrate catabolic process [Term] id: GO:0000274 name: mitochondrial proton-transporting ATP synthase, stator stalk namespace: cellular_component def: "One of two stalks that connect the catalytic core of the hydrogen-transporting ATP synthase to the mitochondrial membrane-associated F0 proteins; is thought to prevent futile rotation of the catalytic core." [GOC:mtg_sensu, PMID:10838056] synonym: "mitochondrial proton-transporting ATP synthase, peripheral stalk" EXACT [] is_a: GO:0045265 ! proton-transporting ATP synthase, stator stalk is_a: GO:0098800 ! inner mitochondrial membrane protein complex intersection_of: GO:0045265 ! proton-transporting ATP synthase, stator stalk intersection_of: part_of GO:0005739 ! mitochondrion relationship: part_of GO:0000276 ! mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) relationship: part_of GO:0005739 ! mitochondrion [Term] id: GO:0000275 name: mitochondrial proton-transporting ATP synthase complex, catalytic core F(1) namespace: cellular_component def: "The catalytic sector of the mitochondrial hydrogen-transporting ATP synthase; it comprises the catalytic core and central stalk, and is peripherally associated with the mitochondrial inner membrane when the entire ATP synthase is assembled." [GOC:mtg_sensu, PMID:10838056] comment: See also the cellular component term 'mitochondrial inner membrane ; GO:0005743'. synonym: "hydrogen-transporting ATP synthase, F1 sector" BROAD [] synonym: "proton-transporting ATP synthase complex, catalytic core F(1)" BROAD [] is_a: GO:0045261 ! proton-transporting ATP synthase complex, catalytic core F(1) is_a: GO:0098800 ! inner mitochondrial membrane protein complex intersection_of: GO:0045261 ! proton-transporting ATP synthase complex, catalytic core F(1) intersection_of: part_of GO:0005739 ! mitochondrion relationship: part_of GO:0005739 ! mitochondrion relationship: part_of GO:0005753 ! mitochondrial proton-transporting ATP synthase complex [Term] id: GO:0000276 name: mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) namespace: cellular_component def: "All non-F1 subunits of the mitochondrial hydrogen-transporting ATP synthase, including integral and peripheral mitochondrial inner membrane proteins." [GOC:mtg_sensu, PMID:10838056] is_a: GO:0045263 ! proton-transporting ATP synthase complex, coupling factor F(o) is_a: GO:0098800 ! inner mitochondrial membrane protein complex intersection_of: GO:0045263 ! proton-transporting ATP synthase complex, coupling factor F(o) intersection_of: part_of GO:0005739 ! mitochondrion relationship: part_of GO:0005739 ! mitochondrion relationship: part_of GO:0005753 ! mitochondrial proton-transporting ATP synthase complex [Term] id: GO:0000277 name: [cytochrome c]-lysine N-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + cytochrome c L-lysine = S-adenosyl-L-homocysteine + cytochrome c N6-methyl-L-lysine. This is the addition of a methyl group to the N6 atom of a lysine residue in cytochrome c." [EC:2.1.1.59] synonym: "cytochrome c (lysine) methyltransferase activity" EXACT [EC:2.1.1.59] synonym: "cytochrome c methyltransferase activity" EXACT [EC:2.1.1.59] synonym: "cytochrome c-lysine N-methyltransferase activity" EXACT [EC:2.1.1.59] synonym: "cytochrome c-specific protein methylase III activity" EXACT [EC:2.1.1.59] synonym: "cytochrome c-specific protein-lysine methyltransferase activity" EXACT [EC:2.1.1.59] synonym: "S-adenosyl-L-methionine:cytochrome c-L-lysine 6-N-methyltransferase activity" EXACT [EC:2.1.1.59] synonym: "S-adenosyl-L-methionine:cytochrome c-L-lysine N6-methyltransferase activity" EXACT [EC:2.1.1.59] xref: EC:2.1.1.59 xref: MetaCyc:2.1.1.59-RXN is_a: GO:0016279 ! protein-lysine N-methyltransferase activity [Term] id: GO:0000278 name: mitotic cell cycle namespace: biological_process def: "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." [GOC:mah, ISBN:0815316194, Reactome:69278] subset: goslim_yeast xref: Reactome:REACT_100451 "Cell Cycle, Mitotic, Taeniopygia guttata" xref: Reactome:REACT_104035 "Cell Cycle, Mitotic, Sus scrofa" xref: Reactome:REACT_104195 "Cell Cycle, Mitotic, Canis familiaris" xref: Reactome:REACT_105856 "Cell Cycle, Mitotic, Danio rerio" xref: Reactome:REACT_108233 "Cell Cycle, Mitotic, Saccharomyces cerevisiae" xref: Reactome:REACT_152 "Cell Cycle, Mitotic, Homo sapiens" xref: Reactome:REACT_28464 "Cell Cycle, Mitotic, Xenopus tropicalis" xref: Reactome:REACT_28953 "Cell Cycle, Mitotic, Bos taurus" xref: Reactome:REACT_33388 "Cell Cycle, Mitotic, Rattus norvegicus" xref: Reactome:REACT_53493 "Cell Cycle, Mitotic, Plasmodium falciparum" xref: Reactome:REACT_79085 "Cell Cycle, Mitotic, Schizosaccharomyces pombe" xref: Reactome:REACT_84794 "Cell Cycle, Mitotic, Caenorhabditis elegans" xref: Reactome:REACT_85137 "Cell Cycle, Mitotic, Gallus gallus" xref: Reactome:REACT_85950 "Cell Cycle, Mitotic, Arabidopsis thaliana" xref: Reactome:REACT_90332 "Cell Cycle, Mitotic, Mus musculus" xref: Reactome:REACT_90846 "Cell Cycle, Mitotic, Oryza sativa" xref: Reactome:REACT_96281 "Cell Cycle, Mitotic, Drosophila melanogaster" xref: Reactome:REACT_97744 "Cell Cycle, Mitotic, Dictyostelium discoideum" xref: Reactome:REACT_98208 "Cell Cycle, Mitotic, Mycobacterium tuberculosis" is_a: GO:0007049 ! cell cycle intersection_of: GO:0007049 ! cell cycle intersection_of: has_part GO:0007067 ! mitotic nuclear division relationship: has_part GO:0007067 ! mitotic nuclear division [Term] id: GO:0000279 name: M phase namespace: biological_process def: "A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase." [GOC:mtg_cell_cycle] comment: Note that this term should not be used for direct annotation. If you are trying to make an annotation to x phase, it is likely that the correct annotation is 'regulation of x/y phase transition' or to a process which occurs during the reported phase (i.e mitotic DNA replication for mitotic S-phase). To capture the phase when a specific location or process is observed, the phase term can be used in an annotation extension (PMID:24885854) applied to a cellular component term (with the relation exists_during) or a biological process term (with the relation happens_during). subset: gocheck_do_not_annotate synonym: "M-phase" EXACT [] xref: Wikipedia:M_phase is_a: GO:0022403 ! cell cycle phase [Term] id: GO:0000280 name: nuclear division namespace: biological_process def: "The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei." [GOC:mah] subset: goslim_pir synonym: "karyokinesis" RELATED [] is_a: GO:0048285 ! organelle fission [Term] id: GO:0000281 name: mitotic cytokinesis namespace: biological_process def: "A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells." [GOC:mtg_cell_cycle] subset: goslim_pombe synonym: "cytokinesis after mitosis" EXACT [] is_a: GO:0061640 ! cytoskeleton-dependent cytokinesis is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0061640 ! cytoskeleton-dependent cytokinesis intersection_of: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0000278 ! mitotic cell cycle [Term] id: GO:0000282 name: cellular bud site selection namespace: biological_process def: "The specification of the site where a daughter cell will form, in organisms that reproduce by budding. An example of this process is found in Saccharomyces cerevisiae." [GOC:mah] comment: Note that this term was split from 'bud site selection/establishment of cell polarity (sensu Saccharomyces) ; GO:0007115' (a sibling term, 'establishment of cell polarity (sensu Saccharomyces) ; GO:0000283', was created but has since been merged with 'establishment of cell polarity' ; GO:0030010). synonym: "bud site selection/establishment of cell polarity" BROAD [] is_a: GO:0030010 ! establishment of cell polarity is_a: GO:1903047 ! mitotic cell cycle process relationship: part_of GO:0000281 ! mitotic cytokinesis [Term] id: GO:0000284 name: obsolete shmoo orientation namespace: biological_process def: "OBSOLETE (was not defined before being made obsolete)." [GOC:elh] comment: This term was made obsolete because it is an organism specific term. The entire branch of the ontology was reorganized to be more generally applicable. synonym: "shmoo orientation" EXACT [] is_obsolete: true replaced_by: GO:0000753 [Term] id: GO:0000285 name: 1-phosphatidylinositol-3-phosphate 5-kinase activity namespace: molecular_function def: "Catalysis of the reaction: a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + ADP + 2 H(+)." [EC:2.7.1.150, RHEA:13612] synonym: "ATP:1-phosphatidyl-1D-myo-inositol-3-phosphate 5-phosphotransferase activity" EXACT [EC:2.7.1.150] synonym: "phosphatidylinositol 3-phosphate 5-kinase activity" EXACT [EC:2.7.1.150] synonym: "phosphatidylinositol-3-phosphate 5-kinase activity" EXACT [] synonym: "type III PIP kinase activity" RELATED [EC:2.7.1.150] xref: EC:2.7.1.150 xref: KEGG:R05802 xref: MetaCyc:2.7.1.150-RXN xref: RHEA:13612 is_a: GO:0016307 ! phosphatidylinositol phosphate kinase activity [Term] id: GO:0000286 name: alanine dehydrogenase activity namespace: molecular_function def: "Catalysis of the reaction: L-alanine + H2O + NAD+ = pyruvate + NH3 + NADH + H(+)." [EC:1.4.1.1] subset: gosubset_prok synonym: "AlaDH" RELATED [EC:1.4.1.1] synonym: "alanine oxidoreductase activity" EXACT [EC:1.4.1.1] synonym: "alpha-alanine dehydrogenase activity" EXACT [EC:1.4.1.1] synonym: "L-alanine dehydrogenase activity" EXACT [EC:1.4.1.1] synonym: "L-alanine:NAD+ oxidoreductase (deaminating)" EXACT [EC:1.4.1.1] synonym: "NAD-dependent alanine dehydrogenase activity" EXACT [EC:1.4.1.1] synonym: "NAD-linked alanine dehydrogenase activity" EXACT [EC:1.4.1.1] synonym: "NADH-dependent alanine dehydrogenase activity" EXACT [EC:1.4.1.1] xref: EC:1.4.1.1 xref: MetaCyc:ALANINE-DEHYDROGENASE-RXN xref: RHEA:18408 is_a: GO:0016638 ! oxidoreductase activity, acting on the CH-NH2 group of donors [Term] id: GO:0000287 name: magnesium ion binding namespace: molecular_function def: "Interacting selectively and non-covalently with magnesium (Mg) ions." [GOC:ai] subset: gosubset_prok synonym: "magnesium binding" EXACT [] is_a: GO:0046872 ! metal ion binding [Term] id: GO:0000288 name: nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay namespace: biological_process def: "A major pathway of degradation of nuclear-transcribed mRNAs that proceeds through a series of ordered steps that includes poly(A) tail shortening and that can regulate mRNA stability." [GOC:jp, GOC:krc] synonym: "deadenylation-dependent mRNA decay" EXACT [] synonym: "mRNA breakdown, deadenylation-dependent decay" EXACT [] synonym: "mRNA catabolic process, deadenylation-dependent" EXACT [] synonym: "mRNA catabolic process, deadenylylation-dependent" EXACT [] synonym: "mRNA catabolism, deadenylation-dependent" EXACT [] synonym: "mRNA catabolism, deadenylylation-dependent" EXACT [] synonym: "mRNA degradation, deadenylation-dependent decay" EXACT [] synonym: "nuclear mRNA catabolic process, deadenylation-dependent decay" EXACT [] xref: Reactome:REACT_102357 "Deadenylation-dependent mRNA decay, Xenopus tropicalis" xref: Reactome:REACT_103296 "Deadenylation-dependent mRNA decay, Gallus gallus" xref: Reactome:REACT_105200 "Deadenylation-dependent mRNA decay, Plasmodium falciparum" xref: Reactome:REACT_110041 "Deadenylation-dependent mRNA decay, Caenorhabditis elegans" xref: Reactome:REACT_20639 "Deadenylation-dependent mRNA decay, Homo sapiens" xref: Reactome:REACT_49520 "Deadenylation-dependent mRNA decay, Rattus norvegicus" xref: Reactome:REACT_79530 "Deadenylation-dependent mRNA decay, Saccharomyces cerevisiae" xref: Reactome:REACT_82315 "Deadenylation-dependent mRNA decay, Sus scrofa" xref: Reactome:REACT_83961 "Deadenylation-dependent mRNA decay, Schizosaccharomyces pombe" xref: Reactome:REACT_89647 "Deadenylation-dependent mRNA decay, Drosophila melanogaster" xref: Reactome:REACT_90397 "Deadenylation-dependent mRNA decay, Mus musculus" xref: Reactome:REACT_93483 "Deadenylation-dependent mRNA decay, Taeniopygia guttata" xref: Reactome:REACT_95045 "Deadenylation-dependent mRNA decay, Oryza sativa" xref: Reactome:REACT_95337 "Deadenylation-dependent mRNA decay, Arabidopsis thaliana" xref: Reactome:REACT_96238 "Deadenylation-dependent mRNA decay, Dictyostelium discoideum" xref: Reactome:REACT_96993 "Deadenylation-dependent mRNA decay, Bos taurus" xref: Reactome:REACT_97186 "Deadenylation-dependent mRNA decay, Canis familiaris" xref: Reactome:REACT_99680 "Deadenylation-dependent mRNA decay, Danio rerio" is_a: GO:0000956 ! nuclear-transcribed mRNA catabolic process [Term] id: GO:0000289 name: nuclear-transcribed mRNA poly(A) tail shortening namespace: biological_process def: "Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length." [GOC:krc] synonym: "3' to 5' mRNA deadenylation" RELATED [] synonym: "mRNA deadenylation" RELATED [] synonym: "nuclear mRNA poly(A) tail shortening" RELATED [] xref: Reactome:REACT_102415 "Deadenylation of mRNA, Rattus norvegicus" xref: Reactome:REACT_104397 "Deadenylation of mRNA, Danio rerio" xref: Reactome:REACT_109691 "Deadenylation of mRNA, Bos taurus" xref: Reactome:REACT_111968 "Deadenylation of mRNA, Drosophila melanogaster" xref: Reactome:REACT_20514 "Deadenylation of mRNA, Homo sapiens" xref: Reactome:REACT_30693 "Deadenylation of mRNA, Xenopus tropicalis" xref: Reactome:REACT_31579 "Deadenylation of mRNA, Canis familiaris" xref: Reactome:REACT_78492 "Deadenylation of mRNA, Mus musculus" xref: Reactome:REACT_83021 "Deadenylation of mRNA, Taeniopygia guttata" is_a: GO:0000956 ! nuclear-transcribed mRNA catabolic process relationship: part_of GO:0000288 ! nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay [Term] id: GO:0000290 name: deadenylation-dependent decapping of nuclear-transcribed mRNA namespace: biological_process def: "Cleavage of the 5'-cap of a nuclear mRNA triggered by shortening of the poly(A) tail to below a minimum functional length." [GOC:krc] synonym: "deadenylation-dependent decapping of nuclear mRNA" EXACT [] synonym: "deadenylylation-dependent decapping" EXACT [] is_a: GO:0000956 ! nuclear-transcribed mRNA catabolic process relationship: part_of GO:0000288 ! nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay [Term] id: GO:0000291 name: nuclear-transcribed mRNA catabolic process, exonucleolytic namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of the transcript body of a nuclear-transcribed mRNA that occurs when the ends are not protected by the 5'-cap or the 3'-poly(A) tail." [GOC:krc] synonym: "exonucleolytic degradation of mRNA" EXACT [] synonym: "mRNA breakdown, exonucleolytic" EXACT [] synonym: "mRNA degradation, exonucleolytic" EXACT [] synonym: "nuclear mRNA catabolic process, exonucleolytic" EXACT [] is_a: GO:0000956 ! nuclear-transcribed mRNA catabolic process [Term] id: GO:0000292 name: RNA fragment catabolic process namespace: biological_process alt_id: GO:0030452 def: "The chemical reactions and pathways resulting in the breakdown of a fragment of RNA, such as excised introns or sequences removed from ribosomal RNA during processing." [GOC:mah] subset: gosubset_prok synonym: "group I intron catabolic process" NARROW [] synonym: "RNA fragment breakdown" EXACT [] synonym: "RNA fragment catabolism" EXACT [GOC:mah] synonym: "RNA fragment degradation" EXACT [] is_a: GO:0006401 ! RNA catabolic process [Term] id: GO:0000293 name: ferric-chelate reductase activity namespace: molecular_function def: "Catalysis of the reaction: 2 Fe2+ + NAD+ = 2 Fe3+ + NADH + H(+)." [EC:1.16.1.7] comment: Note that this function was formerly EC:1.6.99.13. synonym: "Fe(II):NAD+ oxidoreductase activity" EXACT [EC:1.16.1.7] synonym: "ferric chelate reductase activity" EXACT [EC:1.16.1.7] synonym: "iron chelate reductase activity" RELATED [EC:1.16.1.7] synonym: "NADH2:Fe3+ oxidoreductase activity" EXACT [EC:1.16.1.7] synonym: "NADH:Fe(3+) oxidoreductase activity" EXACT [EC:1.16.1.7] synonym: "NADH:Fe(3+)-EDTA reductase activity" EXACT [EC:1.16.1.7] synonym: "NADH:Fe3+ oxidoreductase activity" EXACT [EC:1.16.1.7] synonym: "NADH:Fe3+-EDTA reductase activity" EXACT [EC:1.16.1.7] xref: EC:1.16.1.7 xref: MetaCyc:FERRIC-CHELATE-REDUCTASE-RXN xref: RHEA:15064 is_a: GO:0016723 ! oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor [Term] id: GO:0000294 name: nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay namespace: biological_process def: "A minor degradation pathway nuclear-transcribed mRNAs that begins with an endonucleolytic cleavage to generate unprotected ends." [GOC:krc] synonym: "endonucleolytic mRNA decay" EXACT [] synonym: "mRNA breakdown, endonucleolytic cleavage-dependent decay" EXACT [] synonym: "mRNA catabolic process, endonucleolytic" EXACT [] synonym: "mRNA catabolism, endonucleolytic" EXACT [] synonym: "mRNA degradation, endonucleolytic cleavage-dependent decay" EXACT [] synonym: "nuclear mRNA catabolic process, endonucleolytic cleavage-dependent decay" EXACT [] is_a: GO:0000956 ! nuclear-transcribed mRNA catabolic process [Term] id: GO:0000295 name: adenine nucleotide transmembrane transporter activity namespace: molecular_function def: "Catalysis of the transfer of adenine nucleotides (AMP, ADP, and ATP) from one side of the membrane to the other." [PMID:11566870] xref: Reactome:REACT_101864 "PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP, Bos taurus" xref: Reactome:REACT_107442 "PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP, Rattus norvegicus" xref: Reactome:REACT_113419 "PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP, Oryza sativa" xref: Reactome:REACT_16948 "PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP, Homo sapiens" xref: Reactome:REACT_28950 "PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP, Mus musculus" xref: Reactome:REACT_30244 "PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP, Drosophila melanogaster" xref: Reactome:REACT_33254 "PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP, Dictyostelium discoideum" xref: Reactome:REACT_80715 "PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP, Taeniopygia guttata" xref: Reactome:REACT_83323 "PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP, Gallus gallus" xref: Reactome:REACT_85299 "PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP, Saccharomyces cerevisiae" xref: Reactome:REACT_86138 "PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP, Canis familiaris" xref: Reactome:REACT_86805 "PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP, Danio rerio" xref: Reactome:REACT_89005 "PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP, Sus scrofa" xref: Reactome:REACT_91614 "PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP, Xenopus tropicalis" is_a: GO:0015216 ! purine nucleotide transmembrane transporter activity relationship: part_of GO:0051503 ! adenine nucleotide transport [Term] id: GO:0000296 name: spermine transport namespace: biological_process def: "The directed movement of spermine, N,N-bis(3-aminopropyl)-1,4-diaminobutane, a polyamine formed by the transfer of a propylamine group from decarboxylated S-adenosylmethionine to spermidine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc, ISBN:0198506732] is_a: GO:0015846 ! polyamine transport [Term] id: GO:0000297 name: spermine transmembrane transporter activity namespace: molecular_function def: "Enables the transfer of spermine from one side of the membrane to the other. Spermine is a polybasic amine found in human sperm, in ribosomes and in some viruses, which is involved in nucleic acid packaging. Synthesis is regulated by ornithine decarboxylase which plays a key role in control of DNA replication." [GOC:ai] is_a: GO:0015203 ! polyamine transmembrane transporter activity relationship: part_of GO:1903710 ! spermine transmembrane transport [Term] id: GO:0000298 name: endopolyphosphatase activity namespace: molecular_function def: "Catalysis of the reaction: polyphosphate + n H2O = (n+1) oligophosphate. The product contains 4 or 5 phosphate residues." [EC:3.6.1.10] synonym: "metaphosphatase activity" BROAD [EC:3.6.1.10] synonym: "polymetaphosphatase activity" EXACT [EC:3.6.1.10] synonym: "polyphosphatase activity" BROAD [EC:3.6.1.10] synonym: "polyphosphate depolymerase activity" BROAD [EC:3.6.1.10] synonym: "polyphosphate polyphosphohydrolase activity" EXACT [EC:3.6.1.10] xref: EC:3.6.1.10 xref: MetaCyc:ENDOPOLYPHOSPHATASE-RXN is_a: GO:0016462 ! pyrophosphatase activity [Term] id: GO:0000299 name: obsolete integral to membrane of membrane fraction namespace: cellular_component def: "OBSOLETE: Integral to that fraction of cells, prepared by disruptive biochemical methods, that includes the plasma and other membranes; require detergents, such as Triton X-100, to be released from membranes." [PMID:10512869] comment: This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component. synonym: "integral to membrane of membrane fraction" EXACT [] is_obsolete: true consider: GO:0016021 [Term] id: GO:0000300 name: obsolete peripheral to membrane of membrane fraction namespace: cellular_component def: "OBSOLETE: Peripheral to that fraction of cells, prepared by disruptive biochemical methods, that includes the plasma and other membranes; can be extracted from membrane fraction with high concentrations of salt or high pH." [PMID:10512869] comment: This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component. synonym: "peripheral to membrane of membrane fraction" EXACT [] is_obsolete: true consider: GO:0019898 [Term] id: GO:0000301 name: retrograde transport, vesicle recycling within Golgi namespace: biological_process def: "The retrograde movement of substances within the Golgi, mediated by COP I vesicles. Cis-Golgi vesicles are constantly moving forward through the Golgi stack by cisternal progression, eventually becoming trans-Golgi vesicles. They then selectively transport membrane and luminal proteins from the trans- to the medial-Golgi while leaving others behind in the trans-Golgi cisternae; similarly, they selectively move proteins from the medial- to the cis-Golgi." [ISBN:0716731363] synonym: "retrograde (vesicle recycling within Golgi) transport" EXACT [] is_a: GO:0006891 ! intra-Golgi vesicle-mediated transport [Term] id: GO:0000302 name: response to reactive oxygen species namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals." [GOC:krc] subset: gosubset_prok synonym: "response to active oxygen species" EXACT [] synonym: "response to AOS" EXACT [] synonym: "response to reactive oxidative species" EXACT [] synonym: "response to reactive oxygen intermediate" EXACT [] synonym: "response to ROI" EXACT [] synonym: "response to ROS" EXACT [] is_a: GO:0006979 ! response to oxidative stress is_a: GO:1901700 ! response to oxygen-containing compound [Term] id: GO:0000303 name: response to superoxide namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion." [GOC:krc, ISBN:0198506732] subset: gosubset_prok is_a: GO:0000305 ! response to oxygen radical [Term] id: GO:0000304 name: response to singlet oxygen namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a singlet oxygen stimulus. Singlet oxygen is a dioxygen (O2) molecule in which two 2p electrons have similar spin. Singlet oxygen is more highly reactive than the form in which these electrons are of opposite spin, and it is produced in mutant chloroplasts lacking carotenoids and by leukocytes during metabolic burst." [GOC:krc, ISBN:0124325653, ISBN:0198506732] subset: gosubset_prok is_a: GO:0000302 ! response to reactive oxygen species is_a: GO:0010035 ! response to inorganic substance [Term] id: GO:0000305 name: response to oxygen radical namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen radical stimulus. An oxygen radical is any oxygen species that carries a free electron; examples include hydroxyl radicals and the superoxide anion." [GOC:krc, ISBN:0124325653] subset: gosubset_prok is_a: GO:0000302 ! response to reactive oxygen species is_a: GO:0010035 ! response to inorganic substance [Term] id: GO:0000306 name: extrinsic component of vacuolar membrane namespace: cellular_component def: "The component of a vacuolar membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region." [GOC:dos, GOC:jl, GOC:mah] synonym: "extrinsic to vacuolar membrane" EXACT [] is_a: GO:0031312 ! extrinsic component of organelle membrane is_a: GO:0044437 ! vacuolar part intersection_of: GO:0019898 ! extrinsic component of membrane intersection_of: part_of GO:0005774 ! vacuolar membrane relationship: part_of GO:0005774 ! vacuolar membrane [Term] id: GO:0000307 name: cyclin-dependent protein kinase holoenzyme complex namespace: cellular_component def: "Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner." [GOC:krc, PMID:11602261] subset: goslim_pir synonym: "CDK holoenzyme" EXACT [] is_a: GO:0044424 ! intracellular part is_a: GO:1902554 ! serine/threonine protein kinase complex [Term] id: GO:0000308 name: cytoplasmic cyclin-dependent protein kinase holoenzyme complex namespace: cellular_component def: "Cyclin-dependent protein kinase (CDK) complex found in the cytoplasm." [GOC:krc] synonym: "CDK holoenzyme" BROAD [] is_a: GO:0000307 ! cyclin-dependent protein kinase holoenzyme complex is_a: GO:0044444 ! cytoplasmic part intersection_of: GO:0000307 ! cyclin-dependent protein kinase holoenzyme complex intersection_of: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0000309 name: nicotinamide-nucleotide adenylyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + nicotinamide nucleotide = diphosphate + NAD+." [EC:2.7.7.1] subset: gosubset_prok synonym: "adenosine triphosphate-nicotinamide mononucleotide transadenylase activity" EXACT [EC:2.7.7.1] synonym: "ATP:nicotinamide-nucleotide adenylyltransferase activity" EXACT [] synonym: "ATP:NMN adenylyltransferase activity" EXACT [EC:2.7.7.1] synonym: "diphosphopyridine nucleotide pyrophosphorylase activity" RELATED [EC:2.7.7.1] synonym: "NAD(+) diphosphorylase activity" NARROW [EC:2.7.7.1] synonym: "NAD(+) pyrophosphorylase activity" NARROW [EC:2.7.7.1] synonym: "NAD+ diphosphorylase activity" EXACT [EC:2.7.7.1] synonym: "NAD+ pyrophosphorylase activity" EXACT [EC:2.7.7.1] synonym: "nicotinamide adenine dinucleotide pyrophosphorylase activity" NARROW [EC:2.7.7.1] synonym: "nicotinamide mononucleotide adenylyltransferase activity" NARROW [EC:2.7.7.1] synonym: "NMN adenylyltransferase activity" NARROW [EC:2.7.7.1] synonym: "NMNAT activity" NARROW [EC:2.7.7.1] xref: EC:2.7.7.1 xref: MetaCyc:2.7.7.1-RXN xref: Reactome:REACT_101807 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3], Sus scrofa" xref: Reactome:REACT_102033 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Canis familiaris" xref: Reactome:REACT_103802 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Mus musculus" xref: Reactome:REACT_105839 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1], Xenopus tropicalis" xref: Reactome:REACT_107769 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3], Canis familiaris" xref: Reactome:REACT_107952 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3], Drosophila melanogaster" xref: Reactome:REACT_108630 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1], Sus scrofa" xref: Reactome:REACT_108997 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Sus scrofa" xref: Reactome:REACT_11116 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Homo sapiens" xref: Reactome:REACT_11196 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3], Homo sapiens" xref: Reactome:REACT_112138 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Arabidopsis thaliana" xref: Reactome:REACT_11237 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1], Homo sapiens" xref: Reactome:REACT_112385 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Oryza sativa" xref: Reactome:REACT_114383 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3], Dictyostelium discoideum" xref: Reactome:REACT_114560 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Schizosaccharomyces pombe" xref: Reactome:REACT_114828 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Saccharomyces cerevisiae" xref: Reactome:REACT_115028 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1], Dictyostelium discoideum" xref: Reactome:REACT_29972 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Caenorhabditis elegans" xref: Reactome:REACT_30979 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1], Oryza sativa" xref: Reactome:REACT_31171 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1], Arabidopsis thaliana" xref: Reactome:REACT_31453 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1], Taeniopygia guttata" xref: Reactome:REACT_70840 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3], Saccharomyces cerevisiae" xref: Reactome:REACT_77837 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3], Oryza sativa" xref: Reactome:REACT_78904 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Dictyostelium discoideum" xref: Reactome:REACT_79519 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Rattus norvegicus" xref: Reactome:REACT_79745 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3], Danio rerio" xref: Reactome:REACT_79909 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1], Canis familiaris" xref: Reactome:REACT_80724 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3], Schizosaccharomyces pombe" xref: Reactome:REACT_80917 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Danio rerio" xref: Reactome:REACT_81520 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Taeniopygia guttata" xref: Reactome:REACT_81532 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1], Bos taurus" xref: Reactome:REACT_83285 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1], Mus musculus" xref: Reactome:REACT_84119 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3], Mus musculus" xref: Reactome:REACT_86854 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Xenopus tropicalis" xref: Reactome:REACT_90006 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1], Saccharomyces cerevisiae" xref: Reactome:REACT_92077 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3], Gallus gallus" xref: Reactome:REACT_93517 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1], Drosophila melanogaster" xref: Reactome:REACT_95186 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3], Rattus norvegicus" xref: Reactome:REACT_96395 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1], Schizosaccharomyces pombe" xref: Reactome:REACT_96707 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Gallus gallus" xref: Reactome:REACT_97201 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1], Rattus norvegicus" xref: Reactome:REACT_97323 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3], Taeniopygia guttata" xref: Reactome:REACT_97434 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3], Arabidopsis thaliana" xref: Reactome:REACT_98853 "Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2], Bos taurus" xref: RHEA:21363 is_a: GO:0070566 ! adenylyltransferase activity [Term] id: GO:0000310 name: xanthine phosphoribosyltransferase activity namespace: molecular_function alt_id: GO:0009043 def: "Catalysis of the reaction: 5-phospho-alpha-D-ribose 1-diphosphate + xanthine = (9-D-ribosylxanthine)-5'-phosphate + diphosphate." [EC:2.4.2.22, GOC:clt] subset: gosubset_prok synonym: "5-phospho-alpha-D-ribose-1-diphosphate:xanthine phospho-D-ribosyltransferase activity" EXACT [EC:2.4.2.22] synonym: "Xan phosphoribosyltransferase activity" EXACT [EC:2.4.2.22] synonym: "xanthine-guanine phosphoribosyltransferase activity" EXACT [] synonym: "xanthosine 5'-phosphate pyrophosphorylase activity" EXACT [EC:2.4.2.22] synonym: "xanthylate pyrophosphorylase activity" EXACT [EC:2.4.2.22] synonym: "xanthylic pyrophosphorylase activity" EXACT [EC:2.4.2.22] synonym: "XMP pyrophosphorylase activity" EXACT [EC:2.4.2.22] synonym: "XMP:diphosphate 5-phospho-alpha-D-ribosyltransferase activity" EXACT [EC:2.4.2.22] xref: EC:2.4.2.22 xref: MetaCyc:XANPRIBOSYLTRAN-RXN xref: RHEA:10803 is_a: GO:0016763 ! transferase activity, transferring pentosyl groups [Term] id: GO:0000311 name: plastid large ribosomal subunit namespace: cellular_component def: "The larger of the two subunits of a plastid ribosome. Two sites on the ribosomal large subunit are involved in translation: the aminoacyl site (A site) and peptidyl site (P site)." [GOC:mcc] is_a: GO:0000315 ! organellar large ribosomal subunit is_a: GO:0044435 ! plastid part intersection_of: GO:0015934 ! large ribosomal subunit intersection_of: part_of GO:0009547 ! plastid ribosome relationship: part_of GO:0009547 ! plastid ribosome [Term] id: GO:0000312 name: plastid small ribosomal subunit namespace: cellular_component def: "The smaller of the two subunits of a plastid ribosome." [GOC:mcc] is_a: GO:0000314 ! organellar small ribosomal subunit is_a: GO:0044435 ! plastid part intersection_of: GO:0015935 ! small ribosomal subunit intersection_of: part_of GO:0009547 ! plastid ribosome relationship: part_of GO:0009547 ! plastid ribosome [Term] id: GO:0000313 name: organellar ribosome namespace: cellular_component def: "A ribosome contained within a subcellular membrane-bounded organelle." [GOC:mah, GOC:mcc] is_a: GO:0005840 ! ribosome is_a: GO:0044422 ! organelle part intersection_of: GO:0005840 ! ribosome intersection_of: part_of GO:0043226 ! organelle relationship: part_of GO:0043226 ! organelle [Term] id: GO:0000314 name: organellar small ribosomal subunit namespace: cellular_component def: "The smaller of the two subunits of an organellar ribosome." [GOC:mcc] is_a: GO:0015935 ! small ribosomal subunit intersection_of: GO:0015935 ! small ribosomal subunit intersection_of: part_of GO:0000313 ! organellar ribosome relationship: part_of GO:0000313 ! organellar ribosome [Term] id: GO:0000315 name: organellar large ribosomal subunit namespace: cellular_component def: "The larger of the two subunits of an organellar ribosome. Two sites on the ribosomal large subunit are involved in translation: the aminoacyl site (A site) and peptidyl site (P site)." [GOC:mcc] is_a: GO:0015934 ! large ribosomal subunit intersection_of: GO:0015934 ! large ribosomal subunit intersection_of: part_of GO:0000313 ! organellar ribosome relationship: part_of GO:0000313 ! organellar ribosome [Term] id: GO:0000316 name: sulfite transport namespace: biological_process def: "The directed movement of sulfite into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc] synonym: "sulphite transport" EXACT [] is_a: GO:0015698 ! inorganic anion transport is_a: GO:0072348 ! sulfur compound transport [Term] id: GO:0000319 name: sulfite transmembrane transporter activity namespace: molecular_function def: "Enables the transfer of sulfite ions from one side of a membrane to the other." [GOC:as] synonym: "sulphite transporter activity" EXACT [] is_a: GO:0015103 ! inorganic anion transmembrane transporter activity is_a: GO:1901682 ! sulfur compound transmembrane transporter activity [Term] id: GO:0000320 name: re-entry into mitotic cell cycle namespace: biological_process def: "The resumption of the mitotic cell division cycle by cells that were in a quiescent or other non-dividing state." [GOC:krc] is_a: GO:0022402 ! cell cycle process [Term] id: GO:0000321 name: re-entry into mitotic cell cycle after pheromone arrest namespace: biological_process def: "The resumption of the mitotic cell division cycle by pheromone-arrested cells that have not mated. An example of this process is found in Saccharomyces cerevisiae." [GOC:krc, PMID:9927449] is_a: GO:0000320 ! re-entry into mitotic cell cycle is_a: GO:0000754 ! adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion [Term] id: GO:0000322 name: storage vacuole namespace: cellular_component def: "A vacuole that functions primarily in the storage of materials, including nutrients, pigments, waste products, and small molecules." [GOC:krc] is_a: GO:0005773 ! vacuole [Term] id: GO:0000323 name: lytic vacuole namespace: cellular_component def: "A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases." [GOC:krc] is_a: GO:0005773 ! vacuole [Term] id: GO:0000324 name: fungal-type vacuole namespace: cellular_component def: "A vacuole that has both lytic and storage functions. The fungal vacuole is a large, membrane-bounded organelle that functions as a reservoir for the storage of small molecules (including polyphosphate, amino acids, several divalent cations (e.g. calcium), other ions, and other small molecules) as well as being the primary compartment for degradation. It is an acidic compartment, containing an ensemble of acid hydrolases. At least in S. cerevisiae, there are indications that the morphology of the vacuole is variable and correlated with the cell cycle, with logarithmically growing cells having a multilobed, reticulated vacuole, while stationary phase cells contain a single large structure." [GOC:mah, GOC:mtg_sensu, ISBN:0879693649] synonym: "vacuole, cell cycle-correlated morphology" EXACT [] is_a: GO:0000322 ! storage vacuole is_a: GO:0000323 ! lytic vacuole [Term] id: GO:0000325 name: plant-type vacuole namespace: cellular_component def: "A closed structure that is completely surrounded by a unit membrane, contains liquid, and retains the same shape regardless of cell cycle phase. An example of this structure is found in Arabidopsis thaliana." [GOC:mtg_sensu, ISBN:0815316208] synonym: "vacuole, cell cycle-independent morphology" EXACT [] is_a: GO:0005773 ! vacuole [Term] id: GO:0000326 name: protein storage vacuole namespace: cellular_component def: "A storage vacuole that contains a lytic vacuole; identified in plants." [PMID:11739409] is_a: GO:0000322 ! storage vacuole is_a: GO:0000325 ! plant-type vacuole [Term] id: GO:0000327 name: lytic vacuole within protein storage vacuole namespace: cellular_component def: "A membrane-bounded compartment containing crystals of phytic acid and proteins characteristic of a lytic vacuole, found within a storage vacuole." [PMID:11739490] is_a: GO:0000323 ! lytic vacuole is_a: GO:0044437 ! vacuolar part intersection_of: GO:0000323 ! lytic vacuole intersection_of: part_of GO:0000326 ! protein storage vacuole relationship: part_of GO:0000326 ! protein storage vacuole [Term] id: GO:0000328 name: fungal-type vacuole lumen namespace: cellular_component def: "The volume enclosed within the vacuolar membrane of a vacuole, the shape of which correlates with cell cycle phase. An example of this structure is found in Saccharomyces cerevisiae." [GOC:krc, GOC:mtg_sensu] synonym: "lumen of vacuole with cell cycle-correlated morphology" EXACT [] is_a: GO:0005775 ! vacuolar lumen relationship: part_of GO:0000324 ! fungal-type vacuole [Term] id: GO:0000329 name: fungal-type vacuole membrane namespace: cellular_component def: "The lipid bilayer surrounding a vacuole, the shape of which correlates with cell cycle phase. The membrane separates its contents from the cytoplasm of the cell. An example of this structure is found in Saccharomyces cerevisiae." [GOC:krc, GOC:mtg_sensu] synonym: "fungal-type vacuolar membrane" RELATED [] synonym: "membrane of vacuole with cell cycle-correlated morphology" EXACT [] is_a: GO:0098852 ! lytic vacuole membrane relationship: part_of GO:0000324 ! fungal-type vacuole [Term] id: GO:0000330 name: plant-type vacuole lumen namespace: cellular_component def: "The volume enclosed within the vacuolar membrane of a vacuole that retains the same shape regardless of cell cycle phase. An example of this is found in Arabidopsis thaliana." [GOC:krc, GOC:mtg_sensu] synonym: "lumen of vacuole with cell cycle-independent morphology" EXACT [] is_a: GO:0005775 ! vacuolar lumen relationship: part_of GO:0000325 ! plant-type vacuole [Term] id: GO:0000331 name: contractile vacuole namespace: cellular_component def: "A specialized vacuole of eukaryotic cells, especially Protozoa, that fills with water from the cytoplasm and then discharges this externally by the opening of contractile vacuole pores. Its function is probably osmoregulatory." [GOC:jl, PMID:10503189] xref: Wikipedia:Contractile_vacuole is_a: GO:0005773 ! vacuole is_a: GO:0016023 ! cytoplasmic, membrane-bounded vesicle [Term] id: GO:0000332 name: template for synthesis of G-rich strand of telomere DNA activity namespace: molecular_function def: "Provision of the template used by reverse transcriptase to synthesize the G-rich strand of telomeric DNA." [PMID:11812242] comment: Note that this term describes the activity of an RNA gene product that interacts with other nucleic acid molecules via base pairing; it should not be used to annotate proteins. synonym: "telomerase RNA" EXACT [] synonym: "telomerase, template" EXACT [] is_a: GO:0000497 ! base pairing with DNA relationship: part_of GO:0003720 ! telomerase activity [Term] id: GO:0000333 name: telomerase catalytic core complex namespace: cellular_component def: "The minimal catalytic core of telomerase is a ribonucleoprotein complex composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition." [GOC:BHF-UCL, PMID:11884619, PMID:1808260] synonym: "TERT-TERC complex" RELATED [GOC:nc, PMID:19701182] is_a: GO:0005697 ! telomerase holoenzyme complex [Term] id: GO:0000334 name: 3-hydroxyanthranilate 3,4-dioxygenase activity namespace: molecular_function def: "Catalysis of the reaction: 3-hydroxyanthranilate + O(2) = cis,cis-2-amino-3-(3-oxoprop-1-enyl)but-2-enedioate + H(+)." [EC:1.13.11.6, RHEA:17956] subset: gosubset_prok synonym: "3-hydroxyanthranilate oxygenase activity" EXACT [EC:1.13.11.6] synonym: "3-hydroxyanthranilate:oxygen 3,4-oxidoreductase (decyclizing)" EXACT [EC:1.13.11.6] synonym: "3-hydroxyanthranilic acid dioxygenase activity" EXACT [EC:1.13.11.6] synonym: "3-hydroxyanthranilic acid oxygenase activity" EXACT [EC:1.13.11.6] synonym: "3-hydroxyanthranilic oxygenase activity" EXACT [EC:1.13.11.6] synonym: "3HAO" RELATED [EC:1.13.11.6] xref: EC:1.13.11.6 xref: KEGG:R02665 xref: MetaCyc:1.13.11.6-RXN xref: Reactome:REACT_106067 "3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde, Danio rerio" xref: Reactome:REACT_107237 "3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde, Rattus norvegicus" xref: Reactome:REACT_108663 "3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde, Taeniopygia guttata" xref: Reactome:REACT_108942 "3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde, Canis familiaris" xref: Reactome:REACT_612 "3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde, Homo sapiens" xref: Reactome:REACT_78765 "3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde, Caenorhabditis elegans" xref: Reactome:REACT_81621 "3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde, Sus scrofa" xref: Reactome:REACT_83535 "3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde, Saccharomyces cerevisiae" xref: Reactome:REACT_83862 "3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde, Dictyostelium discoideum" xref: Reactome:REACT_84121 "3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde, Gallus gallus" xref: Reactome:REACT_86308 "3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde, Xenopus tropicalis" xref: Reactome:REACT_93632 "3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde, Bos taurus" xref: Reactome:REACT_94190 "3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde, Mus musculus" xref: RHEA:17956 xref: UM-BBD_reactionID:r1027 is_a: GO:0016702 ! oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen [Term] id: GO:0000335 name: negative regulation of transposition, DNA-mediated namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA transposition." [GOC:dph, GOC:krc, GOC:tb] subset: gosubset_prok synonym: "down regulation of DNA transposition" EXACT [] synonym: "down-regulation of DNA transposition" EXACT [] synonym: "downregulation of DNA transposition" EXACT [] synonym: "inhibition of DNA transposition" NARROW [] synonym: "negative regulation of DNA transposition" EXACT [GOC:dph] is_a: GO:0000337 ! regulation of transposition, DNA-mediated is_a: GO:0010529 ! negative regulation of transposition is_a: GO:0045910 ! negative regulation of DNA recombination intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006313 ! transposition, DNA-mediated relationship: negatively_regulates GO:0006313 ! transposition, DNA-mediated [Term] id: GO:0000336 name: positive regulation of transposition, DNA-mediated namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of DNA transposition." [GOC:dph, GOC:krc] subset: gosubset_prok synonym: "activation of DNA transposition" NARROW [] synonym: "positive regulation of DNA transposition" EXACT [GOC:dph] synonym: "stimulation of DNA transposition" NARROW [] synonym: "up regulation of DNA transposition" EXACT [] synonym: "up-regulation of DNA transposition" EXACT [] synonym: "upregulation of DNA transposition" EXACT [] is_a: GO:0000337 ! regulation of transposition, DNA-mediated is_a: GO:0010530 ! positive regulation of transposition is_a: GO:0045911 ! positive regulation of DNA recombination intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006313 ! transposition, DNA-mediated relationship: positively_regulates GO:0006313 ! transposition, DNA-mediated [Term] id: GO:0000337 name: regulation of transposition, DNA-mediated namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA transposition, the process of transposing (moving to a different location) a segment of a chromosome or a piece of a DNA molecule." [GOC:dph, GOC:krc] subset: gosubset_prok synonym: "regulation of DNA transposition" EXACT [GOC:dph] is_a: GO:0000018 ! regulation of DNA recombination is_a: GO:0010528 ! regulation of transposition intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006313 ! transposition, DNA-mediated relationship: regulates GO:0006313 ! transposition, DNA-mediated [Term] id: GO:0000338 name: protein deneddylation namespace: biological_process def: "The removal of a ubiquitin-like protein of the NEDD8 type from a protein." [GOC:krc] is_a: GO:0070646 ! protein modification by small protein removal [Term] id: GO:0000339 name: RNA cap binding namespace: molecular_function def: "Interacting selectively and non-covalently with a 7-methylguanosine (m7G) group or derivative located at the 5' end of an RNA molecule." [GOC:krc] synonym: "binding to mRNA cap" NARROW [] synonym: "mRNA cap binding" NARROW [] synonym: "snRNA cap binding" NARROW [] is_a: GO:0003723 ! RNA binding [Term] id: GO:0000340 name: RNA 7-methylguanosine cap binding namespace: molecular_function def: "Interacting selectively and non-covalently with the 7-methylguanosine group added cotranscriptionally to the 5' end of RNA molecules transcribed by polymerase II." [GOC:krc] synonym: "RNA m7G cap binding" EXACT [] is_a: GO:0000339 ! RNA cap binding [Term] id: GO:0000341 name: RNA trimethylguanosine cap binding namespace: molecular_function def: "Interacting selectively and non-covalently with the trimethylguanosine (m(3)(2,2,7)-GTP) group located at the 5' end of some RNA molecules. Such trimethylated cap structures, generally produced by posttranscriptional modification of a 7-methylguanosine cap, are often found on snRNAs and snoRNAs transcribed by RNA polymerase II, but have also be found on snRNAs transcribed by RNA polymerase III. They have also been found on a subset of the mRNA population in some species, e.g. C. elegans." [GOC:krc] synonym: "RNA m2,2,7G cap binding" EXACT [] is_a: GO:0000339 ! RNA cap binding [Term] id: GO:0000342 name: RNA cap 4 binding namespace: molecular_function def: "Interacting selectively and non-covalently with a hypermethylated cap structure consisting of 7-methylguanosine (m(7)G) followed by four methylated nucleotides (cap 4): 7-methylguanosine-ppp-N6, N6, 2'-O-trimethyladenosine-p-2'-O-methyladenosine-p-2'-O-methylcytosine-p-N3, 2'-O-dimethyluridine Such caps are known to be found at the 5' ends of SL RNAs of trypanosomatid protozoa." [GOC:krc, PMID:10880518, PMID:12121975] is_a: GO:0000339 ! RNA cap binding [Term] id: GO:0000343 name: plastid-encoded plastid RNA polymerase complex A namespace: cellular_component def: "A plastid-encoded DNA-directed RNA polymerase complex that resembles eubacterial multisubunit RNA polymerases, with a core composed of alpha, beta, and beta-prime subunits. An additional subunit, a sigma factor, is required for promoter recognition. PEP-A is generated from the PEP-B form during chloroplast maturation to generate a complex composed of at least thirteen polypeptides that is not sensitive to the antibiotic rifampicin, like its precursor form the PEP-B complex." [PMID:10946105] synonym: "PEP-A" EXACT [] is_a: GO:0000427 ! plastid-encoded plastid RNA polymerase complex [Term] id: GO:0000344 name: plastid-encoded plastid RNA polymerase complex B namespace: cellular_component def: "A plastid-encoded DNA-directed RNA polymerase complex that resembles eubacterial multisubunit RNA polymerases with a core composed of alpha, beta, and beta-prime subunits. An additional subunit, a sigma factor, is required for promoter recognition. PEP-B is distinguished from PEP-A by its sensitivity to the antibiotic rifampicin. PEP-B is found in both etioplasts and chloroplasts, but is the predominate form in etioplasts. It forms the core of the PEP-A form; the conversion from PEP-B to PEP-A occurs during chloroplast maturation." [PMID:10946105] synonym: "PEP-B" EXACT [] is_a: GO:0000427 ! plastid-encoded plastid RNA polymerase complex [Term] id: GO:0000345 name: cytosolic DNA-directed RNA polymerase complex namespace: cellular_component def: "The eubacterial DNA-directed RNA polymerase is a multisubunit complex with a core composed of the essential subunits beta-prime, beta, and two copies of alpha and a fifth nonessential subunit called omega. An additional subunit, a sigma factor, is required for promoter recognition and specificity." [PMID:11158566] subset: gosubset_prok is_a: GO:0000428 ! DNA-directed RNA polymerase complex is_a: GO:0044445 ! cytosolic part [Term] id: GO:0000346 name: transcription export complex namespace: cellular_component def: "The transcription export (TREX) complex couples transcription elongation by RNA polymerase II to mRNA export. The complex associates with the polymerase and travels with it along the length of the transcribed gene. TREX is composed of the THO transcription elongation complex as well as other proteins that couple THO to mRNA export proteins. The TREX complex is known to be found in a wide range of eukaryotes, including S. cerevisiae and metazoans." [GOC:krc, PMID:11979277] subset: goslim_pir synonym: "TREX complex" EXACT [] is_a: GO:0043234 ! protein complex is_a: GO:0044428 ! nuclear part [Term] id: GO:0000347 name: THO complex namespace: cellular_component def: "The THO complex is a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. The THO complex is also part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm. In S. cerevisiae, it is composed of four subunits: Hpr1p, Tho2p, Thp1p, and Mft1p, while the human complex is composed of 7 subunits." [GOC:krc, PMID:11060033, PMID:11979277, PMID:16983072] subset: goslim_pir is_a: GO:0043234 ! protein complex is_a: GO:0044428 ! nuclear part [Term] id: GO:0000348 name: mRNA branch site recognition namespace: biological_process alt_id: GO:0000370 alt_id: GO:0000371 def: "Recognition of the pre-mRNA branch site sequence by components of the assembling spliceosome." [GOC:krc, ISBN:0879695897] comment: Note that this step represents the formation of the B complex (yeast) or the A complex (mammalian). synonym: "nuclear mRNA branch site recognition" EXACT [GOC:vw] synonym: "spliceosomal A complex biosynthesis" NARROW [] synonym: "spliceosomal A complex formation" NARROW [] synonym: "spliceosomal B complex biosynthesis" NARROW [] synonym: "spliceosomal B complex formation" NARROW [] synonym: "U12-type nuclear mRNA branch site recognition" NARROW [] synonym: "U2-type nuclear mRNA branch site recognition" NARROW [] is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0000245 ! spliceosomal complex assembly [Term] id: GO:0000349 name: generation of catalytic spliceosome for first transesterification step namespace: biological_process alt_id: GO:0000356 alt_id: GO:0000357 def: "Formation of a catalytic spliceosome complex ready to perform the first splicing reaction. This occurs by an ATP-dependent conformational change of the pre-catalytic spliceosome." [GOC:krc, ISBN:0879695897] comment: Note that this step represents the formation of the A2-2 complex (yeast) or the C1 complex (mammalian). synonym: "catalytic spliceosome assembly for first transesterification step" RELATED [] synonym: "formation of catalytic spliceosome for first transesterification step" EXACT [] synonym: "spliceosomal A2-2 complex biosynthesis" NARROW [] synonym: "spliceosomal A2-2 complex formation" NARROW [] synonym: "spliceosomal C1 complex biosynthesis" NARROW [] synonym: "spliceosomal C1 complex formation" NARROW [] synonym: "U12-type catalytic spliceosome formation for first transesterification step" NARROW [] synonym: "U2-type catalytic spliceosome formation for first transesterification step" NARROW [] is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0000393 ! spliceosomal conformational changes to generate catalytic conformation [Term] id: GO:0000350 name: generation of catalytic spliceosome for second transesterification step namespace: biological_process alt_id: GO:0000358 alt_id: GO:0000359 def: "Conformational rearrangement of the spliceosomal complex containing the RNA products from the 1st step of splicing to form the catalytic site for the second step of splicing." [GOC:krc, ISBN:0879695897] comment: Note that this step represents formation of the A2-3 complex (yeast) or the C2 complex (mammalian). synonym: "catalytic spliceosome assembly for second transesterification step" RELATED [] synonym: "formation of catalytic spliceosome for second transesterification step" EXACT [] synonym: "formation of catalytic U12-type spliceosome for second transesterification step" NARROW [] synonym: "formation of catalytic U2-type spliceosome for second transesterification step" NARROW [] synonym: "formation of spliceosomal A2-2 complex" NARROW [] synonym: "formation of spliceosomal C1 complex" NARROW [] synonym: "lariat formation, 5'-splice site cleavage" RELATED [] synonym: "spliceosomal A2-3 complex biosynthesis" NARROW [] synonym: "spliceosomal A2-3 complex formation" NARROW [] synonym: "spliceosomal C2 complex biosynthesis" NARROW [] synonym: "spliceosomal C2 complex formation" NARROW [] is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0000393 ! spliceosomal conformational changes to generate catalytic conformation [Term] id: GO:0000352 name: trans assembly of SL-containing precatalytic spliceosome namespace: biological_process def: "Assembly of a spliceosomal complex containing the SL RNA and the pre-mRNA to be joined, as well as all the spliceosomal snRNPs involved in trans leader splicing. Formation of the trans leader spliceosome brings together the quadruple SL/U4/U5/U6 snRNP and the complex of the U2 snRNP with the splice site of the pre-mRNA." [GOC:krc, GOC:mtg_mpo, ISBN:0879695897] synonym: "trans assembly of spliced leader-containing precatalytic spliceosome" EXACT [] is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0000245 ! spliceosomal complex assembly relationship: part_of GO:0045291 ! mRNA trans splicing, SL addition [Term] id: GO:0000353 name: formation of quadruple SL/U4/U5/U6 snRNP namespace: biological_process def: "Formation of a quadruple snRNP complex composed of the spliced leader (SL) RNA along with the U4/U6-U5 tri-snRNP complex. Interactions that may facilitate this include a duplex between the SL and U6 RNAs and interactions between the U5 RNA and the exon sequence at the 5' splice site within the SL RNA." [GOC:krc, ISBN:0879695897] comment: Note that this step is analogous to 5' splice site selection in cis-splicing. is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0045291 ! mRNA trans splicing, SL addition [Term] id: GO:0000354 name: cis assembly of pre-catalytic spliceosome namespace: biological_process alt_id: GO:0000360 alt_id: GO:0000361 def: "Assembly of a spliceosomal complex containing the intact pre-mRNA and all of the spliceosomal snRNPs. This occurs when the tri-snRNP associates with the pre-mRNA and associated snRNPs in an ATP-dependent manner." [GOC:krc, GOC:mtg_mpo, ISBN:0879695897] comment: Note that this step represents formation of the A2-1 complex (yeast) or the B1 complex (mammals). synonym: "cis assembly of U12-type pre-catalytic spliceosome" NARROW [] synonym: "cis assembly of U2-type pre-catalytic spliceosome" NARROW [] synonym: "formation of spliceosomal A2-1 complex" NARROW [] synonym: "formation of spliceosomal B1 complex" NARROW [] synonym: "spliceosomal A2-1 complex biosynthesis" NARROW [] synonym: "spliceosomal A2-1 complex formation" NARROW [] synonym: "spliceosomal B1 complex biosynthesis" NARROW [] synonym: "spliceosomal B1 complex formation" NARROW [] is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0000245 ! spliceosomal complex assembly relationship: part_of GO:0045292 ! mRNA cis splicing, via spliceosome [Term] id: GO:0000362 name: obsolete first U2-type spliceosomal transesterification activity namespace: molecular_function def: "OBSOLETE. Catalysis of the first transesterification reaction of U2-type spliceosomal mRNA splicing. The intron branch site adenosine is the nucleophile attacking the 5' splice site, resulting in cleavage at this position. In cis splicing, this is the step that forms a lariat structure of the intron RNA, which is still joined to the 3' exon. The catalytic site is thought to be formed by U6 and/or U2 snRNA, and/or associated proteins." [GOC:krc, ISBN:0879695897] comment: This term was made obsolete because the activities used in the U2- and U12-type complexes are the same. The cellular component ontology should (and does) represent the two different complexes, but the molecular function ontology should not. synonym: "first U2-type spliceosomal transesterification activity" EXACT [] synonym: "lariat formation, 5'-splice site cleavage" BROAD [] is_obsolete: true replaced_by: GO:0000384 [Term] id: GO:0000363 name: obsolete first U12-type spliceosomal transesterification activity namespace: molecular_function def: "OBSOLETE. Catalysis of the first transesterification reaction of U12-type spliceosomal mRNA splicing. The intron branch site adenosine is the nucleophile attacking the 5' splice site, resulting in cleavage at this position. In cis splicing, this is the step that forms a lariat structure of the intron RNA, which is still joined to the 3' exon. The catalytic site is thought to be formed by U6atac snRNA and/or U2atac snRNA, and/or associated proteins." [GOC:krc, ISBN:0879695897] comment: This term was made obsolete because the activities used in the U2- and U12-type complexes are the same. The cellular component ontology should (and does) represent the two different complexes, but the molecular function ontology should not. synonym: "first U12-type spliceosomal transesterification activity" EXACT [] synonym: "lariat formation, 5'-splice site cleavage" BROAD [] is_obsolete: true replaced_by: GO:0000384 [Term] id: GO:0000364 name: obsolete second U2-type spliceosomal transesterification activity namespace: molecular_function def: "OBSOLETE. Catalysis of the second transesterification reaction of U2-type spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure. The catalytic site is thought to be formed by U6 and/or U2 snRNAs and/or associated proteins." [GOC:krc, ISBN:0879695897] comment: This term was made obsolete because the activities used in the U2- and U12-type complexes are the same. The cellular component ontology should (and does) represent the two different complexes, but the molecular function ontology should not. synonym: "3'-splice site cleavage, exon ligation" BROAD [] synonym: "second U2-type spliceosomal transesterification activity" EXACT [] is_obsolete: true replaced_by: GO:0000386 [Term] id: GO:0000365 name: mRNA trans splicing, via spliceosome namespace: biological_process def: "The joining together of exons from two different primary transcripts of messenger RNA (mRNA) via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced." [GOC:krc, ISBN:0879695897] synonym: "nuclear mRNA trans splicing, via spliceosome" EXACT [GOC:vw] synonym: "nuclear mRNA trans splicing, via U2-type spliceosome" NARROW [] is_a: GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0000366 name: intergenic mRNA trans splicing namespace: biological_process def: "The joining together of two independently transcribed RNAs from two different genes, each of which also produces mRNA(s) via cis-splicing." [GOC:krc, PMID:11726664, PMID:12110900] synonym: "intergenic nuclear mRNA trans splicing" EXACT [GOC:vw] is_a: GO:0000365 ! mRNA trans splicing, via spliceosome is_a: GO:0000380 ! alternative mRNA splicing, via spliceosome [Term] id: GO:0000367 name: obsolete second U12-type spliceosomal transesterification activity namespace: molecular_function def: "OBSOLETE. Catalysis of the second transesterification reaction of U12-type spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure. The catalytic site is thought to be formed by U6 and/or U2 snRNAs and/or associated proteins." [GOC:krc, ISBN:0879695897] comment: This term was made obsolete because the activities used in the U2- and U12-type complexes are the same. The cellular component ontology should (and does) represent the two different complexes, but the molecular function ontology should not. synonym: "3'-splice site cleavage, exon ligation" BROAD [] synonym: "second U12-type spliceosomal transesterification activity" EXACT [] is_obsolete: true replaced_by: GO:0000386 [Term] id: GO:0000372 name: Group I intron splicing namespace: biological_process def: "The splicing of Group I introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group I introns and involved in determining the locations of the splice sites (there do not appear to be consensus splice site sequences) as well as having a role in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions, generally with exogenous guanosine as the initiating nucleophile. The intron is excised as a linear piece (though it may subsequently circularize)." [GOC:krc, PMID:11377794] comment: Note that Group I introns are known to be found in a number of places: rRNA, mRNA, and tRNA in organelles of fungi, plants, and protists; tRNA and mRNA of bacteria and bacteriophage; rRNA of protists and fungi; and occasionally in mRNA of animal mitochondria (e.g. sea anemone). subset: gosubset_prok synonym: "mRNA splicing" RELATED [] is_a: GO:0000376 ! RNA splicing, via transesterification reactions with guanosine as nucleophile [Term] id: GO:0000373 name: Group II intron splicing namespace: biological_process def: "The splicing of Group II introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group II introns and containing splice site consensus sequences, that is involved in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions (mechanistically similar to those for splicing of nuclear mRNAs) initiated by a bulged adenosine residue within the intron sequence as the initiating nucleophile. The intron is excised as a lariat." [GOC:krc, PMID:11377794] comment: Note that Group II introns are known to be found in a number of places: rRNA, mRNA, and tRNA in organelles of fungi, plants, and protists; and mRNA of bacteria. subset: gosubset_prok synonym: "mRNA splicing" RELATED [] is_a: GO:0000377 ! RNA splicing, via transesterification reactions with bulged adenosine as nucleophile [Term] id: GO:0000374 name: Group III intron splicing namespace: biological_process def: "The splicing of Group III introns. This occurs by a ribozymic mechanism where the intron sequence forms a distinct 3D structure, characteristic of Group III introns, that is involved in catalyzing the splicing reactions, though protein factors are also required in vivo. Splicing occurs by a series of two transesterification reactions begun by a bulged adenosine residue within the intron sequence as the initiating nucleophile. The intron is excised as a lariat. Though very similar in structure and mechanism to Group II introns, Group III introns are smaller and more streamlined and the splice site consensus sequences are not as well conserved." [GOC:krc, PMID:11377794] comment: Note that Group III introns are known to be found in mRNA of plastids of euglenoid protists. subset: gosubset_prok synonym: "mRNA splicing" RELATED [] is_a: GO:0000377 ! RNA splicing, via transesterification reactions with bulged adenosine as nucleophile [Term] id: GO:0000375 name: RNA splicing, via transesterification reactions namespace: biological_process alt_id: GO:0000385 alt_id: GO:0031202 def: "Splicing of RNA via a series of two transesterification reactions." [GOC:krc] comment: Note that nuclear mRNA, Group I, Group II, and Group III introns are all spliced by a series of two transesterification reactions that occur within the RNA itself, or between two RNAs in trans splicing. Some of these require one or more proteins to stabilize the catalytic conformation, while others are autocatalytic. Note that tRNA introns are spliced by a different catalytic mechanism. subset: gosubset_prok synonym: "pre-mRNA splicing factor activity" RELATED [GOC:krc, GOC:mah] synonym: "RNA splicing factor activity, transesterification mechanism" RELATED [GOC:krc, GOC:mah] synonym: "spliceosomal catalysis" RELATED [] is_a: GO:0008380 ! RNA splicing [Term] id: GO:0000376 name: RNA splicing, via transesterification reactions with guanosine as nucleophile namespace: biological_process def: "Splicing of RNA via a series of two transesterification reactions with exogenous guanosine as the initiating nucleophile." [GOC:krc, PMID:11377794] subset: gosubset_prok is_a: GO:0000375 ! RNA splicing, via transesterification reactions [Term] id: GO:0000377 name: RNA splicing, via transesterification reactions with bulged adenosine as nucleophile namespace: biological_process def: "Splicing of RNA via a series of two transesterification reactions with a bulged adenosine residue from the intron branch point as the initiating nucleophile. When the initial RNA for the splicing reaction is a single molecule (cis splicing), the excised intron is released in a lariat structure." [GOC:krc, PMID:11377794] subset: gosubset_prok synonym: "lariat RNA biosynthesis" RELATED [] synonym: "lariat RNA formation" RELATED [] is_a: GO:0000375 ! RNA splicing, via transesterification reactions [Term] id: GO:0000378 name: RNA exon ligation namespace: biological_process def: "The RNA metabolic process that joins two exons, each of which has free ends that were generated by endonucleolytic cleavages, by a ligation reaction." [GOC:krc, ISBN:0879695897] comment: Note that this is not a part of spliceosomal RNA splicing. subset: gosubset_prok is_a: GO:0016070 ! RNA metabolic process relationship: part_of GO:0000394 ! RNA splicing, via endonucleolytic cleavage and ligation [Term] id: GO:0000379 name: tRNA-type intron splice site recognition and cleavage namespace: biological_process def: "RNA processing that begins when the tertiary structure of a tRNA type intron is recognized, and ends when the endonucleolytic cleavage of the RNA at both the 5' and 3' splice sites occurs." [GOC:krc, GOC:mah, ISBN:0879695897] subset: gosubset_prok is_a: GO:0006396 ! RNA processing relationship: part_of GO:0006388 ! tRNA splicing, via endonucleolytic cleavage and ligation [Term] id: GO:0000380 name: alternative mRNA splicing, via spliceosome namespace: biological_process def: "The process of generating multiple mRNA molecules from a given set of exons by differential use of exons from the primary transcript(s) to form multiple mature mRNAs that vary in their exon composition." [GOC:krc, PMID:12110900] comment: Note that this process most commonly occurs in cis, selecting or skipping exons from the same primary transcript, but it has also been observed to occur in trans at low frequency, at least in some mammals. synonym: "alternative nuclear mRNA splicing, via spliceosome" EXACT [GOC:vw] synonym: "splice site selection" BROAD [] is_a: GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0000381 name: regulation of alternative mRNA splicing, via spliceosome namespace: biological_process def: "Any process that modulates the frequency, rate or extent of alternative splicing of nuclear mRNAs." [GOC:krc] synonym: "regulation of alternative nuclear mRNA splicing, via spliceosome" EXACT [GOC:vw] synonym: "splice site selection" BROAD [] is_a: GO:0048024 ! regulation of mRNA splicing, via spliceosome intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0000380 ! alternative mRNA splicing, via spliceosome relationship: regulates GO:0000380 ! alternative mRNA splicing, via spliceosome [Term] id: GO:0000384 name: first spliceosomal transesterification activity namespace: molecular_function def: "Catalysis of the first transesterification reaction of spliceosomal mRNA splicing. The intron branch site adenosine is the nucleophile attacking the 5' splice site, resulting in cleavage at this position. In cis splicing, this is the step that forms a lariat structure of the intron RNA, while it is still joined to the 3' exon." [GOC:krc, ISBN:0879695897] synonym: "lariat formation, 5'-splice site cleavage" RELATED [] is_a: GO:0003824 ! catalytic activity relationship: part_of GO:0000375 ! RNA splicing, via transesterification reactions [Term] id: GO:0000386 name: second spliceosomal transesterification activity namespace: molecular_function def: "Catalysis of the second transesterification reaction of spliceosomal mRNA splicing. Ligation of the two exons occurs via a transesterification reaction where the free 3'-hydroxyl group of the 5' exon is the nucleophile attacking the 3' splice site. Non-expressed sequences are now detached from the exons. In cis splicing, the intron is in a lariat structure." [GOC:krc, ISBN:0879695897] synonym: "3'-splice site cleavage, exon ligation" BROAD [] synonym: "lariat formation, 5'-splice site cleavage" RELATED [] is_a: GO:0003824 ! catalytic activity relationship: part_of GO:0000375 ! RNA splicing, via transesterification reactions [Term] id: GO:0000387 name: spliceosomal snRNP assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of one or more snRNA and multiple protein components to form a ribonucleoprotein complex that is involved in formation of the spliceosome." [GOC:krc, GOC:mah, ISBN:0879695897] synonym: "spliceosomal snRNP biogenesis" RELATED [GOC:mah] xref: Reactome:REACT_10002 "snRNA Cap hypermethylation, Homo sapiens" xref: Reactome:REACT_10041 "Loading and methylation of Sm proteins onto SMN Complexes, Homo sapiens" xref: Reactome:REACT_100869 "snRNP:Snurportin complex formation, Canis familiaris" xref: Reactome:REACT_100915 "snRNP:Snurportin complex formation, Rattus norvegicus" xref: Reactome:REACT_101141 "snRNP Assembly, Mus musculus" xref: Reactome:REACT_102135 "snRNA Cap hypermethylation, Danio rerio" xref: Reactome:REACT_102362 "snRNP complex assembly, Danio rerio" xref: Reactome:REACT_107811 "snRNP Assembly, Gallus gallus" xref: Reactome:REACT_108169 "snRNA Cap hypermethylation, Rattus norvegicus" xref: Reactome:REACT_108689 "snRNP Assembly, Rattus norvegicus" xref: Reactome:REACT_109502 "Loading and methylation of Sm proteins onto SMN Complexes, Danio rerio" xref: Reactome:REACT_11066 "snRNP Assembly, Homo sapiens" xref: Reactome:REACT_112455 "Loading and methylation of Sm proteins onto SMN Complexes, Xenopus tropicalis" xref: Reactome:REACT_29060 "snRNP:Snurportin complex formation, Drosophila melanogaster" xref: Reactome:REACT_29381 "snRNA Cap hypermethylation, Gallus gallus" xref: Reactome:REACT_29703 "snRNP Assembly, Taeniopygia guttata" xref: Reactome:REACT_29866 "snRNP:Snurportin complex formation, Mus musculus" xref: Reactome:REACT_30125 "snRNP complex assembly, Bos taurus" xref: Reactome:REACT_30397 "snRNP Assembly, Sus scrofa" xref: Reactome:REACT_30799 "snRNP:Snurportin complex formation, Danio rerio" xref: Reactome:REACT_30895 "snRNP complex assembly, Canis familiaris" xref: Reactome:REACT_31007 "snRNP complex assembly, Mus musculus" xref: Reactome:REACT_31363 "snRNP complex assembly, Gallus gallus" xref: Reactome:REACT_31615 "snRNP Assembly, Drosophila melanogaster" xref: Reactome:REACT_32359 "snRNP complex assembly, Rattus norvegicus" xref: Reactome:REACT_54083 "snRNA Cap hypermethylation, Bos taurus" xref: Reactome:REACT_77054 "snRNP Assembly, Canis familiaris" xref: Reactome:REACT_79845 "snRNA Cap hypermethylation, Xenopus tropicalis" xref: Reactome:REACT_81235 "Loading and methylation of Sm proteins onto SMN Complexes, Mus musculus" xref: Reactome:REACT_81911 "snRNP complex assembly, Xenopus tropicalis" xref: Reactome:REACT_82745 "snRNA Cap hypermethylation, Drosophila melanogaster" xref: Reactome:REACT_85882 "snRNP Assembly, Danio rerio" xref: Reactome:REACT_86133 "snRNP complex assembly, Drosophila melanogaster" xref: Reactome:REACT_88437 "snRNP Assembly, Xenopus tropicalis" xref: Reactome:REACT_88858 "snRNA Cap hypermethylation, Canis familiaris" xref: Reactome:REACT_93259 "snRNP:Snurportin complex formation, Xenopus tropicalis" xref: Reactome:REACT_93444 "snRNP Assembly, Bos taurus" xref: Reactome:REACT_93869 "snRNP:Snurportin complex formation, Gallus gallus" xref: Reactome:REACT_95210 "snRNA Cap hypermethylation, Mus musculus" xref: Reactome:REACT_99021 "snRNP:Snurportin complex formation, Bos taurus" xref: Reactome:REACT_9946 "snRNP:Snurportin complex formation, Homo sapiens" xref: Reactome:REACT_9957 "snRNP complex assembly, Homo sapiens" is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0000388 name: spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) namespace: biological_process alt_id: GO:0000396 alt_id: GO:0000397 def: "Rearrangement of the pre-catalytic spliceosome containing U4 (or U4atac) and U1 (or U11) snRNPs to unpair U4 (or U4atac) from U6 (or U6atac) and release it from the spliceosomal complex along with U1 (or U11)." [GOC:krc, ISBN:0879695897] comment: Note that this step represents formation of the A1 complex (yeast) or the B2 complex (mammalian). synonym: "3'-splice site cleavage, exon ligation" BROAD [] synonym: "spliceosomal A1 complex biosynthesis" NARROW [] synonym: "spliceosomal A1 complex formation" NARROW [] synonym: "spliceosomal B2 complex biosynthesis" NARROW [] synonym: "spliceosomal B2 complex formation" NARROW [] synonym: "U12-type spliceosome conformational change to release U4atac and U11" NARROW [] synonym: "U2-type spliceosome conformational change to release U4 and U1" NARROW [] is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0000393 ! spliceosomal conformational changes to generate catalytic conformation [Term] id: GO:0000389 name: mRNA 3'-splice site recognition namespace: biological_process alt_id: GO:0000382 alt_id: GO:0000383 def: "Recognition of the intron 3'-splice site by components of the assembling U2- or U12-type spliceosome." [GOC:krc, ISBN:0879695897] synonym: "nuclear mRNA 3'-splice site recognition" EXACT [GOC:vw] synonym: "U12-type nuclear mRNA 3'-splice site recognition" NARROW [] synonym: "U2-type nuclear mRNA 3'-splice site recognition" NARROW [] is_a: GO:0006376 ! mRNA splice site selection [Term] id: GO:0000390 name: spliceosomal complex disassembly namespace: biological_process alt_id: GO:0000391 alt_id: GO:0000392 def: "Disassembly of a spliceosomal complex with the ATP-dependent release of the product RNAs, one of which is composed of the joined exons. In cis splicing, the other product is the excised sequence, often a single intron, in a lariat structure." [GOC:krc, ISBN:0879695897] synonym: "spliceosome complex disassembly" EXACT [] synonym: "spliceosome disassembly" BROAD [] synonym: "U12-type spliceosome disassembly" NARROW [] synonym: "U2-type spliceosome disassembly" NARROW [] is_a: GO:0032988 ! ribonucleoprotein complex disassembly relationship: part_of GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0000393 name: spliceosomal conformational changes to generate catalytic conformation namespace: biological_process def: "Structural rearrangements of the spliceosome complex, containing RNA to be spliced, to generate a catalytic conformation." [GOC:krc] synonym: "3'-splice site cleavage, exon ligation" BROAD [] is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0000398 ! mRNA splicing, via spliceosome [Term] id: GO:0000394 name: RNA splicing, via endonucleolytic cleavage and ligation namespace: biological_process def: "Splicing of RNA via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons." [GOC:krc, ISBN:0879695897] comment: Note that while typically associated with tRNA splicing, this mechanism of splicing is known to be used for some non-tRNA substrates, e.g. HAC1 (YFL031W) in S. cerevisiae and an intron in the 23S rRNA of the Archaeal species Desulfurococcus mobilis. subset: gosubset_prok synonym: "mRNA splicing" BROAD [] is_a: GO:0008380 ! RNA splicing [Term] id: GO:0000395 name: mRNA 5'-splice site recognition namespace: biological_process alt_id: GO:0000368 alt_id: GO:0000369 def: "Recognition of the intron 5'-splice site by components of the assembling spliceosome." [GOC:krc, ISBN:0879695897] comment: Note that this step represents formation of the Commitment Complex (CC, in yeast) or the E complex (mammalian). synonym: "nuclear mRNA 5' splice site recognition" EXACT [] synonym: "nuclear mRNA 5'-splice site recognition" EXACT [GOC:vw] synonym: "spliceosomal CC complex biosynthesis" NARROW [] synonym: "spliceosomal CC complex formation" NARROW [] synonym: "spliceosomal commitment complex biosynthesis" NARROW [] synonym: "spliceosomal commitment complex formation" NARROW [] synonym: "spliceosomal E complex biosynthesis" NARROW [] synonym: "spliceosomal E complex formation" NARROW [] synonym: "U12-type nuclear mRNA 5' splice site recognition" NARROW [] synonym: "U12-type nuclear mRNA 5'-splice site recognition" NARROW [] synonym: "U2-type nuclear mRNA 5' splice site recognition" NARROW [] synonym: "U2-type nuclear mRNA 5'-splice site recognition" NARROW [] is_a: GO:0006376 ! mRNA splice site selection relationship: part_of GO:0045292 ! mRNA cis splicing, via spliceosome [Term] id: GO:0000398 name: mRNA splicing, via spliceosome namespace: biological_process alt_id: GO:0006374 alt_id: GO:0006375 def: "The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced." [GOC:krc, ISBN:0198506732, ISBN:0879695897] comment: Note that although the many U12-type introns have the sequence AT-AC at the intron termini, some introns with these terminal sequences are spliced by the U2-type spliceosome. The distinguishing characteristics are sequences near the 5' splice site and the branch point sequences of the intron. Note that although the majority of U2-type introns have the sequence GU-AG at the intron termini, some introns with these terminal sequences are spliced by the U12-type spliceosome. The distinguishing characteristics are sequences near the 5' splice site and the branch point sequences of the intron. synonym: "mRNA splicing" BROAD [] synonym: "nuclear mRNA splicing via U12-type spliceosome" NARROW [] synonym: "nuclear mRNA splicing via U2-type spliceosome" NARROW [] synonym: "nuclear mRNA splicing, via spliceosome" EXACT [GOC:krc, GOC:vw] synonym: "pre-mRNA splicing" BROAD [] synonym: "splicing AT-AC intron" RELATED [] synonym: "splicing GT-AG intron" RELATED [] xref: Reactome:REACT_101135 "mRNA Splicing - Minor Pathway, Drosophila melanogaster" xref: Reactome:REACT_101749 "mRNA Splicing - Minor Pathway, Caenorhabditis elegans" xref: Reactome:REACT_106268 "mRNA Splicing - Major Pathway, Gallus gallus" xref: Reactome:REACT_107907 "mRNA Splicing - Minor Pathway, Schizosaccharomyces pombe" xref: Reactome:REACT_109091 "mRNA Splicing - Minor Pathway, Rattus norvegicus" xref: Reactome:REACT_112200 "mRNA Splicing - Major Pathway, Arabidopsis thaliana" xref: Reactome:REACT_114266 "mRNA Splicing - Major Pathway, Oryza sativa" xref: Reactome:REACT_114738 "mRNA Splicing - Major Pathway, Taeniopygia guttata" xref: Reactome:REACT_1753 "mRNA Splicing - Minor Pathway, Homo sapiens" xref: Reactome:REACT_30984 "mRNA Splicing - Minor Pathway, Plasmodium falciparum" xref: Reactome:REACT_32449 "mRNA Splicing - Minor Pathway, Canis familiaris" xref: Reactome:REACT_34020 "mRNA Splicing - Minor Pathway, Dictyostelium discoideum" xref: Reactome:REACT_467 "mRNA Splicing - Major Pathway, Homo sapiens" xref: Reactome:REACT_81417 "mRNA Splicing - Major Pathway, Canis familiaris" xref: Reactome:REACT_82149 "mRNA Splicing - Minor Pathway, Danio rerio" xref: Reactome:REACT_85452 "mRNA Splicing - Major Pathway, Bos taurus" xref: Reactome:REACT_86489 "mRNA Splicing - Minor Pathway, Mus musculus" xref: Reactome:REACT_88186 "mRNA Splicing - Minor Pathway, Oryza sativa" xref: Reactome:REACT_89168 "mRNA Splicing - Minor Pathway, Gallus gallus" xref: Reactome:REACT_90296 "mRNA Splicing - Major Pathway, Danio rerio" xref: Reactome:REACT_91088 "mRNA Splicing - Minor Pathway, Arabidopsis thaliana" xref: Reactome:REACT_91611 "mRNA Splicing - Major Pathway, Drosophila melanogaster" xref: Reactome:REACT_91773 "mRNA Splicing - Minor Pathway, Bos taurus" xref: Reactome:REACT_93740 "mRNA Splicing - Major Pathway, Caenorhabditis elegans" xref: Reactome:REACT_93843 "mRNA Splicing - Major Pathway, Rattus norvegicus" xref: Reactome:REACT_95764 "mRNA Splicing - Major Pathway, Mus musculus" xref: Reactome:REACT_99123 "mRNA Splicing - Major Pathway, Xenopus tropicalis" xref: Reactome:REACT_99763 "mRNA Splicing - Minor Pathway, Xenopus tropicalis" is_a: GO:0000377 ! RNA splicing, via transesterification reactions with bulged adenosine as nucleophile is_a: GO:0006397 ! mRNA processing [Term] id: GO:0000399 name: cellular bud neck septin structure namespace: cellular_component def: "Any of a series of septin structures that are localized in the bud neck of a budding fungal cell during the cell cycle." [GOC:krc] is_a: GO:0032155 ! cell division site part relationship: part_of GO:0005935 ! cellular bud neck [Term] id: GO:0000400 name: four-way junction DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with DNA containing four-way junctions, also known as Holliday junctions, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices." [GOC:krc, ISBN:0815332181, PMID:15563464] synonym: "forked DNA binding" BROAD [] synonym: "Holliday junction binding" EXACT [] is_a: GO:0000217 ! DNA secondary structure binding [Term] id: GO:0000401 name: open form four-way junction DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with DNA containing the open form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The open form of a four-way junction can be diagrammed without any of the strands crossing over." [GOC:krc, ISBN:0815332181, PMID:15563464] synonym: "open form Holliday junction binding" EXACT [] is_a: GO:0000400 ! four-way junction DNA binding [Term] id: GO:0000402 name: crossed form four-way junction DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with DNA containing the crossed form of a four-way junction, also known as a Holliday junction, a structure where two DNA double strands are held together by reciprocal exchange of two of the four strands, one strand each from the two original helices. The crossed form of a four-way junction cannot be diagrammed without any of the strands crossing over, and instead contains a single crossover between two of the strands." [GOC:krc, ISBN:0815332181, PMID:15563464] synonym: "crossed form Holliday junction binding" EXACT [] is_a: GO:0000400 ! four-way junction DNA binding [Term] id: GO:0000403 name: Y-form DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with segment of DNA shaped like a Y. This shape occurs when DNA contains a region of paired double-stranded DNA on one end and a region of unpaired DNA strands on the opposite end." [GOC:elh, PMID:16781730] synonym: "forked DNA binding" BROAD [] synonym: "splayed Y-form DNA binding" EXACT [] is_a: GO:0000217 ! DNA secondary structure binding [Term] id: GO:0000404 name: heteroduplex DNA loop binding namespace: molecular_function def: "Interacting selectively and non-covalently with DNA containing a loop. A loop occurs when DNA contains a large insertion or deletion that causes a region of unpaired single-stranded DNA to loop out, while the rest of the DNA is in a paired double-stranded configuration." [GOC:elh, PMID:16781730] synonym: "loop DNA binding" RELATED [GOC:jh] is_a: GO:0000217 ! DNA secondary structure binding is_a: GO:0032135 ! DNA insertion or deletion binding [Term] id: GO:0000405 name: bubble DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with DNA that contains a bubble. A bubble occurs when DNA contains a region of unpaired, single-stranded DNA flanked on both sides by regions of paired, double-stranded DNA." [GOC:elh, GOC:vw, PMID:16781730] is_a: GO:0000217 ! DNA secondary structure binding [Term] id: GO:0000406 name: double-strand/single-strand DNA junction binding namespace: molecular_function def: "Interacting selectively and non-covalently with a region of DNA that contains double-stranded DNA flanked by a region of single-stranded DNA." [GOC:elh, PMID:16781730] is_a: GO:0000217 ! DNA secondary structure binding [Term] id: GO:0000407 name: pre-autophagosomal structure namespace: cellular_component def: "A punctate structure localized in the vicinity of the vacuole that is required for the formation of autophagosomes." [GOC:elh, PMID:11689437, PMID:12048214, PMID:12554655] synonym: "isolation membrane" RELATED [] synonym: "PAS" EXACT [] synonym: "perivacuolar space" NARROW [] synonym: "phagophore" RELATED [GOC:bf] synonym: "phagophore assembly site" RELATED [] is_a: GO:0044444 ! cytoplasmic part [Term] id: GO:0000408 name: EKC/KEOPS complex namespace: cellular_component def: "A protein complex involved in t6A tRNA modification; originally proposed to be involved in transcription as well as promoting telomere uncapping and telomere elongation. For example, in Saccharomyces cerevisiae the complex contains Bud32p, Kae1p, Gon7p, Cgi121p, and Pcc1p." [GOC:elh, GOC:vw, PMID:16564010, PMID:16874308, PMID:21183954, PMID:23945934] synonym: "Endopeptidase-like Kinase Chromatin-associated protein complex" EXACT [] synonym: "KEOPS/EKC complex" EXACT [PMID:21183954, PMID:23945934] synonym: "Kinase, putative Endopeptidase and Other Proteins of Small size protein complex" EXACT [] is_a: GO:0043234 ! protein complex is_a: GO:0044424 ! intracellular part [Term] id: GO:0000409 name: regulation of transcription by galactose namespace: biological_process def: "Any process involving galactose that modulates the frequency, rate or extent or transcription." [GOC:go_curators] subset: gosubset_prok is_a: GO:0006355 ! regulation of transcription, DNA-templated [Term] id: GO:0000410 name: negative regulation of transcription by galactose namespace: biological_process def: "Any process involving galactose that stops, prevents or reduces the rate of transcription." [GOC:mah] synonym: "down regulation of transcription by galactose" EXACT [] synonym: "down-regulation of transcription by galactose" EXACT [] synonym: "downregulation of transcription by galactose" EXACT [] synonym: "inhibition of transcription by galactose" NARROW [] is_a: GO:0000409 ! regulation of transcription by galactose is_a: GO:0045013 ! carbon catabolite repression of transcription [Term] id: GO:0000411 name: positive regulation of transcription by galactose namespace: biological_process def: "Any process involving galactose that activates or increases the rate of transcription." [GOC:go_curators] synonym: "activation of transcription by galactose" NARROW [] synonym: "stimulation of transcription by galactose" NARROW [] synonym: "up regulation of transcription by galactose" EXACT [] synonym: "up-regulation of transcription by galactose" EXACT [] synonym: "upregulation of transcription by galactose" EXACT [] is_a: GO:0000409 ! regulation of transcription by galactose is_a: GO:0045991 ! carbon catabolite activation of transcription [Term] id: GO:0000412 name: histone peptidyl-prolyl isomerization namespace: biological_process def: "The modification of a histone by cis-trans isomerization of a proline residue." [GOC:krc] synonym: "histone proline isomerization" EXACT [] is_a: GO:0000413 ! protein peptidyl-prolyl isomerization is_a: GO:0016570 ! histone modification [Term] id: GO:0000413 name: protein peptidyl-prolyl isomerization namespace: biological_process def: "The modification of a protein by cis-trans isomerization of a proline residue." [GOC:krc, PMID:16959570] synonym: "protein proline isomerization" EXACT [] is_a: GO:0018208 ! peptidyl-proline modification [Term] id: GO:0000414 name: regulation of histone H3-K36 methylation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3." [GOC:krc] is_a: GO:0031060 ! regulation of histone methylation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0010452 ! histone H3-K36 methylation relationship: regulates GO:0010452 ! histone H3-K36 methylation [Term] id: GO:0000415 name: negative regulation of histone H3-K36 methylation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3." [GOC:krc] synonym: "down regulation of histone H3-K36 methylation" EXACT [] synonym: "down-regulation of histone H3-K36 methylation" EXACT [] synonym: "downregulation of histone H3-K36 methylation" EXACT [] synonym: "inhibition of histone H3-K36 methylation" NARROW [] is_a: GO:0000414 ! regulation of histone H3-K36 methylation is_a: GO:0031061 ! negative regulation of histone methylation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0010452 ! histone H3-K36 methylation relationship: negatively_regulates GO:0010452 ! histone H3-K36 methylation [Term] id: GO:0000416 name: positive regulation of histone H3-K36 methylation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 36 of histone H3." [GOC:krc] synonym: "activation of histone H3-K36 methylation" NARROW [] synonym: "stimulation of histone H3-K36 methylation" NARROW [] synonym: "up regulation of histone H3-K36 methylation" EXACT [] synonym: "up-regulation of histone H3-K36 methylation" EXACT [] synonym: "upregulation of histone H3-K36 methylation" EXACT [] is_a: GO:0000414 ! regulation of histone H3-K36 methylation is_a: GO:0031062 ! positive regulation of histone methylation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0010452 ! histone H3-K36 methylation relationship: positively_regulates GO:0010452 ! histone H3-K36 methylation [Term] id: GO:0000417 name: HIR complex namespace: cellular_component def: "A protein complex proposed to be involved in replication-independent nucleosome assembly, by promoting histone deposition onto DNA. For example, in Saccharomyces, the complex contains Hir1p, Hir2p, Hir3p, and Hpc2p." [GOC:elh, GOC:mah, PMID:16303565, PMID:17180700] synonym: "HIRA complex" EXACT [PMID:19620282, PMID:20976105] is_a: GO:0043234 ! protein complex [Term] id: GO:0000418 name: DNA-directed RNA polymerase IV complex namespace: cellular_component alt_id: GO:0000420 def: "RNA polymerase IV is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Pol IV is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. The largest and second-largest subunits of Pol IV are the catalytic subunits and share similarity with the corresponding subunits of other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase V, while the largest subunit is found only in RNAP IV complex." [GOC:krc, GOC:mtg_sensu, PMID:15692015, PMID:15766525, PMID:16140984, PMID:19110459] synonym: "DNA-directed RNA polymerase IVa complex" EXACT [] is_a: GO:0044451 ! nucleoplasm part is_a: GO:0055029 ! nuclear DNA-directed RNA polymerase complex [Term] id: GO:0000419 name: DNA-directed RNA polymerase V complex namespace: cellular_component alt_id: GO:0080137 def: "RNA polymerase V is a multisubunit RNA polymerase complex found in the nucleus of plants and involved in accumulation of siRNAs and in DNA methylation-dependent silencing of endogenous repeated sequences. Pol V is composed of subunits that are paralogous or identical to the 12 subunits of Pol II. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The second largest subunit is also found in RNA polymerase IVa, while the largest subunit is found only in the IVa complex and contains an extended C-terminal domain (CTD) that includes multiple repeats of a 16 amino-acid consensus sequence as well as other sequences. The remainder of the complex is composed of smaller subunits." [GOC:krc, GOC:mtg_sensu, PMID:16140984, PMID:19110459] synonym: "DNA-directed RNA polymerase IVb complex" EXACT [] is_a: GO:0055029 ! nuclear DNA-directed RNA polymerase complex [Term] id: GO:0000421 name: autophagosome membrane namespace: cellular_component def: "The lipid bilayer surrounding an autophagosome, a double-membrane-bounded vesicle in which endogenous cellular material is sequestered." [GOC:autophagy, GOC:isa_complete] synonym: "autophagic vacuole membrane" EXACT [GOC:autophagy] is_a: GO:0005774 ! vacuolar membrane relationship: part_of GO:0005776 ! autophagosome [Term] id: GO:0000422 name: mitophagy namespace: biological_process def: "The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions." [GOC:autophagy, PMID:15798367, PMID:19289147, PMID:23065344] synonym: "mitochondrion autophagy" EXACT [GOC:autophagy] xref: Wikipedia:Autophagy_(cellular)#Selective_autophagy xref: Wikipedia:Mitophagy is_a: GO:0006914 ! autophagy is_a: GO:0007005 ! mitochondrion organization is_a: GO:0061726 ! mitochondrion disassembly [Term] id: GO:0000423 name: macromitophagy namespace: biological_process def: "Degradation of a mitochondrion by macroautophagy." [PMID:15798367] is_a: GO:0000422 ! mitophagy is_a: GO:0016236 ! macroautophagy [Term] id: GO:0000424 name: microautophagy of mitochondrion namespace: biological_process def: "Degradation of a mitochondrion by lysosomal microautophagy." [PMID:15798367, PMID:27003723] synonym: "micromitophagy" BROAD [PMID:27003723] is_a: GO:0000422 ! mitophagy is_a: GO:0016237 ! lysosomal microautophagy [Term] id: GO:0000425 name: macropexophagy namespace: biological_process def: "Degradation of a peroxisome by macroautophagy." [PMID:12914914, PMID:16973210] is_a: GO:0016236 ! macroautophagy is_a: GO:0030242 ! pexophagy [Term] id: GO:0000426 name: micropexophagy namespace: biological_process def: "Degradation of a peroxisome by lysosomal microautophagy." [GOC:autophagy, GOC:pad, PMID:12914914, PMID:15350980, PMID:16973210] is_a: GO:0016237 ! lysosomal microautophagy is_a: GO:0030242 ! pexophagy [Term] id: GO:0000427 name: plastid-encoded plastid RNA polymerase complex namespace: cellular_component def: "An RNA polymerase complex containing polypeptides encoded by the plastid genome. Plastid-encoded DNA-directed RNA polymerases resemble eubacterial multisubunit RNA polymerases, with a core composed of alpha, beta, and beta-prime subunits. Some forms contain multiple additional subunits. An additional sigma factor subunit is required for promoter recognition." [GOC:krc, GOC:mah, GOC:pj] is_a: GO:0000428 ! DNA-directed RNA polymerase complex is_a: GO:0044435 ! plastid part intersection_of: GO:0000428 ! DNA-directed RNA polymerase complex intersection_of: part_of GO:0009536 ! plastid relationship: part_of GO:0009536 ! plastid [Term] id: GO:0000428 name: DNA-directed RNA polymerase complex namespace: cellular_component def: "A protein complex that possesses DNA-directed RNA polymerase activity." [GOC:krc] is_a: GO:0030880 ! RNA polymerase complex [Term] id: GO:0000429 name: carbon catabolite regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A transcription regulation process in which the presence of one carbon source leads to the modulation of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources." [GOC:krc, GOC:mah] synonym: "regulation of transcription from RNA polymerase II promoter by carbon catabolites" EXACT [GOC:mah] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0045990 ! carbon catabolite regulation of transcription [Term] id: GO:0000430 name: regulation of transcription from RNA polymerase II promoter by glucose namespace: biological_process def: "Any process involving glucose that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc] is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter is_a: GO:0046015 ! regulation of transcription by glucose [Term] id: GO:0000431 name: regulation of transcription from RNA polymerase II promoter by galactose namespace: biological_process def: "Any process involving galactose that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc] is_a: GO:0000409 ! regulation of transcription by galactose is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter [Term] id: GO:0000432 name: positive regulation of transcription from RNA polymerase II promoter by glucose namespace: biological_process def: "Any process involving glucose that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:krc] synonym: "activation of transcription from RNA polymerase II promoter by glucose" NARROW [] synonym: "stimulation of transcription from RNA polymerase II promoter by glucose" NARROW [] synonym: "up regulation of transcription from RNA polymerase II promoter by glucose" EXACT [] synonym: "up-regulation of transcription from RNA polymerase II promoter by glucose" EXACT [] synonym: "upregulation of transcription from RNA polymerase II promoter by glucose" EXACT [] is_a: GO:0000430 ! regulation of transcription from RNA polymerase II promoter by glucose is_a: GO:0000436 ! carbon catabolite activation of transcription from RNA polymerase II promoter is_a: GO:0046016 ! positive regulation of transcription by glucose [Term] id: GO:0000433 name: negative regulation of transcription from RNA polymerase II promoter by glucose namespace: biological_process def: "Any process involving glucose that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter." [GOC:krc] synonym: "down regulation of transcription from RNA polymerase II promoter by glucose" EXACT [] synonym: "down-regulation of transcription from RNA polymerase II promoter by glucose" EXACT [] synonym: "downregulation of transcription from RNA polymerase II promoter by glucose" EXACT [] synonym: "inhibition of transcription from RNA polymerase II promoter by glucose" NARROW [] is_a: GO:0000430 ! regulation of transcription from RNA polymerase II promoter by glucose is_a: GO:0000437 ! carbon catabolite repression of transcription from RNA polymerase II promoter is_a: GO:0045014 ! negative regulation of transcription by glucose [Term] id: GO:0000434 name: negative regulation of transcription from RNA polymerase II promoter by galactose namespace: biological_process def: "Any process involving galactose that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter." [GOC:krc] synonym: "down regulation of transcription from RNA polymerase II promoter by galactose" EXACT [] synonym: "down-regulation of transcription from RNA polymerase II promoter by galactose" EXACT [] synonym: "downregulation of transcription from RNA polymerase II promoter by galactose" EXACT [] synonym: "inhibition of transcription from RNA polymerase II promoter by galactose" NARROW [] is_a: GO:0000410 ! negative regulation of transcription by galactose is_a: GO:0000431 ! regulation of transcription from RNA polymerase II promoter by galactose is_a: GO:0000437 ! carbon catabolite repression of transcription from RNA polymerase II promoter [Term] id: GO:0000435 name: positive regulation of transcription from RNA polymerase II promoter by galactose namespace: biological_process def: "Any process involving galactose that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:krc] synonym: "activation of transcription from RNA polymerase II promoter by galactose" NARROW [] synonym: "stimulation of transcription from RNA polymerase II promoter by galactose" NARROW [] synonym: "up regulation of transcription from RNA polymerase II promoter by galactose" EXACT [] synonym: "up-regulation of transcription from RNA polymerase II promoter by galactose" EXACT [] synonym: "upregulation of transcription from RNA polymerase II promoter by galactose" EXACT [] is_a: GO:0000411 ! positive regulation of transcription by galactose is_a: GO:0000431 ! regulation of transcription from RNA polymerase II promoter by galactose is_a: GO:0000436 ! carbon catabolite activation of transcription from RNA polymerase II promoter [Term] id: GO:0000436 name: carbon catabolite activation of transcription from RNA polymerase II promoter namespace: biological_process def: "Any process involving carbon catabolites that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc] synonym: "positive regulation of transcription from RNA polymerase II promoter by carbon catabolites" EXACT [GOC:mah] is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter is_a: GO:0045991 ! carbon catabolite activation of transcription is_a: GO:1901522 ! positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus [Term] id: GO:0000437 name: carbon catabolite repression of transcription from RNA polymerase II promoter namespace: biological_process def: "A transcription regulation process in which the presence of one carbon source leads to a decrease in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other carbon sources." [GOC:krc] synonym: "negative regulation of transcription from RNA polymerase II promoter by carbon catabolites" EXACT [GOC:mah] is_a: GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter is_a: GO:0000429 ! carbon catabolite regulation of transcription from RNA polymerase II promoter is_a: GO:0045013 ! carbon catabolite repression of transcription [Term] id: GO:0000438 name: core TFIIH complex portion of holo TFIIH complex namespace: cellular_component alt_id: GO:0000443 def: "The core TFIIH complex when it is part of the general transcription factor TFIIH." [GOC:ew, GOC:krc, PMID:14500720, PMID:22308316, PMID:22572993, PMID:7813015] synonym: "SSL2-core TFIIH complex portion of holo TFIIH complex" EXACT [] is_a: GO:0000439 ! core TFIIH complex is_a: GO:0044451 ! nucleoplasm part intersection_of: GO:0000439 ! core TFIIH complex intersection_of: part_of GO:0005675 ! holo TFIIH complex relationship: part_of GO:0005675 ! holo TFIIH complex [Term] id: GO:0000439 name: core TFIIH complex namespace: cellular_component alt_id: GO:0000441 def: "The 7 subunit core of TFIIH that is a part of either the general transcription factor holo-TFIIH or the nucleotide-excision repair factor 3 complex. In S. cerevisiae/humans the complex is composed of: Ssl2/XPB, Tfb1/p62, Tfb2/p52, Ssl1/p44, Tfb4/p34, Tfb5/p8 and Rad3/XPD." [GOC:ew, GOC:krc, PMID:14500720, PMID:17215295, PMID:22308316, PMID:22572993, PMID:23028141, PMID:7813015] subset: goslim_pir synonym: "SSL2-core TFIIH complex" EXACT [] is_a: GO:0043234 ! protein complex is_a: GO:0044428 ! nuclear part [Term] id: GO:0000440 name: core TFIIH complex portion of NEF3 complex namespace: cellular_component alt_id: GO:0000442 def: "The core TFIIH complex when it is part of the nucleotide-excision repair factor 3 (NEF3)." [GOC:ew, GOC:krc, PMID:14500720, PMID:22308316, PMID:22572993, PMID:7813015] synonym: "SSL2-core TFIIH complex portion of NEF3 complex" EXACT [] is_a: GO:0000439 ! core TFIIH complex intersection_of: GO:0000439 ! core TFIIH complex intersection_of: part_of GO:0000112 ! nucleotide-excision repair factor 3 complex relationship: part_of GO:0000112 ! nucleotide-excision repair factor 3 complex [Term] id: GO:0000444 name: MIS12/MIND type complex namespace: cellular_component def: "A multiprotein kinetochore subcomplex that binds to centromeric chromatin and forms part of the inner kinetochore. It helps to recruit outer kinetochore subunits that will bind to microtubules. In humans, it consists of MIS12, DSN1, NSL1 and PMF1." [GOC:krc, PMID:14633972, PMID:16585270] synonym: "Mis12 complex" NARROW [] is_a: GO:0043234 ! protein complex is_a: GO:0044427 ! chromosomal part relationship: part_of GO:0000777 ! condensed chromosome kinetochore [Term] id: GO:0000445 name: THO complex part of transcription export complex namespace: cellular_component def: "The THO complex when it is part of the TREX (TRanscription EXport) complex that is involved in coupling transcription to export of mRNAs to the cytoplasm. In S. cerevisiae, it is composed of four subunits: Hpr1, Tho2, Thp1, and Mft1, while the human complex is composed of 7 subunits." [GOC:krc, PMID:11060033, PMID:11979277, PMID:16983072] synonym: "THO complex part of TREX complex" EXACT [] is_a: GO:0000347 ! THO complex intersection_of: GO:0000347 ! THO complex intersection_of: part_of GO:0000346 ! transcription export complex relationship: part_of GO:0000346 ! transcription export complex [Term] id: GO:0000446 name: nucleoplasmic THO complex namespace: cellular_component def: "The THO complex when it is acting as a nuclear complex that is required for transcription elongation through genes containing tandemly repeated DNA sequences. In S. cerevisiae, it is composed of four subunits: Hpr1, Tho2, Thp2, and Mft1, while the human complex is composed of 7 subunits." [GOC:krc, GOC:se, PMID:11060033, PMID:11979277, PMID:16983072] is_a: GO:0000347 ! THO complex is_a: GO:0008023 ! transcription elongation factor complex [Term] id: GO:0000447 name: endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage between the SSU-rRNA and the 5.8S rRNA of an rRNA molecule originally produced as a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:curators, PMID:10690410] synonym: "endonucleolytic cleavage at A2" NARROW [] is_a: GO:0000479 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) relationship: part_of GO:0000462 ! maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) relationship: part_of GO:0000466 ! maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000448 name: cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process alt_id: GO:0000490 def: "Endonucleolytic cleavage within ITS2 between the 5.8S rRNA and the LSU-rRNA of an rRNA molecule originally produced as a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:curators, PMID:10690410] synonym: "cleavage at C2" RELATED [] synonym: "cleavage in ITS2 of tricistronic rRNA transcript to separate 5.8S and LSU rRNAs (SSU-rRNA, 5.8S rRNA, LSU-rRNA)" EXACT [] is_a: GO:0000479 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) relationship: part_of GO:0000463 ! maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) relationship: part_of GO:0000466 ! maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000449 name: endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 5S) namespace: biological_process def: "Endonucleolytic cleavage of a pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the Large Subunit (LSU) rRNA, and the 5S rRNA, in that order, from 5' to 3' along the primary transcript. For example, primary ribosomal RNA transcripts containing three genes, in this order, are produced in E. coli and other prokaryotic species. Note that the use of the word tricistronic refers only to the number of mature rRNA molecules which will be produced from the primary transcript and ignores tRNAs that may also be present within the primary transcript." [GOC:curators] is_a: GO:0000478 ! endonucleolytic cleavage involved in rRNA processing [Term] id: GO:0000450 name: cleavage of bicistronic rRNA transcript (SSU-rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage of pre-rRNAs originally produced as a bicistronic rRNA transcript that contains the SSU-rRNA and the LSU-rRNA in that order from 5' to 3' along the primary transcript. Primary ribosomal RNA transcripts with two genes in this order are produced in Archaeal species." [GOC:curators] is_a: GO:0000478 ! endonucleolytic cleavage involved in rRNA processing [Term] id: GO:0000451 name: rRNA 2'-O-methylation namespace: biological_process def: "The addition of a methyl group to the 2'-oxygen atom of a nucleotide residue in an rRNA molecule during ribosome biogenesis." [GOC:curators, ISBN:1555811337] is_a: GO:0031167 ! rRNA methylation [Term] id: GO:0000452 name: snoRNA guided rRNA 2'-O-methylation namespace: biological_process def: "The posttranscriptional addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis using a snoRNA guide that targets the position of methylation." [GOC:curators, ISBN:1555811337] synonym: "snoRNA guided rRNA 2'-O-ribose methylation" RELATED [GOC:ascb_2009, GOC:dph, GOC:tb] is_a: GO:0000451 ! rRNA 2'-O-methylation is_a: GO:0016074 ! snoRNA metabolic process [Term] id: GO:0000453 name: enzyme-directed rRNA 2'-O-methylation namespace: biological_process def: "The addition of methyl groups to the 2'-oxygen atom of nucleotide residues in an rRNA molecule during ribosome biogenesis where the methylase specifies the site that becomes methylated without using a guide RNA." [GOC:curators, ISBN:1555811337] is_a: GO:0000451 ! rRNA 2'-O-methylation [Term] id: GO:0000454 name: snoRNA guided rRNA pseudouridine synthesis namespace: biological_process def: "The intramolecular conversion of uridine to pseudouridine in an rRNA molecule during ribosome biogenesis using a snoRNA guide that targets the position of pseudouridylation." [GOC:curators, ISBN:1555811337] is_a: GO:0016074 ! snoRNA metabolic process is_a: GO:0031118 ! rRNA pseudouridine synthesis [Term] id: GO:0000455 name: enzyme-directed rRNA pseudouridine synthesis namespace: biological_process def: "The intramolecular conversion of uridine to pseudouridine during ribosome biogenesis where the enzyme specifies the site that becomes pseudouridylated without using a guide RNA." [GOC:curators, ISBN:1555811337] is_a: GO:0031118 ! rRNA pseudouridine synthesis [Term] id: GO:0000456 name: dimethylation involved in SSU-rRNA maturation namespace: biological_process def: "Dimethylation of the N6 amino groups of two consecutive adenosine residues near the 3'-end of the SSU rRNA. This process has been conserved from bacteria to eukaryotes." [GOC:curators, GOC:dph, GOC:tb, ISBN:1555811337] is_a: GO:0031167 ! rRNA methylation relationship: part_of GO:0030490 ! maturation of SSU-rRNA [Term] id: GO:0000457 name: endonucleolytic cleavage between SSU-rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 5S) namespace: biological_process def: "Endonucleolytic cleavage to separate a pre-SSU-rRNA from a pre-LSU-rRNA originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the Large Subunit (LSU) rRNA, and the 5S rRNA, in that order, from 5' to 3' along the primary transcript. Note that the use of the word tricistronic refers only to the number of mature rRNA molecules which will be produced from the primary transcript and ignores tRNAs that may also be present within the primary transcript." [GOC:curators] is_a: GO:0000449 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 5S) relationship: part_of GO:0002108 ! maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) relationship: part_of GO:0002109 ! maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) [Term] id: GO:0000458 name: endonucleolytic cleavage between LSU-rRNA and 5S rRNA of tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 5S) namespace: biological_process def: "Endonucleolytic cleavage to separate a pre-LSU-rRNA from a pre-5S rRNA originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the Large Subunit (LSU) rRNA, and the 5S rRNA, in that order, from 5' to 3' along the primary transcript. Note that the use of the word tricistronic refers only to the number of mature rRNA molecules which will be produced from the primary transcript and ignores tRNAs that may also be present within the primary transcript." [GOC:curators] is_a: GO:0000449 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 5S) relationship: part_of GO:0002108 ! maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA,5S) [Term] id: GO:0000459 name: exonucleolytic trimming involved in rRNA processing namespace: biological_process def: "Exonucleolytic digestion of a pre-rRNA molecule in the process to generate a mature rRNA molecule." [GOC:curators] synonym: "exonucleolytic trimming during rRNA processing" RELATED [GOC:dph, GOC:tb] is_a: GO:0000469 ! cleavage involved in rRNA processing is_a: GO:0090503 ! RNA phosphodiester bond hydrolysis, exonucleolytic intersection_of: GO:0090503 ! RNA phosphodiester bond hydrolysis, exonucleolytic intersection_of: part_of GO:0006364 ! rRNA processing relationship: part_of GO:0006364 ! rRNA processing [Term] id: GO:0000460 name: maturation of 5.8S rRNA namespace: biological_process def: "Any process involved in the maturation of a precursor 5.8S ribosomal RNA (rRNA) molecule into a mature 5.8S rRNA molecule." [GOC:curators] is_a: GO:0006364 ! rRNA processing [Term] id: GO:0000461 name: endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage at the 3'-end of the SSU-rRNA from an originally tricistronic rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA." [GOC:krc, PMID:10690410] synonym: "endonucleolytic cleavage at site D" NARROW [] is_a: GO:0000479 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) is_a: GO:0031125 ! rRNA 3'-end processing relationship: part_of GO:0000462 ! maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000462 name: maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process alt_id: GO:1990041 def: "Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and the Large Subunit (LSU) in that order from 5' to 3' along the primary transcript." [GOC:curators] synonym: "maturation of 18S rRNA" NARROW [] is_a: GO:0030490 ! maturation of SSU-rRNA [Term] id: GO:0000463 name: maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and Large Subunit (LSU) in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0000470 ! maturation of LSU-rRNA [Term] id: GO:0000464 name: endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage within Internal Transcribed Spacer 1 (ITS1) upstream of the 5.8S rRNA derived from an originally tricistronic rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript. In S. cerevisiae, this endonucleolytic cleavage within ITS1 initiates the maturation of the LSU and the 5.8S rRNAs." [GOC:krc, PMID:10690410] synonym: "endonucleolytic cleavage at A3" NARROW [] is_a: GO:0000479 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) relationship: part_of GO:0000463 ! maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) relationship: part_of GO:0000466 ! maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000465 name: exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Exonucleolytic digestion of a pre-rRNA molecule to generate the mature 5'-end of a 5.8S rRNA molecule derived from an originally tricistronic pre-rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript." [GOC:krc, PMID:10690410] is_a: GO:0000459 ! exonucleolytic trimming involved in rRNA processing is_a: GO:0000967 ! rRNA 5'-end processing relationship: part_of GO:0000466 ! maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000466 name: maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Any process involved in the maturation of an rRNA molecule originally produced as part of a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:curators, PMID:10690410] is_a: GO:0000460 ! maturation of 5.8S rRNA [Term] id: GO:0000467 name: exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Exonucleolytic digestion of a pre-rRNA molecule to generate the mature 3'-end of a 5.8S rRNA molecule derived from an originally tricistronic pre-rRNA transcript that contained the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript." [GOC:krc, PMID:10690410] is_a: GO:0000459 ! exonucleolytic trimming involved in rRNA processing is_a: GO:0031125 ! rRNA 3'-end processing relationship: part_of GO:0000466 ! maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000468 name: generation of mature 3'-end of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Any process involved in generating the mature 3'-end of an LSU-rRNA derived from a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:krc, PMID:10690410] synonym: "processing at B2" NARROW [] is_a: GO:0031125 ! rRNA 3'-end processing relationship: part_of GO:0000463 ! maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000469 name: cleavage involved in rRNA processing namespace: biological_process def: "Any phosphodiester bond hydrolysis involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA molecule." [GOC:curators] synonym: "cleavage during rRNA processing" RELATED [GOC:dph, GOC:tb] is_a: GO:0090501 ! RNA phosphodiester bond hydrolysis intersection_of: GO:0090501 ! RNA phosphodiester bond hydrolysis intersection_of: part_of GO:0006364 ! rRNA processing relationship: part_of GO:0006364 ! rRNA processing [Term] id: GO:0000470 name: maturation of LSU-rRNA namespace: biological_process def: "Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule." [GOC:curators] is_a: GO:0006364 ! rRNA processing relationship: part_of GO:0042273 ! ribosomal large subunit biogenesis [Term] id: GO:0000471 name: endonucleolytic cleavage in 3'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage within the 3'-External Transcribed Spacer (ETS) of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript. In S. cerevisiae, endonucleolytic cleavage within the 3'-ETS of the pre-RNA, which may occur cotranscriptionally, is the first step in rRNA processing, and initiates a cascade of subsequent processing and modification events." [GOC:krc, PMID:10690410] is_a: GO:0000479 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000472 name: endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage between the 5'-External Transcribed Spacer (5'-ETS) and the 5' end of the SSU-rRNA of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript, to produce the mature end of the SSU-rRNA." [GOC:curators, PMID:10690410] synonym: "endonucleolytic cleavage at A1" NARROW [] is_a: GO:0000479 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) is_a: GO:0000967 ! rRNA 5'-end processing relationship: part_of GO:0000462 ! maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000473 name: maturation of LSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) namespace: biological_process def: "Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule from the pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8 S rRNA, 2S rRNA, and Large Subunit (LSU) in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0000470 ! maturation of LSU-rRNA [Term] id: GO:0000474 name: maturation of SSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) namespace: biological_process def: "Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule from the pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8 S rRNA, 2S rRNA, and Large Subunit (LSU) in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0030490 ! maturation of SSU-rRNA [Term] id: GO:0000475 name: maturation of 2S rRNA namespace: biological_process def: "Any process involved in the maturation of a precursor 2S ribosomal RNA (rRNA) molecule into a mature 2S rRNA molecule." [GOC:curators] is_a: GO:0006364 ! rRNA processing [Term] id: GO:0000476 name: maturation of 4.5S rRNA namespace: biological_process def: "Any process involved in the maturation of a precursor 4.5S ribosomal RNA (rRNA) molecule into a mature 4.5S rRNA molecule." [GOC:curators] is_a: GO:0006364 ! rRNA processing [Term] id: GO:0000477 name: generation of mature 5'-end of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Cleavage within ITS2 to generate the mature 5'-end of an LSU-rRNA derived from a tricistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:curators, PMID:10690410] synonym: "processing at C1" NARROW [] is_a: GO:0000469 ! cleavage involved in rRNA processing is_a: GO:0000967 ! rRNA 5'-end processing relationship: part_of GO:0000463 ! maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000478 name: endonucleolytic cleavage involved in rRNA processing namespace: biological_process def: "Any endonucleolytic cleavage involved in the conversion of a primary ribosomal RNA (rRNA) transcript into a mature rRNA molecule. Some endonucleolytic cleavages produce the mature end, while others are a step in the process of generating the mature end from the pre-rRNA." [GOC:krc, PMID:10690410] synonym: "endonucleolytic cleavage during rRNA processing" RELATED [GOC:dph, GOC:tb] is_a: GO:0000469 ! cleavage involved in rRNA processing is_a: GO:0090502 ! RNA phosphodiester bond hydrolysis, endonucleolytic intersection_of: GO:0090502 ! RNA phosphodiester bond hydrolysis, endonucleolytic intersection_of: part_of GO:0006364 ! rRNA processing relationship: part_of GO:0006364 ! rRNA processing [Term] id: GO:0000479 name: endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage of a pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small SubUnit (SSU) rRNA, the 5.8S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript. Primary ribosomal RNA transcripts with three genes, in this order, are produced in the nuclei of many eukaryotic species, including S. cerevisiae." [GOC:curators, PMID:10690410] is_a: GO:0000478 ! endonucleolytic cleavage involved in rRNA processing [Term] id: GO:0000480 name: endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage within the 5'-External Transcribed Spacer (ETS) of a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 5.8S rRNA, and the Large Subunit (LSU) rRNA in that order from 5' to 3' along the primary transcript. Endonucleolytic cleavage within the 5'-ETS of the pre-RNA is conserved as one of the early steps of rRNA processing in all eukaryotes, but the specific position of cleavage is variable." [GOC:curators, PMID:10690410, PMID:15282326] synonym: "endonucleolytic cleavage at A-prime" NARROW [PMID:15282326] synonym: "endonucleolytic cleavage at A0" NARROW [] is_a: GO:0000479 ! endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) relationship: part_of GO:0000462 ! maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) [Term] id: GO:0000481 name: maturation of 5S rRNA namespace: biological_process def: "Any process involved in the maturation of a precursor 5S ribosomal RNA (rRNA) molecule into a mature 5S rRNA molecule." [GOC:curators] is_a: GO:0006364 ! rRNA processing [Term] id: GO:0000482 name: maturation of 5S rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) namespace: biological_process def: "Any process involved in the maturation of a precursor 5S ribosomal RNA (rRNA) molecule into a mature 5S rRNA molecule from the pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, Large Subunit (LSU) the 4.5S rRNA, and the 5S rRNA in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0000481 ! maturation of 5S rRNA [Term] id: GO:0000483 name: endonucleolytic cleavage of tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage of a pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small SubUnit (SSU) rRNA, the 5.8S rRNA, 2S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript. Primary ribosomal RNA transcripts with four genes, in this order, are produced in the nuclei of D. melanogaster as well as in those of other dipteran species." [GOC:curators] is_a: GO:0000478 ! endonucleolytic cleavage involved in rRNA processing [Term] id: GO:0000484 name: cleavage between SSU-rRNA and 5.8S rRNA of tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage between the SSU-rRNA and the 5.8S rRNA of an rRNA molecule originally produced as a tetracistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, 2S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0000483 ! endonucleolytic cleavage of tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) relationship: part_of GO:0000474 ! maturation of SSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) relationship: part_of GO:0000487 ! maturation of 5.8S rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) [Term] id: GO:0000485 name: cleavage between 2S rRNA and LSU-rRNA of tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage between the LSU-rRNA and the 2S rRNA of an rRNA molecule originally produced as a tetracistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, 2S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:curators, PMID:768488] is_a: GO:0000483 ! endonucleolytic cleavage of tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) relationship: part_of GO:0000473 ! maturation of LSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) relationship: part_of GO:0000475 ! maturation of 2S rRNA [Term] id: GO:0000486 name: cleavage between 5.8S rRNA and 2S rRNA of tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) namespace: biological_process def: "Endonucleolytic cleavage between the 5.8S rRNA and the 2S rRNA of an rRNA molecule originally produced as a tetracistronic rRNA transcript that contained the Small SubUnit (SSU) rRNA, the 5.8S rRNA, 2S rRNA, and the Large SubUnit (LSU) rRNA, in that order, from 5' to 3' along the primary transcript." [GOC:curators, PMID:768488] is_a: GO:0000483 ! endonucleolytic cleavage of tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) relationship: part_of GO:0000475 ! maturation of 2S rRNA relationship: part_of GO:0000487 ! maturation of 5.8S rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) [Term] id: GO:0000487 name: maturation of 5.8S rRNA from tetracistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, 2S rRNA, LSU-rRNA) namespace: biological_process def: "Any process involved in the maturation of a precursor 5.8S ribosomal RNA (rRNA) molecule into a mature 5.8S rRNA molecule from the pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, the 8.8S rRNA, the 2S rRNA, and the Large Subunit (LSU) in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0000460 ! maturation of 5.8S rRNA [Term] id: GO:0000488 name: maturation of LSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) namespace: biological_process def: "Any process involved in the maturation of a precursor Large SubUnit (LSU) ribosomal RNA (rRNA) molecule into a mature LSU-rRNA molecule from the pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, Large Subunit (LSU) the 4.5S rRNA, and the 5S rRNA in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0000470 ! maturation of LSU-rRNA [Term] id: GO:0000489 name: maturation of SSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) namespace: biological_process def: "Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule from the pre-rRNA molecule originally produced as a tetracistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, Large Subunit (LSU) the 4.5S rRNA, and the 5S rRNA in that order from 5' to 3' along the primary transcript." [GOC:curators] is_a: GO:0030490 ! maturation of SSU-rRNA [Term] id: GO:0000491 name: small nucleolar ribonucleoprotein complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins and a snoRNA to form a small nucleolar ribonucleoprotein (snoRNP) complex." [GOC:krc] synonym: "snoRNP assembly" EXACT [] is_a: GO:0022618 ! ribonucleoprotein complex assembly [Term] id: GO:0000492 name: box C/D snoRNP assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins and a box C/D snoRNA to form a box C/D small nucleolar ribonucleoprotein (snoRNP) complex." [GOC:krc] synonym: "box C/D small nucleolar ribonucleoprotein complex assembly" EXACT [] is_a: GO:0000491 ! small nucleolar ribonucleoprotein complex assembly [Term] id: GO:0000493 name: box H/ACA snoRNP assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins and a box H/ACA snoRNA to form a box H/ACA small nucleolar ribonucleoprotein (snoRNP) complex." [GOC:krc, PMID:12515383] synonym: "box H/ACA small nucleolar ribonucleoprotein complex assembly" EXACT [] is_a: GO:0000491 ! small nucleolar ribonucleoprotein complex assembly [Term] id: GO:0000494 name: box C/D snoRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of a box C/D snoRNA molecule." [GOC:krc] synonym: "box C/D snoRNA 3' end processing" EXACT [] is_a: GO:0031126 ! snoRNA 3'-end processing is_a: GO:0034963 ! box C/D snoRNA processing [Term] id: GO:0000495 name: box H/ACA snoRNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of a box H/ACA snoRNA molecule." [GOC:krc] synonym: "box H/ACA snoRNA 3' end processing" EXACT [] is_a: GO:0031126 ! snoRNA 3'-end processing is_a: GO:0034964 ! box H/ACA snoRNA processing [Term] id: GO:0000496 name: base pairing namespace: molecular_function def: "Interacting selectively and non-covalently with nucleic acid via hydrogen bonds between the bases of a gene product molecule and the bases of a target nucleic acid molecule." [GOC:krc] comment: Note that with respect to annotation, "base pairing" and its child terms are intended to be used to annotate the activity of gene products composed of nucleic acid, presumably RNA, to interact with other nucleic acid molecules via base pairing. Internal base pairing with itself is considered part of the secondary structure of the molecule and is not within the scope of GO function. xref: Wikipedia:Base_pair is_a: GO:0003676 ! nucleic acid binding [Term] id: GO:0000497 name: base pairing with DNA namespace: molecular_function def: "Interacting selectively and non-covalently with nucleic acid via hydrogen bonds between the bases of a gene product molecule and the bases of a target DNA molecule." [GOC:krc] comment: Note that with respect to annotation, "base pairing" and its child terms are intended to be used to annotate the activity of gene products composed of nucleic acid, presumably RNA, to interact with DNA molecules via base pairing. Internal base pairing with itself is considered part of the secondary structure of the molecule and is not within the scope of GO function. is_a: GO:0000496 ! base pairing is_a: GO:0003677 ! DNA binding [Term] id: GO:0000498 name: base pairing with RNA namespace: molecular_function def: "Interacting selectively and non-covalently with ribonucleic acid (RNA) via hydrogen bonds between the bases of a gene product molecule and the bases of a target RNA molecule." [GOC:krc] comment: Note that with respect to annotation, "base pairing with RNA" and its child terms are intended to be used to annotate the activity of gene products composed of nucleic acid, presumably RNA, to interact with other RNA molecules via base pairing. Internal base pairing with itself is considered part of the secondary structure of the molecule and is not within the scope of GO function. is_a: GO:0000496 ! base pairing is_a: GO:0003723 ! RNA binding [Term] id: GO:0000499 name: base pairing with mRNA namespace: molecular_function def: "Interacting selectively and non-covalently with messenger ribonucleic acid (mRNA) via hydrogen bonds between the bases of a gene product molecule and the bases of a target mRNA molecule." [GOC:krc] comment: Note that with respect to annotation, "base pairing with RNA" and its child terms are intended to be used to annotate the activity of gene products composed of nucleic acid, presumably RNA, to interact with other RNA molecules via base pairing. Internal base pairing with itself is considered part of the secondary structure of the molecule and is not within the scope of GO function. is_a: GO:0000498 ! base pairing with RNA [Term] id: GO:0000500 name: RNA polymerase I upstream activating factor complex namespace: cellular_component def: "A complex required for the transcription of rDNA by RNA polymerase I. In yeast the complex consists of Rrrn5p, Rrn9p, Rrn10p, histones H3 and H4, and Uaf30p." [PMID:11500378] synonym: "RNA polymerase I upstream activation factor complex" EXACT [] synonym: "UAF" EXACT [] is_a: GO:0000120 ! RNA polymerase I transcription factor complex [Term] id: GO:0000501 name: flocculation via cell wall protein-carbohydrate interaction namespace: biological_process def: "The reversible, non-sexual aggregation of cells mediated by the binding of proteins in the cell wall of one cell to carbohydrates in the cell wall of another cell. An example of this process is found in Saccharomyces cerevisiae, in which it is pH- and calcium-dependent." [GOC:mcc, GOC:sgd_curators, GOC:vw, PMID:21114594] subset: gosubset_prok is_a: GO:0000128 ! flocculation [Term] id: GO:0000502 name: proteasome complex namespace: cellular_component def: "A large multisubunit complex which catalyzes protein degradation, found in eukaryotes, archaea and some bacteria. In eukaryotes, this complex consists of the barrel shaped proteasome core complex and one or two associated proteins or complexes that act in regulating entry into or exit from the core." [GOC:rb, http://en.wikipedia.org/wiki/Proteasome] subset: goslim_pir synonym: "26S proteasome" NARROW [] synonym: "proteasome" EXACT [GOC:cjm] is_a: GO:0044424 ! intracellular part is_a: GO:1905369 ! endopeptidase complex [Term] id: GO:0000504 name: obsolete proteasome regulatory particle (sensu Bacteria) namespace: cellular_component def: "OBSOLETE. A multisubunit complex that recognizes and unfolds ubiquitinated proteins, and translocates them to the core complex in an ATP dependent manner. As in, but not restricted to, the taxon Bacteria (Bacteria, ncbi_taxonomy_id:2)." [GOC:rb] comment: This term was made obsolete because there is no ubiquitin in bacteria and they do not have proteasome regulatory particles. Instead they have proteasome-activating nucleotidase. synonym: "26S proteasome" NARROW [] synonym: "proteasome regulatory particle (sensu Bacteria)" EXACT [] is_obsolete: true [Term] id: GO:0000506 name: glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex namespace: cellular_component def: "An enzyme complex that catalyzes the transfer of GlcNAc from UDP-GlcNAc to an acceptor phosphatidylinositol, the first step in the production of GPI anchors for cell surface proteins. The complex contains PIG-A, PIG-C, PIG-H, PIG-Q, PIG-P, and DPM2 in human, and Eri1p, Gpi1p, Gpi2p, Gpi15p, Gpi19p, and Spt14p in budding yeast." [GOC:kp, GOC:rb, PMID:10944123, PMID:15163411] comment: Note that this term should not be confused with 'GPI-anchor transamidase complex ; GO:0042765', which represents a distinct complex with a different catalytic activity. synonym: "GPI-GlcNAc transferase complex" EXACT [] synonym: "GPI-GnT complex" EXACT [] synonym: "GPI-N-acetylglucosaminyltransferase complex" EXACT [] is_a: GO:0043234 ! protein complex is_a: GO:0044432 ! endoplasmic reticulum part [Term] id: GO:0000578 name: embryonic axis specification namespace: biological_process def: "The establishment, maintenance and elaboration of a pattern along a line or a point in an embryo." [GOC:dph, GOC:go_curators, GOC:sdb_2009, GOC:tb] synonym: "embryonic axis determination" RELATED [] is_a: GO:0009798 ! axis specification is_a: GO:0009880 ! embryonic pattern specification [Term] id: GO:0000700 name: mismatch base pair DNA N-glycosylase activity namespace: molecular_function def: "Catalysis of the removal of single bases present in mismatches by the cleavage the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site." [GOC:elh, PMID:9224623] is_a: GO:0019104 ! DNA N-glycosylase activity [Term] id: GO:0000701 name: purine-specific mismatch base pair DNA N-glycosylase activity namespace: molecular_function def: "Catalysis of the removal of purines present in mismatches, especially opposite oxidized purines, by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic (AP) site." [GOC:elh, PMID:9224623] synonym: "A/G-specific adenine DNA glycosylase activity" NARROW [] xref: EC:3.2.2.- is_a: GO:0000700 ! mismatch base pair DNA N-glycosylase activity [Term] id: GO:0000702 name: oxidized base lesion DNA N-glycosylase activity namespace: molecular_function def: "Catalysis of the removal of oxidized bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site." [GOC:elh, PMID:11554296] subset: gosubset_prok is_a: GO:0019104 ! DNA N-glycosylase activity [Term] id: GO:0000703 name: oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity namespace: molecular_function alt_id: GO:0019004 def: "Catalysis of the removal oxidized pyrimidine bases by cleaving the N-C1' glycosidic bond between the oxidized pyrimidine and the deoxyribose sugar. The reaction involves formation of a covalent enzyme-pyrimidine base intermediate. Release of the enzyme and free base by a beta-elimination or a beta, gamma-elimination mechanism results in the cleavage of the DNA backbone 3' of the apyrimidinic (AP) site." [GOC:elh, PMID:11554296] comment: Consider also annotating to the molecular function term 'DNA-(apurinic or apyrimidinic site) lyase activity ; GO:0003906'. subset: gosubset_prok synonym: "bifunctional DNA glycosylase" BROAD [] synonym: "DNA glycosylase/AP-lyase" BROAD [] synonym: "DNA glycosylase/beta-lyase" BROAD [] synonym: "endodeoxyribonuclease III" RELATED [] synonym: "endonuclease III" RELATED [] synonym: "endonuclease VIII activity" RELATED [] synonym: "oxidized pyrimidine base lesion DNA N-glycosylase activity" EXACT [GOC:go_curators] synonym: "pyrimidine-specific oxidized base lesion DNA N-glycosylase activity" RELATED [] xref: Reactome:REACT_101001 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Plasmodium falciparum" xref: Reactome:REACT_101090 "Cleavage of dihydrouracil by hNTH1 glycosylase, Escherichia coli" xref: Reactome:REACT_101315 "Cleavage of cytosine glycol by hNTH1 glycosylase, Danio rerio" xref: Reactome:REACT_101744 "Cleavage of thymine glycol by hNTH1 glycosylase, Mus musculus" xref: Reactome:REACT_102306 "Cleavage of cytosine glycol by hNTH1 glycosylase, Schizosaccharomyces pombe" xref: Reactome:REACT_103688 "Cleavage of thymine glycol by hNTH1 glycosylase, Gallus gallus" xref: Reactome:REACT_103837 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Saccharomyces cerevisiae" xref: Reactome:REACT_104179 "Cleavage of cytosine glycol by hNTH1 glycosylase, Oryza sativa" xref: Reactome:REACT_104266 "Cleavage of thymine glycol by hNTH1 glycosylase, Saccharomyces cerevisiae" xref: Reactome:REACT_104313 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Staphylococcus aureus N315" xref: Reactome:REACT_105538 "Cleavage of cytosine glycol by hNTH1 glycosylase, Arabidopsis thaliana" xref: Reactome:REACT_105622 "Cleavage of thymine glycol by hNTH1 glycosylase, Xenopus tropicalis" xref: Reactome:REACT_105635 "Cleavage of cytosine glycol by hNTH1 glycosylase, Escherichia coli" xref: Reactome:REACT_105967 "Cleavage of thymine glycol by hNTH1 glycosylase, Schizosaccharomyces pombe" xref: Reactome:REACT_106253 "Cleavage of thymine glycol by hNTH1 glycosylase, Taeniopygia guttata" xref: Reactome:REACT_107207 "Cleavage of cytosine glycol by hNTH1 glycosylase, Bos taurus" xref: Reactome:REACT_107703 "Cleavage of dihydrouracil by hNTH1 glycosylase, Taeniopygia guttata" xref: Reactome:REACT_107763 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Danio rerio" xref: Reactome:REACT_108637 "Cleavage of cytosine glycol by hNTH1 glycosylase, Canis familiaris" xref: Reactome:REACT_108860 "Cleavage of dihydrouracil by hNTH1 glycosylase, Mycobacterium tuberculosis" xref: Reactome:REACT_109023 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Bos taurus" xref: Reactome:REACT_109743 "Cleavage of cytosine glycol by hNTH1 glycosylase, Gallus gallus" xref: Reactome:REACT_2021 "Cleavage of cytosine glycol by hNTH1 glycosylase, Homo sapiens" xref: Reactome:REACT_2157 "Cleavage of dihydrouracil by hNTH1 glycosylase, Homo sapiens" xref: Reactome:REACT_2255 "Cleavage of thymine glycol by hNTH1 glycosylase, Homo sapiens" xref: Reactome:REACT_28127 "Cleavage of cytosine glycol by hNTH1 glycosylase, Mus musculus" xref: Reactome:REACT_28180 "Cleavage of thymine glycol by hNTH1 glycosylase, Caenorhabditis elegans" xref: Reactome:REACT_29323 "Cleavage of dihydrouracil by hNTH1 glycosylase, Schizosaccharomyces pombe" xref: Reactome:REACT_29518 "Cleavage of cytosine glycol by hNTH1 glycosylase, Xenopus tropicalis" xref: Reactome:REACT_30621 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Mus musculus" xref: Reactome:REACT_30642 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Oryza sativa" xref: Reactome:REACT_30750 "Cleavage of dihydrouracil by hNTH1 glycosylase, Arabidopsis thaliana" xref: Reactome:REACT_32240 "Cleavage of cytosine glycol by hNTH1 glycosylase, Drosophila melanogaster" xref: Reactome:REACT_32421 "Cleavage of thymine glycol by hNTH1 glycosylase, Danio rerio" xref: Reactome:REACT_32931 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Escherichia coli" xref: Reactome:REACT_33078 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Taeniopygia guttata" xref: Reactome:REACT_33307 "Cleavage of cytosine glycol by hNTH1 glycosylase, Dictyostelium discoideum" xref: Reactome:REACT_33417 "Cleavage of cytosine glycol by hNTH1 glycosylase, Plasmodium falciparum" xref: Reactome:REACT_33820 "Cleavage of thymine glycol by hNTH1 glycosylase, Bos taurus" xref: Reactome:REACT_33839 "Cleavage of thymine glycol by hNTH1 glycosylase, Arabidopsis thaliana" xref: Reactome:REACT_33951 "Cleavage of dihydrouracil by hNTH1 glycosylase, Drosophila melanogaster" xref: Reactome:REACT_34296 "Cleavage of dihydrouracil by hNTH1 glycosylase, Xenopus tropicalis" xref: Reactome:REACT_77336 "Cleavage of cytosine glycol by hNTH1 glycosylase, Rattus norvegicus" xref: Reactome:REACT_77526 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Dictyostelium discoideum" xref: Reactome:REACT_78108 "Cleavage of cytosine glycol by hNTH1 glycosylase, Mycobacterium tuberculosis" xref: Reactome:REACT_78298 "Cleavage of dihydrouracil by hNTH1 glycosylase, Saccharomyces cerevisiae" xref: Reactome:REACT_78343 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Sus scrofa" xref: Reactome:REACT_78458 "Cleavage of dihydrouracil by hNTH1 glycosylase, Danio rerio" xref: Reactome:REACT_78529 "Cleavage of dihydrouracil by hNTH1 glycosylase, Gallus gallus" xref: Reactome:REACT_79663 "Cleavage of dihydrouracil by hNTH1 glycosylase, Dictyostelium discoideum" xref: Reactome:REACT_79864 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Arabidopsis thaliana" xref: Reactome:REACT_80155 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Schizosaccharomyces pombe" xref: Reactome:REACT_81464 "Cleavage of dihydrouracil by hNTH1 glycosylase, Rattus norvegicus" xref: Reactome:REACT_81531 "Cleavage of thymine glycol by hNTH1 glycosylase, Oryza sativa" xref: Reactome:REACT_82850 "Cleavage of dihydrouracil by hNTH1 glycosylase, Sus scrofa" xref: Reactome:REACT_83701 "Cleavage of thymine glycol by hNTH1 glycosylase, Dictyostelium discoideum" xref: Reactome:REACT_83784 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Gallus gallus" xref: Reactome:REACT_84042 "Cleavage of dihydrouracil by hNTH1 glycosylase, Plasmodium falciparum" xref: Reactome:REACT_84141 "Cleavage of cytosine glycol by hNTH1 glycosylase, Caenorhabditis elegans" xref: Reactome:REACT_84471 "Cleavage of dihydrouracil by hNTH1 glycosylase, Staphylococcus aureus N315" xref: Reactome:REACT_85485 "Cleavage of dihydrouracil by hNTH1 glycosylase, Oryza sativa" xref: Reactome:REACT_87055 "Cleavage of cytosine glycol by hNTH1 glycosylase, Saccharomyces cerevisiae" xref: Reactome:REACT_87146 "Cleavage of cytosine glycol by hNTH1 glycosylase, Sus scrofa" xref: Reactome:REACT_87389 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Caenorhabditis elegans" xref: Reactome:REACT_87494 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Mycobacterium tuberculosis" xref: Reactome:REACT_87850 "Cleavage of thymine glycol by hNTH1 glycosylase, Rattus norvegicus" xref: Reactome:REACT_87925 "Cleavage of dihydrouracil by hNTH1 glycosylase, Caenorhabditis elegans" xref: Reactome:REACT_890 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Homo sapiens" xref: Reactome:REACT_89137 "Cleavage of dihydrouracil by hNTH1 glycosylase, Bos taurus" xref: Reactome:REACT_89396 "Cleavage of cytosine glycol by hNTH1 glycosylase, Taeniopygia guttata" xref: Reactome:REACT_90163 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Drosophila melanogaster" xref: Reactome:REACT_90552 "Cleavage of thymine glycol by hNTH1 glycosylase, Canis familiaris" xref: Reactome:REACT_92193 "Cleavage of dihydrouracil by hNTH1 glycosylase, Canis familiaris" xref: Reactome:REACT_92466 "Cleavage of cytosine glycol by hNTH1 glycosylase, Staphylococcus aureus N315" xref: Reactome:REACT_93244 "Cleavage of thymine glycol by hNTH1 glycosylase, Sus scrofa" xref: Reactome:REACT_93473 "Cleavage of dihydrouracil by hNTH1 glycosylase, Mus musculus" xref: Reactome:REACT_94304 "Cleavage of thymine glycol by hNTH1 glycosylase, Staphylococcus aureus N315" xref: Reactome:REACT_95145 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Rattus norvegicus" xref: Reactome:REACT_96277 "Cleavage of thymine glycol by hNTH1 glycosylase, Escherichia coli" xref: Reactome:REACT_96754 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Xenopus tropicalis" xref: Reactome:REACT_97913 "Cleavage of thymine glycol by hNTH1 glycosylase, Drosophila melanogaster" xref: Reactome:REACT_97922 "Cleavage of thymine glycol by hNTH1 glycosylase, Plasmodium falciparum" xref: Reactome:REACT_98089 "Cleavage of formamidopyrimidine by hNTH1 glycosylase, Canis familiaris" xref: Reactome:REACT_99032 "Cleavage of thymine glycol by hNTH1 glycosylase, Mycobacterium tuberculosis" is_a: GO:0000702 ! oxidized base lesion DNA N-glycosylase activity is_a: GO:0003906 ! DNA-(apurinic or apyrimidinic site) lyase activity [Term] id: GO:0000704 name: pyrimidine dimer DNA N-glycosylase activity namespace: molecular_function def: "Catalysis of the removal of pyrimidine dimers by removing the 5' pyrimidine of the dimer by cleaving the N-C1' glycosidic bond between the 5' pyrimidine of the dimer and the deoxyribose sugar. The reaction releases the 5' pyrimidine of the dimer and leaves an apurinic (AP) site. The reaction involves the formation of a covalent enzyme substrate intermediate. Release of the enzyme and free base by a beta-elimination or a beta, gamma-elimination mechanism results in the cleavage of the DNA backbone 3' of the apyrimidinic (AP) site." [GOC:elh, PMID:9224623] is_a: GO:0003906 ! DNA-(apurinic or apyrimidinic site) lyase activity is_a: GO:0019104 ! DNA N-glycosylase activity [Term] id: GO:0000705 name: achiasmate meiosis I namespace: biological_process def: "The first division of meiosis in which homologous chromosomes are paired and segregated from each other, occurring in the constitutive absence of chiasmata." [GOC:elh, GOC:sart, PMID:10690419] is_a: GO:0007127 ! meiosis I [Term] id: GO:0000706 name: meiotic DNA double-strand break processing namespace: biological_process def: "The cell cycle process in which the 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang occurs. This takes place during meiosis." [GOC:elh, PMID:9334324] is_a: GO:0000729 ! DNA double-strand break processing is_a: GO:1903046 ! meiotic cell cycle process intersection_of: GO:0000729 ! DNA double-strand break processing intersection_of: part_of GO:0051321 ! meiotic cell cycle relationship: part_of GO:0051321 ! meiotic cell cycle [Term] id: GO:0000707 name: meiotic DNA recombinase assembly namespace: biological_process def: "During meiosis, the aggregation, arrangement and bonding together of strand exchange proteins (recombinases) to form higher order oligomers on single-stranded DNA." [GOC:elh, PMID:11459983] is_a: GO:0000730 ! DNA recombinase assembly is_a: GO:1903046 ! meiotic cell cycle process intersection_of: GO:0000730 ! DNA recombinase assembly intersection_of: part_of GO:0051321 ! meiotic cell cycle relationship: part_of GO:0007127 ! meiosis I relationship: part_of GO:0051321 ! meiotic cell cycle [Term] id: GO:0000708 name: meiotic strand invasion namespace: biological_process def: "The cell cycle process in which the nucleoprotein complex (composed of the broken single-strand DNA and the recombinase) searches and identifies a region of homology in intact duplex DNA. The broken single-strand DNA displaces the like strand and forms Watson-Crick base pairs with its complement, forming a duplex in which each strand is from one of the two recombining DNA molecules. This occurs during meiosis." [GOC:elh, PMID:10915877] synonym: "meiotic D-loop biosynthesis" RELATED [] synonym: "meiotic D-loop formation" RELATED [] synonym: "meiotic displacement loop biosynthesis" RELATED [GOC:mah, GOC:vw] synonym: "meiotic displacement loop formation" RELATED [GOC:mah, GOC:vw] is_a: GO:0042148 ! strand invasion is_a: GO:1903046 ! meiotic cell cycle process intersection_of: GO:0042148 ! strand invasion intersection_of: part_of GO:0051321 ! meiotic cell cycle relationship: part_of GO:0007127 ! meiosis I relationship: part_of GO:0051321 ! meiotic cell cycle [Term] id: GO:0000709 name: meiotic joint molecule formation namespace: biological_process def: "The conversion of the paired broken DNA and homologous duplex DNA into a four-stranded branched intermediate, known as a joint molecule, formed during meiotic recombination. These joint molecules contain Holliday junctions on either side of heteroduplex DNA." [GOC:elh, PMID:8521495] is_a: GO:1903046 ! meiotic cell cycle process relationship: part_of GO:0007131 ! reciprocal meiotic recombination [Term] id: GO:0000710 name: meiotic mismatch repair namespace: biological_process def: "A system for the identification and correction of base-base mismatches, small insertion-deletion loops, and regions of heterology that are present in duplex DNA formed with strands from two recombining molecules. Correction of the mismatch can result in non-Mendelian segregation of alleles following meiosis." [GOC:elh, PMID:10357855] is_a: GO:0006298 ! mismatch repair is_a: GO:1903046 ! meiotic cell cycle process intersection_of: GO:0006298 ! mismatch repair intersection_of: part_of GO:0051321 ! meiotic cell cycle relationship: part_of GO:0007127 ! meiosis I relationship: part_of GO:0051321 ! meiotic cell cycle [Term] id: GO:0000711 name: meiotic DNA repair synthesis namespace: biological_process def: "During meiosis, the synthesis of DNA proceeding from the broken 3' single-strand DNA end that uses the homologous intact duplex as the template." [GOC:elh, PMID:9334324] is_a: GO:0000731 ! DNA synthesis involved in DNA repair is_a: GO:1903046 ! meiotic cell cycle process relationship: part_of GO:0007127 ! meiosis I [Term] id: GO:0000712 name: resolution of meiotic recombination intermediates namespace: biological_process def: "The cleavage and rejoining of intermediates, such as Holliday junctions, formed during meiotic recombination to produce two intact molecules in which genetic material has been exchanged." [GOC:elh, PMID:11733053] synonym: "resolution of meiotic joint molecules as recombinants" NARROW [GOC:elh, GOC:mah] is_a: GO:1903046 ! meiotic cell cycle process relationship: part_of GO:0007131 ! reciprocal meiotic recombination relationship: part_of GO:0051307 ! meiotic chromosome separation [Term] id: GO:0000713 name: meiotic heteroduplex formation namespace: biological_process def: "During meiosis, the formation of a stable duplex DNA that contains one strand from each of the two recombining DNA molecules." [GOC:elh, PMID:9334324] is_a: GO:0030491 ! heteroduplex formation is_a: GO:1903046 ! meiotic cell cycle process intersection_of: GO:0030491 ! heteroduplex formation intersection_of: part_of GO:0051321 ! meiotic cell cycle relationship: part_of GO:0006310 ! DNA recombination relationship: part_of GO:0007127 ! meiosis I relationship: part_of GO:0051321 ! meiotic cell cycle [Term] id: GO:0000714 name: meiotic strand displacement namespace: biological_process def: "The cell cycle process in which the broken 3' single-strand DNA molecule that formed heteroduplex DNA with its complement in an intact duplex DNA is rejected. The Watson-Crick base pairing in the original duplex is restored. The rejected 3' single-strand DNA molecule reanneals with its original complement to reform two intact duplex molecules. This occurs during meiosis." [GOC:elh, PMID:10357855] synonym: "meiotic D-loop dissociation" RELATED [GOC:mah, GOC:vw] synonym: "meiotic D-loop processing" RELATED [GOC:mah, GOC:vw] synonym: "meiotic displacement loop dissociation" RELATED [GOC:mah, GOC:vw] synonym: "meiotic displacement loop processing" RELATED [GOC:mah, GOC:vw] is_a: GO:0000732 ! strand displacement is_a: GO:1903046 ! meiotic cell cycle process intersection_of: GO:0000732 ! strand displacement intersection_of: part_of GO:0051321 ! meiotic cell cycle relationship: part_of GO:0007127 ! meiosis I relationship: part_of GO:0051321 ! meiotic cell cycle [Term] id: GO:0000715 name: nucleotide-excision repair, DNA damage recognition namespace: biological_process def: "The identification of lesions in DNA, such as pyrimidine-dimers, intrastrand cross-links, and bulky adducts. The wide range of substrate specificity suggests the repair complex recognizes distortions in the DNA helix." [GOC:elh, PMID:10197977] subset: gosubset_prok synonym: "pyrimidine-dimer repair, DNA damage recognition" RELATED [] xref: Reactome:REACT_107456 "DNA Damage Recognition in GG-NER, Drosophila melanogaster" xref: Reactome:REACT_112311 "DNA Damage Recognition in GG-NER, Caenorhabditis elegans" xref: Reactome:REACT_115249 "DNA Damage Recognition in GG-NER, Xenopus tropicalis" xref: Reactome:REACT_115544 "DNA damage recognition in global genomic repair, Gallus gallus" xref: Reactome:REACT_29640 "DNA Damage Recognition in GG-NER, Dictyostelium discoideum" xref: Reactome:REACT_30130 "DNA Damage Recognition in GG-NER, Rattus norvegicus" xref: Reactome:REACT_31764 "DNA Damage Recognition in GG-NER, Taeniopygia guttata" xref: Reactome:REACT_476 "DNA Damage Recognition in GG-NER, Homo sapiens" xref: Reactome:REACT_77558 "DNA Damage Recognition in GG-NER, Danio rerio" xref: Reactome:REACT_81184 "DNA Damage Recognition in GG-NER, Bos taurus" xref: Reactome:REACT_82635 "DNA Damage Recognition in GG-NER, Canis familiaris" xref: Reactome:REACT_86796 "DNA Damage Recognition in GG-NER, Gallus gallus" xref: Reactome:REACT_89770 "DNA Damage Recognition in GG-NER, Arabidopsis thaliana" xref: Reactome:REACT_92224 "DNA Damage Recognition in GG-NER, Mus musculus" xref: Reactome:REACT_94418 "DNA Damage Recognition in GG-NER, Sus scrofa" xref: Reactome:REACT_95988 "DNA Damage Recognition in GG-NER, Saccharomyces cerevisiae" xref: Reactome:REACT_97740 "DNA Damage Recognition in GG-NER, Oryza sativa" xref: Reactome:REACT_98000 "DNA Damage Recognition in GG-NER, Schizosaccharomyces pombe" is_a: GO:0051276 ! chromosome organization relationship: part_of GO:0006289 ! nucleotide-excision repair [Term] id: GO:0000716 name: transcription-coupled nucleotide-excision repair, DNA damage recognition namespace: biological_process def: "The identification of lesions on the actively transcribed strand of the DNA duplex as well as a small subset of lesions not recognized by the general nucleotide-excision repair pathway." [GOC:elh, PMID:10197977] subset: gosubset_prok synonym: "pyrimidine-dimer repair, DNA damage recognition" RELATED [] xref: Reactome:REACT_100470 "RNA Pol II is blocked by the lesion leading to reduced transcription, Plasmodium falciparum" xref: Reactome:REACT_100673 "RNA Pol II is blocked by the lesion leading to reduced transcription, Dictyostelium discoideum" xref: Reactome:REACT_100817 "RNA Pol II is blocked by the lesion leading to reduced transcription, Mus musculus" xref: Reactome:REACT_101583 "RNA Pol II is blocked by the lesion leading to reduced transcription, Drosophila melanogaster" xref: Reactome:REACT_103224 "RNA Pol II is blocked by the lesion leading to reduced transcription, Saccharomyces cerevisiae" xref: Reactome:REACT_104426 "RNA Pol II is blocked by the lesion leading to reduced transcription, Oryza sativa" xref: Reactome:REACT_106854 "RNA Pol II is blocked by the lesion leading to reduced transcription, Schizosaccharomyces pombe" xref: Reactome:REACT_1947 "RNA Pol II is blocked by the lesion leading to reduced transcription, Homo sapiens" xref: Reactome:REACT_78581 "RNA Pol II is blocked by the lesion leading to reduced transcription, Gallus gallus" xref: Reactome:REACT_78888 "RNA Pol II is blocked by the lesion leading to reduced transcription, Canis familiaris" xref: Reactome:REACT_80099 "RNA Pol II is blocked by the lesion leading to reduced transcription, Xenopus tropicalis" xref: Reactome:REACT_86060 "RNA Pol II is blocked by the lesion leading to reduced transcription, Bos taurus" xref: Reactome:REACT_86572 "RNA Pol II is blocked by the lesion leading to reduced transcription, Taeniopygia guttata" xref: Reactome:REACT_86848 "RNA Pol II is blocked by the lesion leading to reduced transcription, Caenorhabditis elegans" xref: Reactome:REACT_88150 "RNA Pol II is blocked by the lesion leading to reduced transcription, Danio rerio" xref: Reactome:REACT_90318 "RNA Pol II is blocked by the lesion leading to reduced transcription, Arabidopsis thaliana" xref: Reactome:REACT_96982 "RNA Pol II is blocked by the lesion leading to reduced transcription, Rattus norvegicus" is_a: GO:0000715 ! nucleotide-excision repair, DNA damage recognition relationship: part_of GO:0006283 ! transcription-coupled nucleotide-excision repair [Term] id: GO:0000717 name: nucleotide-excision repair, DNA duplex unwinding namespace: biological_process def: "The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage." [GOC:elh, PMID:10197977] subset: gosubset_prok xref: Reactome:REACT_101247 "Formation of open bubble structure in DNA by helicases, Bos taurus" xref: Reactome:REACT_101644 "Formation of open bubble structure in DNA by helicases, Oryza sativa" xref: Reactome:REACT_1033 "Formation of open bubble structure in DNA by helicases, Homo sapiens" xref: Reactome:REACT_106346 "Formation of open bubble structure in DNA by helicases, Taeniopygia guttata" xref: Reactome:REACT_107072 "Formation of open bubble structure in DNA by helicases, Mus musculus" xref: Reactome:REACT_110827 "Formation of open bubble structure in DNA by helicases, Danio rerio" xref: Reactome:REACT_113177 "Formation of open bubble structure in DNA by helicases, Caenorhabditis elegans" xref: Reactome:REACT_29217 "Formation of open bubble structure in DNA by helicases, Xenopus tropicalis" xref: Reactome:REACT_34016 "Formation of open bubble structure in DNA by helicases, Rattus norvegicus" xref: Reactome:REACT_78462 "Formation of open bubble structure in DNA by helicases, Drosophila melanogaster" xref: Reactome:REACT_81682 "Formation of open bubble structure in DNA by helicases, Canis familiaris" xref: Reactome:REACT_83794 "Formation of open bubble structure in DNA by helicases, Gallus gallus" xref: Reactome:REACT_84565 "Formation of open bubble structure in DNA by helicases, Schizosaccharomyces pombe" xref: Reactome:REACT_89030 "Formation of open bubble structure in DNA by helicases, Saccharomyces cerevisiae" xref: Reactome:REACT_95993 "Formation of open bubble structure in DNA by helicases, Arabidopsis thaliana" xref: Reactome:REACT_98302 "Formation of open bubble structure in DNA by helicases, Sus scrofa" is_a: GO:0032508 ! DNA duplex unwinding intersection_of: GO:0032508 ! DNA duplex unwinding intersection_of: part_of GO:0006289 ! nucleotide-excision repair relationship: part_of GO:0006289 ! nucleotide-excision repair [Term] id: GO:0000718 name: nucleotide-excision repair, DNA damage removal namespace: biological_process def: "The removal of the oligonucleotide that contains the DNA damage. The oligonucleotide is formed by dual incisions that flank the site of DNA damage." [GOC:elh, PMID:10197977] subset: gosubset_prok xref: Reactome:REACT_102444 "Dual incision reaction in GG-NER, Oryza sativa" xref: Reactome:REACT_104645 "Dual incision reaction in GG-NER, Taeniopygia guttata" xref: Reactome:REACT_109019 "Dual incision reaction in GG-NER, Bos taurus" xref: Reactome:REACT_30192 "Dual incision reaction in GG-NER, Xenopus tropicalis" xref: Reactome:REACT_311 "Dual incision reaction in GG-NER, Homo sapiens" xref: Reactome:REACT_31322 "Dual incision reaction in GG-NER, Saccharomyces cerevisiae" xref: Reactome:REACT_32014 "Dual incision reaction in GG-NER, Danio rerio" xref: Reactome:REACT_52725 "Dual incision reaction in GG-NER, Gallus gallus" xref: Reactome:REACT_89200 "Dual incision reaction in GG-NER, Sus scrofa" xref: Reactome:REACT_90961 "Dual incision reaction in GG-NER, Arabidopsis thaliana" xref: Reactome:REACT_91383 "Dual incision reaction in GG-NER, Drosophila melanogaster" xref: Reactome:REACT_92216 "Dual incision reaction in GG-NER, Canis familiaris" xref: Reactome:REACT_92900 "Dual incision reaction in GG-NER, Rattus norvegicus" xref: Reactome:REACT_93068 "Dual incision reaction in GG-NER, Schizosaccharomyces pombe" xref: Reactome:REACT_96787 "Dual incision reaction in GG-NER, Caenorhabditis elegans" xref: Reactome:REACT_99802 "Dual incision reaction in GG-NER, Mus musculus" is_a: GO:0044349 ! DNA excision relationship: part_of GO:0006289 ! nucleotide-excision repair [Term] id: GO:0000719 name: photoreactive repair namespace: biological_process def: "The repair of UV-induced T-T, C-T and C-C dimers by directly reversing the damage to restore the original pyrimidines." [GOC:elh, PMID:10915863] subset: gosubset_prok synonym: "pyrimidine-dimer repair by photolyase" NARROW [] is_a: GO:0006290 ! pyrimidine dimer repair [Term] id: GO:0000720 name: pyrimidine dimer repair by nucleotide-excision repair namespace: biological_process def: "The repair of UV-induced T-T, C-T, and C-C dimers by the recognition and removal of the damaged DNA strand from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase." [GOC:elh] comment: Note that the repair of pyrimidine dimers by nucleotide excision repair involves the same gene products that are involved in general nucleotide excision repair. Consider also annotating to other children of the biological process term 'nucleotide-excision repair ; GO:0006289'. subset: gosubset_prok is_a: GO:0006289 ! nucleotide-excision repair is_a: GO:0006290 ! pyrimidine dimer repair [Term] id: GO:0000721 name: (R,R)-butanediol dehydrogenase activity namespace: molecular_function def: "Catalysis of the reversible reaction: (R,R)-butane-2,3-diol + NAD+ = (R)-acetoin + NADH + H(+)." [EC:1.1.1.4] subset: gosubset_prok synonym: "(R)-2,3-butanediol dehydrogenase activity" EXACT [EC:1.1.1.4] synonym: "(R)-diacetyl reductase activity" EXACT [EC:1.1.1.4] synonym: "1-amino-2-propanol dehydrogenase activity" EXACT [EC:1.1.1.4] synonym: "1-amino-2-propanol oxidoreductase activity" EXACT [EC:1.1.1.4] synonym: "2,3-butanediol dehydrogenase activity" EXACT [EC:1.1.1.4] synonym: "aminopropanol oxidoreductase activity" EXACT [EC:1.1.1.4] synonym: "butylene glycol dehydrogenase activity" EXACT [EC:1.1.1.4] synonym: "butyleneglycol dehydrogenase activity" EXACT [EC:1.1.1.4] synonym: "D-(-)-butanediol dehydrogenase activity" EXACT [EC:1.1.1.4] synonym: "D-1-amino-2-propanol dehydrogenase activity" EXACT [EC:1.1.1.4] synonym: "D-1-amino-2-propanol:NAD(2) oxidoreductase activity" EXACT [EC:1.1.1.4] synonym: "D-aminopropanol dehydrogenase activity" EXACT [EC:1.1.1.4] synonym: "D-butanediol dehydrogenase activity" EXACT [EC:1.1.1.4] synonym: "diacetyl (acetoin) reductase activity" RELATED [EC:1.1.1.4] xref: EC:1.1.1.4 xref: MetaCyc:RR-BUTANEDIOL-DEHYDROGENASE-RXN xref: RHEA:24343 is_a: GO:0016616 ! oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor [Term] id: GO:0000722 name: telomere maintenance via recombination namespace: biological_process def: "Any recombinational process that contributes to the maintenance of proper telomeric length." [GOC:elh, PMID:11850777] synonym: "telomerase-independent telomere maintenance" RELATED [] xref: Reactome:REACT_101373 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Xenopus tropicalis" xref: Reactome:REACT_101439 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Danio rerio" xref: Reactome:REACT_101498 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Oryza sativa" xref: Reactome:REACT_101756 "Polymerase switching on the C-strand of the telomere, Arabidopsis thaliana" xref: Reactome:REACT_101953 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Oryza sativa" xref: Reactome:REACT_102170 "Polymerase switching on the C-strand of the telomere, Drosophila melanogaster" xref: Reactome:REACT_102248 "RPA binds to the Flap on the C-strand, Danio rerio" xref: Reactome:REACT_102860 "Polymerase switching on the C-strand of the telomere, Canis familiaris" xref: Reactome:REACT_102881 "Removal of the Flap Intermediate from the C-strand, Oryza sativa" xref: Reactome:REACT_103207 "Telomere C-strand synthesis initiation, Dictyostelium discoideum" xref: Reactome:REACT_103350 "Telomere C-strand synthesis initiation, Schizosaccharomyces pombe" xref: Reactome:REACT_103501 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Xenopus tropicalis" xref: Reactome:REACT_103857 "Recruitment of Dna2 endonuclease to the C strand, Sus scrofa" xref: Reactome:REACT_104171 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Danio rerio" xref: Reactome:REACT_104453 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Dictyostelium discoideum" xref: Reactome:REACT_104638 "Polymerase switching on the C-strand of the telomere, Caenorhabditis elegans" xref: Reactome:REACT_104914 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Rattus norvegicus" xref: Reactome:REACT_105177 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Mus musculus" xref: Reactome:REACT_105258 "Formation of Processive Complex on the C-strand of the telomere, Mus musculus" xref: Reactome:REACT_105462 "Formation of C-strand Okazaki fragments, Sus scrofa" xref: Reactome:REACT_105491 "Formation of Processive Complex on the C-strand of the telomere, Xenopus tropicalis" xref: Reactome:REACT_106206 "Removal of the Flap Intermediate from the C-strand, Schizosaccharomyces pombe" xref: Reactome:REACT_106874 "Polymerase switching on the C-strand of the telomere, Xenopus tropicalis" xref: Reactome:REACT_106919 "Joining of adjacent Okazaki fragments of the C-strand, Oryza sativa" xref: Reactome:REACT_106924 "Removal of remaining Flap from the C-strand, Bos taurus" xref: Reactome:REACT_106994 "Formation of C-strand Okazaki fragments, Schizosaccharomyces pombe" xref: Reactome:REACT_107163 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Dictyostelium discoideum" xref: Reactome:REACT_107299 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Gallus gallus" xref: Reactome:REACT_107682 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Saccharomyces cerevisiae" xref: Reactome:REACT_108058 "Formation of Processive Complex on the C-strand of the telomere, Oryza sativa" xref: Reactome:REACT_108279 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Rattus norvegicus" xref: Reactome:REACT_108285 "Processive synthesis on the C-strand of the telomere, Oryza sativa" xref: Reactome:REACT_108323 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Plasmodium falciparum" xref: Reactome:REACT_108876 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Caenorhabditis elegans" xref: Reactome:REACT_109084 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Bos taurus" xref: Reactome:REACT_109593 "Formation of C-strand Okazaki fragments, Mus musculus" xref: Reactome:REACT_109676 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Bos taurus" xref: Reactome:REACT_110206 "Recruitment of Dna2 endonuclease to the C strand, Canis familiaris" xref: Reactome:REACT_110252 "Formation of C-strand Okazaki fragments, Canis familiaris" xref: Reactome:REACT_110586 "Removal of remaining Flap from the C-strand, Xenopus tropicalis" xref: Reactome:REACT_110741 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Saccharomyces cerevisiae" xref: Reactome:REACT_28103 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Schizosaccharomyces pombe" xref: Reactome:REACT_28301 "Removal of remaining Flap from the C-strand, Danio rerio" xref: Reactome:REACT_28337 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Rattus norvegicus" xref: Reactome:REACT_28438 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Danio rerio" xref: Reactome:REACT_28735 "Formation of the Flap Intermediate on the C-strand, Oryza sativa" xref: Reactome:REACT_28845 "Removal of the Flap Intermediate from the C-strand, Xenopus tropicalis" xref: Reactome:REACT_29030 "Formation of C-strand Okazaki fragments, Danio rerio" xref: Reactome:REACT_29091 "Removal of RNA primer and dissociation of RPA and Dna2 from the C-strand, Danio rerio" xref: Reactome:REACT_29268 "Polymerase switching on the C-strand of the telomere, Saccharomyces cerevisiae" xref: Reactome:REACT_29498 "Joining of adjacent Okazaki fragments of the C-strand, Mus musculus" xref: Reactome:REACT_29561 "Telomere C-strand synthesis initiation, Caenorhabditis elegans" xref: Reactome:REACT_29730 "Processive synthesis on the C-strand of the telomere, Rattus norvegicus" xref: Reactome:REACT_29736 "Removal of remaining Flap from the C-strand, Oryza sativa" xref: Reactome:REACT_30132 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Arabidopsis thaliana" xref: Reactome:REACT_30146 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Canis familiaris" xref: Reactome:REACT_30357 "Recruitment of Dna2 endonuclease to the C strand, Oryza sativa" xref: Reactome:REACT_30676 "Processive synthesis on the C-strand of the telomere, Taeniopygia guttata" xref: Reactome:REACT_31415 "Polymerase switching on the C-strand of the telomere, Gallus gallus" xref: Reactome:REACT_31855 "Recruitment of Dna2 endonuclease to the C strand, Xenopus tropicalis" xref: Reactome:REACT_31896 "Removal of RNA primer and dissociation of RPA and Dna2 from the C-strand, Mus musculus" xref: Reactome:REACT_32409 "Formation of Processive Complex on the C-strand of the telomere, Bos taurus" xref: Reactome:REACT_32656 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Oryza sativa" xref: Reactome:REACT_32714 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Arabidopsis thaliana" xref: Reactome:REACT_32801 "Recruitment of Dna2 endonuclease to the C strand, Schizosaccharomyces pombe" xref: Reactome:REACT_33015 "Formation of the Flap Intermediate on the C-strand, Sus scrofa" xref: Reactome:REACT_33071 "Polymerase switching on the C-strand of the telomere, Bos taurus" xref: Reactome:REACT_33514 "Recruitment of Dna2 endonuclease to the C strand, Danio rerio" xref: Reactome:REACT_33663 "Processive synthesis on the C-strand of the telomere, Mus musculus" xref: Reactome:REACT_33974 "Formation of the Flap Intermediate on the C-strand, Mus musculus" xref: Reactome:REACT_34757 "Polymerase switching on the C-strand of the telomere, Taeniopygia guttata" xref: Reactome:REACT_57279 "Processive synthesis on the C-strand of the telomere, Bos taurus" xref: Reactome:REACT_77128 "Formation of C-strand Okazaki fragments, Oryza sativa" xref: Reactome:REACT_77820 "Formation of Processive Complex on the C-strand of the telomere, Arabidopsis thaliana" xref: Reactome:REACT_77906 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Plasmodium falciparum" xref: Reactome:REACT_77925 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Plasmodium falciparum" xref: Reactome:REACT_78056 "Formation of the Flap Intermediate on the C-strand, Rattus norvegicus" xref: Reactome:REACT_78182 "Telomere C-strand synthesis initiation, Rattus norvegicus" xref: Reactome:REACT_78501 "Formation of the Flap Intermediate on the C-strand, Bos taurus" xref: Reactome:REACT_78969 "Joining of adjacent Okazaki fragments of the C-strand, Bos taurus" xref: Reactome:REACT_79008 "Recruitment of Dna2 endonuclease to the C strand, Arabidopsis thaliana" xref: Reactome:REACT_79101 "Removal of the Flap Intermediate from the C-strand, Danio rerio" xref: Reactome:REACT_7949 "RPA binds to the Flap on the C-strand, Homo sapiens" xref: Reactome:REACT_7955 "Removal of RNA primer and dissociation of RPA and Dna2 from the C-strand, Homo sapiens" xref: Reactome:REACT_7967 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Homo sapiens" xref: Reactome:REACT_7973 "Formation of the Flap Intermediate on the C-strand, Homo sapiens" xref: Reactome:REACT_7975 "Removal of remaining Flap from the C-strand, Homo sapiens" xref: Reactome:REACT_7979 "Formation of Processive Complex on the C-strand of the telomere, Homo sapiens" xref: Reactome:REACT_7987 "Polymerase switching on the C-strand of the telomere, Homo sapiens" xref: Reactome:REACT_7993 "Telomere C-strand synthesis initiation, Homo sapiens" xref: Reactome:REACT_7994 "Joining of adjacent Okazaki fragments of the C-strand, Homo sapiens" xref: Reactome:REACT_79977 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Saccharomyces cerevisiae" xref: Reactome:REACT_7998 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Homo sapiens" xref: Reactome:REACT_7999 "Removal of the Flap Intermediate from the C-strand, Homo sapiens" xref: Reactome:REACT_8000 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Homo sapiens" xref: Reactome:REACT_8004 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Homo sapiens" xref: Reactome:REACT_8008 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Homo sapiens" xref: Reactome:REACT_8015 "Recruitment of Dna2 endonuclease to the C strand, Homo sapiens" xref: Reactome:REACT_80165 "Removal of the Flap Intermediate from the C-strand, Taeniopygia guttata" xref: Reactome:REACT_8027 "Processive synthesis on the C-strand of the telomere, Homo sapiens" xref: Reactome:REACT_8029 "Formation of C-strand Okazaki fragments, Homo sapiens" xref: Reactome:REACT_80513 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Dictyostelium discoideum" xref: Reactome:REACT_80567 "Polymerase switching on the C-strand of the telomere, Mus musculus" xref: Reactome:REACT_80653 "Telomere C-strand synthesis initiation, Sus scrofa" xref: Reactome:REACT_80757 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Saccharomyces cerevisiae" xref: Reactome:REACT_80999 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Schizosaccharomyces pombe" xref: Reactome:REACT_81201 "Removal of remaining Flap from the C-strand, Mus musculus" xref: Reactome:REACT_81258 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Schizosaccharomyces pombe" xref: Reactome:REACT_81387 "Formation of Processive Complex on the C-strand of the telomere, Rattus norvegicus" xref: Reactome:REACT_81697 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Taeniopygia guttata" xref: Reactome:REACT_81968 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Sus scrofa" xref: Reactome:REACT_81990 "Joining of adjacent Okazaki fragments of the C-strand, Danio rerio" xref: Reactome:REACT_82014 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Caenorhabditis elegans" xref: Reactome:REACT_82097 "Processive synthesis on the C-strand of the telomere, Schizosaccharomyces pombe" xref: Reactome:REACT_82246 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Drosophila melanogaster" xref: Reactome:REACT_82465 "Processive synthesis on the C-strand of the telomere, Arabidopsis thaliana" xref: Reactome:REACT_82605 "Telomere C-strand synthesis initiation, Canis familiaris" xref: Reactome:REACT_82834 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Canis familiaris" xref: Reactome:REACT_83118 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Plasmodium falciparum" xref: Reactome:REACT_83299 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Danio rerio" xref: Reactome:REACT_83482 "Removal of RNA primer and dissociation of RPA and Dna2 from the C-strand, Xenopus tropicalis" xref: Reactome:REACT_83617 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Oryza sativa" xref: Reactome:REACT_83805 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Drosophila melanogaster" xref: Reactome:REACT_84276 "Recruitment of Dna2 endonuclease to the C strand, Taeniopygia guttata" xref: Reactome:REACT_84292 "Removal of RNA primer and dissociation of RPA and Dna2 from the C-strand, Bos taurus" xref: Reactome:REACT_84527 "Joining of adjacent Okazaki fragments of the C-strand, Xenopus tropicalis" xref: Reactome:REACT_84864 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Mus musculus" xref: Reactome:REACT_85303 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Arabidopsis thaliana" xref: Reactome:REACT_85614 "Removal of RNA primer and dissociation of RPA and Dna2 from the C-strand, Rattus norvegicus" xref: Reactome:REACT_85781 "Joining of adjacent Okazaki fragments of the C-strand, Schizosaccharomyces pombe" xref: Reactome:REACT_85910 "Joining of adjacent Okazaki fragments of the C-strand, Canis familiaris" xref: Reactome:REACT_85945 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Xenopus tropicalis" xref: Reactome:REACT_86438 "Removal of the Flap Intermediate from the C-strand, Mus musculus" xref: Reactome:REACT_86551 "Formation of the Flap Intermediate on the C-strand, Danio rerio" xref: Reactome:REACT_86566 "RPA binds to the Flap on the C-strand, Mus musculus" xref: Reactome:REACT_86673 "Processive synthesis on the C-strand of the telomere, Xenopus tropicalis" xref: Reactome:REACT_86894 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Bos taurus" xref: Reactome:REACT_87128 "Processive synthesis on the C-strand of the telomere, Canis familiaris" xref: Reactome:REACT_87148 "Recruitment of Dna2 endonuclease to the C strand, Rattus norvegicus" xref: Reactome:REACT_87271 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Xenopus tropicalis" xref: Reactome:REACT_87564 "Recruitment of Dna2 endonuclease to the C strand, Mus musculus" xref: Reactome:REACT_87776 "Removal of the Flap Intermediate from the C-strand, Canis familiaris" xref: Reactome:REACT_87852 "Removal of RNA primer and dissociation of RPA and Dna2 from the C-strand, Canis familiaris" xref: Reactome:REACT_87982 "Removal of the Flap Intermediate from the C-strand, Arabidopsis thaliana" xref: Reactome:REACT_88080 "Telomere C-strand synthesis initiation, Mus musculus" xref: Reactome:REACT_88200 "Formation of the Flap Intermediate on the C-strand, Canis familiaris" xref: Reactome:REACT_88586 "RPA binds to the Flap on the C-strand, Rattus norvegicus" xref: Reactome:REACT_88760 "Removal of remaining Flap from the C-strand, Sus scrofa" xref: Reactome:REACT_88793 "RPA binds to the Flap on the C-strand, Bos taurus" xref: Reactome:REACT_88811 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Danio rerio" xref: Reactome:REACT_89109 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Canis familiaris" xref: Reactome:REACT_89136 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Schizosaccharomyces pombe" xref: Reactome:REACT_89422 "RPA binds to the Flap on the C-strand, Xenopus tropicalis" xref: Reactome:REACT_89618 "Joining of adjacent Okazaki fragments of the C-strand, Rattus norvegicus" xref: Reactome:REACT_89731 "Polymerase switching on the C-strand of the telomere, Rattus norvegicus" xref: Reactome:REACT_89859 "Polymerase switching on the C-strand of the telomere, Danio rerio" xref: Reactome:REACT_89896 "Formation of C-strand Okazaki fragments, Bos taurus" xref: Reactome:REACT_90432 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Caenorhabditis elegans" xref: Reactome:REACT_90507 "Polymerase switching on the C-strand of the telomere, Schizosaccharomyces pombe" xref: Reactome:REACT_90656 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Rattus norvegicus" xref: Reactome:REACT_91124 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Caenorhabditis elegans" xref: Reactome:REACT_91185 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Bos taurus" xref: Reactome:REACT_91218 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Oryza sativa" xref: Reactome:REACT_91365 "Formation of C-strand Okazaki fragments, Rattus norvegicus" xref: Reactome:REACT_91568 "Recruitment of Dna2 endonuclease to the C strand, Bos taurus" xref: Reactome:REACT_91624 "Telomere C-strand synthesis initiation, Saccharomyces cerevisiae" xref: Reactome:REACT_91633 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Gallus gallus" xref: Reactome:REACT_91661 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Caenorhabditis elegans" xref: Reactome:REACT_92017 "Telomere C-strand synthesis initiation, Arabidopsis thaliana" xref: Reactome:REACT_92092 "Joining of adjacent Okazaki fragments of the C-strand, Sus scrofa" xref: Reactome:REACT_92189 "Processive synthesis on the C-strand of the telomere, Danio rerio" xref: Reactome:REACT_92339 "Removal of remaining Flap from the C-strand, Rattus norvegicus" xref: Reactome:REACT_92420 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Sus scrofa" xref: Reactome:REACT_92505 "Removal of the Flap Intermediate from the C-strand, Rattus norvegicus" xref: Reactome:REACT_92773 "Formation of Processive Complex on the C-strand of the telomere, Schizosaccharomyces pombe" xref: Reactome:REACT_93121 "Polymerase switching on the C-strand of the telomere, Sus scrofa" xref: Reactome:REACT_93535 "Formation of C-strand Okazaki fragments, Arabidopsis thaliana" xref: Reactome:REACT_93603 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Taeniopygia guttata" xref: Reactome:REACT_93674 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Dictyostelium discoideum" xref: Reactome:REACT_93682 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Arabidopsis thaliana" xref: Reactome:REACT_93745 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Schizosaccharomyces pombe" xref: Reactome:REACT_93828 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Canis familiaris" xref: Reactome:REACT_93893 "Removal of the Flap Intermediate from the C-strand, Bos taurus" xref: Reactome:REACT_94317 "Joining of adjacent Okazaki fragments of the C-strand, Arabidopsis thaliana" xref: Reactome:REACT_94323 "The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere, Canis familiaris" xref: Reactome:REACT_94685 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Xenopus tropicalis" xref: Reactome:REACT_94878 "Formation of the Flap Intermediate on the C-strand, Xenopus tropicalis" xref: Reactome:REACT_94930 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Drosophila melanogaster" xref: Reactome:REACT_95256 "Polymerase switching on the C-strand of the telomere, Dictyostelium discoideum" xref: Reactome:REACT_95355 "Polymerase switching on the C-strand of the telomere, Oryza sativa" xref: Reactome:REACT_95570 "RPA binds to the Flap on the C-strand, Canis familiaris" xref: Reactome:REACT_95593 "Telomere C-strand synthesis initiation, Bos taurus" xref: Reactome:REACT_95767 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Plasmodium falciparum" xref: Reactome:REACT_95954 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Mus musculus" xref: Reactome:REACT_96276 "Removal of remaining Flap from the C-strand, Schizosaccharomyces pombe" xref: Reactome:REACT_96429 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Arabidopsis thaliana" xref: Reactome:REACT_96454 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Saccharomyces cerevisiae" xref: Reactome:REACT_96676 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Mus musculus" xref: Reactome:REACT_96810 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Drosophila melanogaster" xref: Reactome:REACT_97064 "The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere, Bos taurus" xref: Reactome:REACT_97146 "Removal of remaining Flap from the C-strand, Arabidopsis thaliana" xref: Reactome:REACT_97211 "Telomere C-strand synthesis initiation, Drosophila melanogaster" xref: Reactome:REACT_97260 "Formation of C-strand Okazaki fragments, Xenopus tropicalis" xref: Reactome:REACT_97574 "Formation of the Flap Intermediate on the C-strand, Arabidopsis thaliana" xref: Reactome:REACT_97781 "Telomere C-strand synthesis initiation, Danio rerio" xref: Reactome:REACT_97849 "Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere, Dictyostelium discoideum" xref: Reactome:REACT_98163 "RFC dissociates after sliding clamp formation on the C-strand of the telomere, Mus musculus" xref: Reactome:REACT_98508 "Telomere C-strand synthesis initiation, Oryza sativa" xref: Reactome:REACT_98514 "Telomere C-strand synthesis initiation, Xenopus tropicalis" xref: Reactome:REACT_98606 "Formation of Processive Complex on the C-strand of the telomere, Danio rerio" xref: Reactome:REACT_98653 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Drosophila melanogaster" xref: Reactome:REACT_98674 "Formation of Processive Complex on the C-strand of the telomere, Canis familiaris" xref: Reactome:REACT_98759 "RFC binding displaces Pol Alpha on the C-strand of the telomere, Rattus norvegicus" xref: Reactome:REACT_98885 "Formation of the Flap Intermediate on the C-strand, Schizosaccharomyces pombe" xref: Reactome:REACT_99121 "Removal of the Flap Intermediate from the C-strand, Sus scrofa" xref: Reactome:REACT_99658 "Processive synthesis on the C-strand of the telomere, Sus scrofa" xref: Reactome:REACT_99801 "Polymerase switching on the C-strand of the telomere, Plasmodium falciparum" xref: Reactome:REACT_99836 "Telomere C-strand synthesis initiation, Plasmodium falciparum" is_a: GO:0000723 ! telomere maintenance is_a: GO:0006312 ! mitotic recombination [Term] id: GO:0000723 name: telomere maintenance namespace: biological_process def: "Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences." [GOC:BHF, GOC:BHF_telomere, GOC:elh, GOC:rl, PMID:11092831] synonym: "regulation of telomere length" RELATED [GOC:dph, GOC:tb] xref: Reactome:REACT_102051 "Telomere Maintenance, Sus scrofa" xref: Reactome:REACT_102166 "Telomere Maintenance, Schizosaccharomyces pombe" xref: Reactome:REACT_103257 "Telomere Maintenance, Bos taurus" xref: Reactome:REACT_103618 "Telomere Maintenance, Canis familiaris" xref: Reactome:REACT_104398 "Telomere Maintenance, Dictyostelium discoideum" xref: Reactome:REACT_105276 "Disassociation of Processive Complex and Completed Telomere End, Canis familiaris" xref: Reactome:REACT_105401 "Packaging Of Telomere Ends, Rattus norvegicus" xref: Reactome:REACT_105641 "Disassociation of Processive Complex and Completed Telomere End, Mus musculus" xref: Reactome:REACT_107344 "Disassociation of Processive Complex and Completed Telomere End, Xenopus tropicalis" xref: Reactome:REACT_109055 "Disassociation of Processive Complex and Completed Telomere End, Schizosaccharomyces pombe" xref: Reactome:REACT_110319 "Telomere Maintenance, Rattus norvegicus" xref: Reactome:REACT_115102 "Packaging Of Telomere Ends, Canis familiaris" xref: Reactome:REACT_115503 "Packaging Of Telomere Ends, Danio rerio" xref: Reactome:REACT_115535 "Telomere maintenance, Gallus gallus" xref: Reactome:REACT_31996 "Disassociation of Processive Complex and Completed Telomere End, Rattus norvegicus" xref: Reactome:REACT_32322 "Packaging Of Telomere Ends, Sus scrofa" xref: Reactome:REACT_78001 "Telomere Maintenance, Danio rerio" xref: Reactome:REACT_78680 "Telomere Maintenance, Saccharomyces cerevisiae" xref: Reactome:REACT_7954 "Disassociation of Processive Complex and Completed Telomere End, Homo sapiens" xref: Reactome:REACT_7963 "Packaging Of Telomere Ends, Homo sapiens" xref: Reactome:REACT_7970 "Telomere Maintenance, Homo sapiens" xref: Reactome:REACT_80940 "Telomere Maintenance, Plasmodium falciparum" xref: Reactome:REACT_82431 "Disassociation of Processive Complex and Completed Telomere End, Danio rerio" xref: Reactome:REACT_83277 "Disassociation of Processive Complex and Completed Telomere End, Bos taurus" xref: Reactome:REACT_84888 "Telomere Maintenance, Mus musculus" xref: Reactome:REACT_85317 "Disassociation of Processive Complex and Completed Telomere End, Oryza sativa" xref: Reactome:REACT_85782 "Telomere Maintenance, Arabidopsis thaliana" xref: Reactome:REACT_86038 "Telomere Maintenance, Drosophila melanogaster" xref: Reactome:REACT_86194 "Disassociation of Processive Complex and Completed Telomere End, Arabidopsis thaliana" xref: Reactome:REACT_87184 "Telomere Maintenance, Caenorhabditis elegans" xref: Reactome:REACT_88530 "Packaging Of Telomere Ends, Mus musculus" xref: Reactome:REACT_94176 "Telomere Maintenance, Gallus gallus" xref: Reactome:REACT_94707 "Telomere Maintenance, Oryza sativa" xref: Reactome:REACT_96013 "Telomere Maintenance, Taeniopygia guttata" xref: Reactome:REACT_96166 "Telomere Maintenance, Xenopus tropicalis" is_a: GO:0006259 ! DNA metabolic process is_a: GO:0032200 ! telomere organization is_a: GO:0060249 ! anatomical structure homeostasis [Term] id: GO:0000724 name: double-strand break repair via homologous recombination namespace: biological_process alt_id: GO:0016924 def: "The error-free repair of a double-strand break in DNA in which the broken DNA molecule is repaired using homologous sequences. A strand in the broken DNA searches for a homologous region in an intact chromosome to serve as the template for DNA synthesis. The restoration of two intact DNA molecules results in the exchange, reciprocal or nonreciprocal, of genetic material between the intact DNA molecule and the broken DNA molecule." [GOC:elh, PMID:10357855] subset: gosubset_prok synonym: "HDR" EXACT [GOC:vk] synonym: "homologous recombinational repair" EXACT [] synonym: "homology-directed repair" EXACT [GOC:vk] synonym: "HRR" EXACT [] synonym: "Rad51-dependent recombinational repair" EXACT [GOC:mah] synonym: "Rhp51-dependent recombinational repair" EXACT [] xref: Reactome:REACT_103005 "Homologous Recombination Repair, Caenorhabditis elegans" xref: Reactome:REACT_108237 "Homologous Recombination Repair, Saccharomyces cerevisiae" xref: Reactome:REACT_115539 "Recruitment of repair and signaling proteins to double-strand breaks, Gallus gallus" xref: Reactome:REACT_115585 "Homologous recombination repair of replication-dependent double-strand breaks, Gallus gallus" xref: Reactome:REACT_115626 "Homologous DNA pairing and strand exchange, Gallus gallus" xref: Reactome:REACT_115651 "ATM mediated response to DNA double-strand break, Gallus gallus" xref: Reactome:REACT_115715 "ATM mediated phosphorylation of repair proteins, Gallus gallus" xref: Reactome:REACT_115769 "Homologous recombination repair, Gallus gallus" xref: Reactome:REACT_115931 "Processing of DNA double-strand break ends, Gallus gallus" xref: Reactome:REACT_115936 "Homologous recombination repair (HRR) of replication-independent double-strand breaks, Gallus gallus" xref: Reactome:REACT_1874 "Homologous Recombination Repair, Homo sapiens" xref: Reactome:REACT_29815 "Homologous Recombination Repair, Sus scrofa" xref: Reactome:REACT_33853 "Homologous Recombination Repair, Oryza sativa" xref: Reactome:REACT_42307 "Homologous Recombination Repair, Gallus gallus" xref: Reactome:REACT_80576 "Homologous Recombination Repair, Schizosaccharomyces pombe" xref: Reactome:REACT_82771 "Homologous Recombination Repair, Xenopus tropicalis" xref: Reactome:REACT_83941 "Homologous Recombination Repair, Plasmodium falciparum" xref: Reactome:REACT_84594 "Homologous Recombination Repair, Dictyostelium discoideum" xref: Reactome:REACT_84793 "Homologous Recombination Repair, Danio rerio" xref: Reactome:REACT_85965 "Homologous Recombination Repair, Drosophila melanogaster" xref: Reactome:REACT_87979 "Homologous Recombination Repair, Mycobacterium tuberculosis" xref: Reactome:REACT_90944 "Homologous Recombination Repair, Mus musculus" xref: Reactome:REACT_92384 "Homologous Recombination Repair, Canis familiaris" xref: Reactome:REACT_92897 "Homologous Recombination Repair, Arabidopsis thaliana" xref: Reactome:REACT_97339 "Homologous Recombination Repair, Taeniopygia guttata" xref: Reactome:REACT_99066 "Homologous Recombination Repair, Rattus norvegicus" xref: Reactome:REACT_99423 "Homologous Recombination Repair, Bos taurus" is_a: GO:0000725 ! recombinational repair is_a: GO:0006302 ! double-strand break repair [Term] id: GO:0000725 name: recombinational repair namespace: biological_process def: "A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC:elh] subset: gosubset_prok xref: Wikipedia:Recombinational_repair is_a: GO:0006281 ! DNA repair is_a: GO:0006310 ! DNA recombination [Term] id: GO:0000726 name: non-recombinational repair namespace: biological_process def: "A DNA repair process in which that does not require the exchange of genetic material between the broken DNA molecule and a homologous region of DNA." [GOC:elh] subset: gosubset_prok is_a: GO:0006281 ! DNA repair [Term] id: GO:0000727 name: double-strand break repair via break-induced replication namespace: biological_process def: "The error-free repair of a double-strand break in DNA in which the centromere-proximal end of a broken chromosome searches for a homologous region in an intact chromosome. DNA synthesis initiates from the 3' end of the invading DNA strand, using the intact chromosome as the template, and progresses to the end of the chromosome." [GOC:elh, PMID:10357855] subset: gosubset_prok is_a: GO:0000724 ! double-strand break repair via homologous recombination [Term] id: GO:0000728 name: gene conversion at mating-type locus, DNA double-strand break formation namespace: biological_process def: "The site-specific endonucleolytic cleavage of DNA at the mating-type locus which initiates the conversion of one mating-type allele to another." [GOC:elh, PMID:7646483] is_a: GO:0022414 ! reproductive process is_a: GO:0090305 ! nucleic acid phosphodiester bond hydrolysis relationship: part_of GO:0007534 ! gene conversion at mating-type locus [Term] id: GO:0000729 name: DNA double-strand break processing namespace: biological_process def: "The 5' to 3' exonucleolytic resection of the DNA at the site of the break to form a 3' single-strand DNA overhang." [PMID:10357855] xref: Reactome:REACT_172 "Resection of double-strand break ends, Homo sapiens" is_a: GO:0006259 ! DNA metabolic process relationship: has_part GO:0035312 ! 5'-3' exodeoxyribonuclease activity relationship: part_of GO:0006302 ! double-strand break repair [Term] id: GO:0000730 name: DNA recombinase assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of strand exchange proteins (recombinases) into higher order oligomers on single-stranded DNA." [PMID:10357855] synonym: "Rad51 nucleoprotein filament formation" EXACT [GOC:elh, GOC:vw] xref: Reactome:REACT_100225 "Assembly of the RAD51-ssDNA nucleoprotein complex, Gallus gallus" xref: Reactome:REACT_100616 "Assembly of the RAD51-ssDNA nucleoprotein complex, Plasmodium falciparum" xref: Reactome:REACT_101062 "Assembly of the RAD51-ssDNA nucleoprotein complex, Arabidopsis thaliana" xref: Reactome:REACT_102016 "Assembly of the RAD51-ssDNA nucleoprotein complex, Dictyostelium discoideum" xref: Reactome:REACT_103788 "Assembly of the RAD51-ssDNA nucleoprotein complex, Drosophila melanogaster" xref: Reactome:REACT_104366 "Assembly of the RAD51-ssDNA nucleoprotein complex, Schizosaccharomyces pombe" xref: Reactome:REACT_106498 "Assembly of the RAD51-ssDNA nucleoprotein complex, Taeniopygia guttata" xref: Reactome:REACT_110494 "Assembly of the RAD51-ssDNA nucleoprotein complex, Mus musculus" xref: Reactome:REACT_2141 "Assembly of the RAD51-ssDNA nucleoprotein complex, Homo sapiens" xref: Reactome:REACT_28107 "Assembly of the RAD51-ssDNA nucleoprotein complex, Saccharomyces cerevisiae" xref: Reactome:REACT_32257 "Assembly of the RAD51-ssDNA nucleoprotein complex, Bos taurus" xref: Reactome:REACT_78586 "Assembly of the RAD51-ssDNA nucleoprotein complex, Canis familiaris" xref: Reactome:REACT_79561 "Assembly of the RAD51-ssDNA nucleoprotein complex, Sus scrofa" xref: Reactome:REACT_81810 "Assembly of the RAD51-ssDNA nucleoprotein complex, Xenopus tropicalis" xref: Reactome:REACT_82066 "Assembly of the RAD51-ssDNA nucleoprotein complex, Caenorhabditis elegans" xref: Reactome:REACT_85201 "Assembly of the RAD51-ssDNA nucleoprotein complex, Oryza sativa" xref: Reactome:REACT_88197 "Assembly of the RAD51-ssDNA nucleoprotein complex, Rattus norvegicus" xref: Reactome:REACT_96901 "Assembly of the RAD51-ssDNA nucleoprotein complex, Danio rerio" is_a: GO:0065004 ! protein-DNA complex assembly relationship: part_of GO:0045003 ! double-strand break repair via synthesis-dependent strand annealing [Term] id: GO:0000731 name: DNA synthesis involved in DNA repair namespace: biological_process def: "Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template." [PMID:10357855] subset: gosubset_prok synonym: "DNA repair synthesis" BROAD [] synonym: "DNA synthesis during DNA repair" RELATED [GOC:dph, GOC:tb] synonym: "mitotic DNA repair synthesis" NARROW [GOC:mah] xref: Reactome:REACT_973 "DNA repair synthesis, Homo sapiens" is_a: GO:0071897 ! DNA biosynthetic process intersection_of: GO:0071897 ! DNA biosynthetic process intersection_of: part_of GO:0006281 ! DNA repair relationship: part_of GO:0006281 ! DNA repair [Term] id: GO:0000732 name: strand displacement namespace: biological_process def: "The rejection of the broken 3' single-strand DNA molecule that formed heteroduplex DNA with its complement in an intact duplex DNA. The Watson-Crick base pairing in the original duplex is restored. The rejected 3' single-strand DNA molecule reanneals with its original complement to reform two intact duplex molecules." [PMID:10357855] subset: gosubset_prok synonym: "D-loop dissociation" RELATED [GOC:mah, GOC:vw] synonym: "D-loop processing" RELATED [GOC:mah, GOC:vw] synonym: "displacement loop dissociation" RELATED [GOC:mah, GOC:vw] synonym: "displacement loop processing" RELATED [GOC:mah, GOC:vw] xref: Reactome:REACT_287 "Dissociation of the extended strands, Homo sapiens" is_a: GO:0006259 ! DNA metabolic process relationship: part_of GO:0006310 ! DNA recombination [Term] id: GO:0000733 name: DNA strand renaturation namespace: biological_process def: "The identification and annealing of complementary base pairs in single-strand DNA." [GOC:elh] subset: gosubset_prok is_a: GO:0006259 ! DNA metabolic process [Term] id: GO:0000734 name: gene conversion at mating-type locus, DNA repair synthesis namespace: biological_process def: "Synthesis of DNA that proceeds from the broken 3' single-strand DNA end uses the homologous intact duplex as the template during gene conversion at the mating-type locus." [GOC:elh] is_a: GO:0000731 ! DNA synthesis involved in DNA repair is_a: GO:0022414 ! reproductive process intersection_of: GO:0000731 ! DNA synthesis involved in DNA repair intersection_of: part_of GO:0007534 ! gene conversion at mating-type locus relationship: part_of GO:0007534 ! gene conversion at mating-type locus [Term] id: GO:0000735 name: removal of nonhomologous ends namespace: biological_process def: "The removal of nonhomologous sequences at the broken 3' single-strand DNA end before DNA repair synthesis can occur." [PMID:10357855] is_a: GO:0006259 ! DNA metabolic process relationship: has_part GO:0004520 ! endodeoxyribonuclease activity [Term] id: GO:0000736 name: double-strand break repair via single-strand annealing, removal of nonhomologous ends namespace: biological_process def: "During DSBR via single-strand annealing, the removal of nonhomologous sequences at the broken 3' single-strand DNA end before DNA repair synthesis can occur." [PMID:10357855] subset: gosubset_prok is_a: GO:0000735 ! removal of nonhomologous ends intersection_of: GO:0000735 ! removal of nonhomologous ends intersection_of: part_of GO:0045002 ! double-strand break repair via single-strand annealing relationship: part_of GO:0045002 ! double-strand break repair via single-strand annealing [Term] id: GO:0000737 name: DNA catabolic process, endonucleolytic namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides." [GOC:elh, GOC:mah] subset: gosubset_prok synonym: "DNA breakdown, endonucleolytic" EXACT [] synonym: "DNA degradation, endonucleolytic" EXACT [] synonym: "endonucleolytic degradation of DNA" EXACT [] synonym: "endonucleolytic DNA catabolism" EXACT [] is_a: GO:0006308 ! DNA catabolic process is_a: GO:0090305 ! nucleic acid phosphodiester bond hydrolysis relationship: has_part GO:0004520 ! endodeoxyribonuclease activity [Term] id: GO:0000738 name: DNA catabolic process, exonucleolytic namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of terminal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides." [GOC:elh, GOC:mah] subset: gosubset_prok synonym: "DNA breakdown, exonucleolytic" EXACT [] synonym: "DNA degradation, exonucleolytic" EXACT [] synonym: "exonucleolytic degradation of DNA" EXACT [] is_a: GO:0006308 ! DNA catabolic process is_a: GO:0090305 ! nucleic acid phosphodiester bond hydrolysis relationship: has_part GO:0004529 ! exodeoxyribonuclease activity [Term] id: GO:0000739 name: obsolete DNA strand annealing activity namespace: molecular_function def: "OBSOLETE. Facilitates the base-pairing of complementary single-stranded DNA." [GOC:elh] comment: This term was made obsolete because it describes a process and not an activity. synonym: "DNA strand annealing activity" EXACT [] is_obsolete: true consider: GO:0000733 consider: GO:0036292 consider: GO:0036310 [Term] id: GO:0000740 name: nuclear membrane fusion namespace: biological_process def: "The joining of 2 or more lipid bilayer membranes that surround the nucleus." [GOC:elh] is_a: GO:0000741 ! karyogamy is_a: GO:0090174 ! organelle membrane fusion [Term] id: GO:0000741 name: karyogamy namespace: biological_process alt_id: GO:0007335 def: "The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei." [GOC:elh] synonym: "nuclear fusion" EXACT [] synonym: "nuclear fusion during karyogamy" EXACT [] xref: Wikipedia:Karyogamy is_a: GO:0048284 ! organelle fusion relationship: part_of GO:0006997 ! nucleus organization [Term] id: GO:0000742 name: karyogamy involved in conjugation with cellular fusion namespace: biological_process def: "During sexual reproduction, the creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei. This occurs after cytogamy." [GOC:elh] synonym: "karyogamy during conjugation with cellular fusion" RELATED [GOC:dph, GOC:tb] is_a: GO:0000741 ! karyogamy is_a: GO:0022414 ! reproductive process intersection_of: GO:0000741 ! karyogamy intersection_of: part_of GO:0000747 ! conjugation with cellular fusion relationship: part_of GO:0000747 ! conjugation with cellular fusion [Term] id: GO:0000743 name: nuclear migration involved in conjugation with cellular fusion namespace: biological_process alt_id: GO:0006946 def: "The microtubule-based movement of nuclei towards one another as a prelude to karyogamy in organisms undergoing conjugation with cellular fusion." [GOC:clt, GOC:vw, PMID:16380440] synonym: "nuclear congression" EXACT [GOC:vw] synonym: "nuclear migration during conjugation with cellular fusion" RELATED [GOC:dph, GOC:tb] is_a: GO:0030473 ! nuclear migration along microtubule is_a: GO:0044702 ! single organism reproductive process intersection_of: GO:0007097 ! nuclear migration intersection_of: part_of GO:0000747 ! conjugation with cellular fusion relationship: part_of GO:0000747 ! conjugation with cellular fusion [Term] id: GO:0000744 name: karyogamy involved in conjugation with mutual genetic exchange namespace: biological_process def: "During sexual reproduction, the creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei. This occurs after the mutual exchange of nuclei." [GOC:elh] synonym: "karyogamy involved in conjugation without cellular fusion" EXACT [GOC:dph, GOC:tb] is_a: GO:0000741 ! karyogamy intersection_of: GO:0000741 ! karyogamy intersection_of: part_of GO:0000748 ! conjugation with mutual genetic exchange relationship: part_of GO:0000748 ! conjugation with mutual genetic exchange [Term] id: GO:0000745 name: nuclear migration involved in conjugation with mutual genetic exchange namespace: biological_process def: "The net movement of nuclei towards one another, leading to the bilateral transfer of genetic material in organisms undergoing conjugation without cellular fusion." [GOC:clt, GOC:mah] synonym: "nuclear exchange during conjugation without cellular fusion" RELATED [] synonym: "nuclear migration involved in conjugation without cellular fusion" EXACT [GOC:dph, GOC:tb] is_a: GO:0007097 ! nuclear migration intersection_of: GO:0007097 ! nuclear migration intersection_of: part_of GO:0000748 ! conjugation with mutual genetic exchange relationship: part_of GO:0000744 ! karyogamy involved in conjugation with mutual genetic exchange relationship: part_of GO:0000748 ! conjugation with mutual genetic exchange [Term] id: GO:0000746 name: conjugation namespace: biological_process def: "The union or introduction of genetic information from compatible mating types that results in a genetically different individual. Conjugation requires direct cellular contact between the organisms." [GOC:elh] subset: goslim_aspergillus subset: goslim_candida subset: goslim_pir subset: goslim_yeast subset: gosubset_prok xref: Wikipedia:Conjugation is_a: GO:0044764 ! multi-organism cellular process [Term] id: GO:0000747 name: conjugation with cellular fusion namespace: biological_process alt_id: GO:0007322 alt_id: GO:0007333 alt_id: GO:0030461 alt_id: GO:0030477 def: "A conjugation process that results in the union of cellular and genetic information from compatible mating types. An example of this process is found in Saccharomyces cerevisiae." [GOC:elh] subset: goslim_pombe synonym: "cell fusion" RELATED [] synonym: "mating" RELATED [] is_a: GO:0000746 ! conjugation is_a: GO:0019953 ! sexual reproduction [Term] id: GO:0000748 name: conjugation with mutual genetic exchange namespace: biological_process def: "A conjugation process that results in the mutual exchange and union of only genetic information between compatible mating types. Conjugation without cellular fusion requires direct cellular contact between the organisms without plasma membrane fusion. The organisms involved in conjugation without cellular fusion separate after nuclear exchange." [GOC:elh] synonym: "conjugation without cellular fusion" EXACT [] is_a: GO:0000746 ! conjugation [Term] id: GO:0000749 name: response to pheromone involved in conjugation with cellular fusion namespace: biological_process alt_id: GO:0007328 alt_id: GO:0030434 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pheromone stimulus that contributes to the process of conjugation with cellular fusion. An example of this process is found in Saccharomyces cerevisiae." [GOC:clt] synonym: "response to pheromone during conjugation with cellular fusion" RELATED [GOC:dph] is_a: GO:0022414 ! reproductive process is_a: GO:0071444 ! cellular response to pheromone intersection_of: GO:0019236 ! response to pheromone intersection_of: part_of GO:0000747 ! conjugation with cellular fusion relationship: part_of GO:0000747 ! conjugation with cellular fusion [Term] id: GO:0000750 name: pheromone-dependent signal transduction involved in conjugation with cellular fusion namespace: biological_process alt_id: GO:0007330 alt_id: GO:0030454 def: "A signal transduction process resulting in the relay, amplification or dampening of a signal generated in response to pheromone exposure in organisms that undergo conjugation with cellular fusion. An example of this process is found in Saccharomyces cerevisiae." [GOC:clt] synonym: "transduction of mating signal" BROAD [] is_a: GO:0007186 ! G-protein coupled receptor signaling pathway is_a: GO:0032005 ! signal transduction involved in conjugation with cellular fusion relationship: part_of GO:0000749 ! response to pheromone involved in conjugation with cellular fusion [Term] id: GO:0000751 name: mitotic cell cycle arrest in response to pheromone namespace: biological_process alt_id: GO:0030571 def: "The cell cycle regulatory process in which the mitotic cell cycle is halted during one of the normal phases (G1, S, G2, M) as a result of a pheromone stimulus. An example of this process is found in Saccharomyces cerevisiae." [GOC:clt, GOC:dph, GOC:mah, GOC:tb] synonym: "cell cycle arrest in response to pheromone" BROAD [] is_a: GO:0022414 ! reproductive process is_a: GO:0071850 ! mitotic cell cycle arrest relationship: part_of GO:0000749 ! response to pheromone involved in conjugation with cellular fusion [Term] id: GO:0000752 name: agglutination involved in conjugation with cellular fusion namespace: biological_process alt_id: GO:0007334 def: "During conjugation with cellular fusion, the aggregation or adhesion of compatible mating types via complementary cell-cell interactions. An example of this process is agglutination in Saccharomyces cerevisiae." [GOC:elh] synonym: "agglutination" BROAD [] synonym: "cell-cell adhesion during conjugation with cellular fusion" EXACT [] synonym: "cell-cell adhesion during mating" EXACT [] is_a: GO:0000771 ! agglutination involved in conjugation is_a: GO:0044703 ! multi-organism reproductive process is_a: GO:0098630 ! aggregation of unicellular organisms intersection_of: GO:0098610 ! adhesion between unicellular organisms intersection_of: part_of GO:0000747 ! conjugation with cellular fusion relationship: part_of GO:0000747 ! conjugation with cellular fusion relationship: part_of GO:0000749 ! response to pheromone involved in conjugation with cellular fusion [Term] id: GO:0000753 name: cell morphogenesis involved in conjugation with cellular fusion namespace: biological_process alt_id: GO:0007332 def: "The change in form (cell shape and size) that occurs during sexual reproduction in order to facilitate direct contact between the compatible mating types in organisms that undergo conjugation cellular fusion." [GOC:clt] synonym: "shmoo orientation" NARROW [] synonym: "shmooing" NARROW [] is_a: GO:0000767 ! cell morphogenesis involved in conjugation is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0044702 ! single organism reproductive process intersection_of: GO:0000902 ! cell morphogenesis intersection_of: part_of GO:0000747 ! conjugation with cellular fusion relationship: part_of GO:0000747 ! conjugation with cellular fusion relationship: part_of GO:0000749 ! response to pheromone involved in conjugation with cellular fusion [Term] id: GO:0000754 name: adaptation of signaling pathway by response to pheromone involved in conjugation with cellular fusion namespace: biological_process alt_id: GO:0007331 alt_id: GO:0030453 def: "In organisms that undergo conjugation with cellular fusion, the process resulting in desensitization following exposure to pheromone stimulus that act to down-regulate further stimulation or block initial conjugation responses. An example of this is the adaptation to pheromone during conjugation with cellular fusion in Saccharomyces cerevisiae." [GOC:clt] synonym: "adaptation of signalling pathway by response to pheromone involved in conjugation with cellular fusion" EXACT [GOC:mah] synonym: "adaptation to pheromone during conjugation with cellular fusion" RELATED [GOC:dph, GOC:tb] synonym: "desensitization to pheromone during conjugation with cellular fusion" EXACT [] is_a: GO:0022414 ! reproductive process is_a: GO:0023058 ! adaptation of signaling pathway relationship: part_of GO:0000749 ! response to pheromone involved in conjugation with cellular fusion [Term] id: GO:0000755 name: cytogamy namespace: biological_process alt_id: GO:0000218 alt_id: GO:0030462 def: "During conjugation with cellular fusion, the process resulting in creating a single cell from complementary mating types. The localized remodeling and dissolution of external protective structures allow the fusion of the plasma membranes and cytoplasmic mixing. An example of this process is found in Saccharomyces cerevisiae." [GOC:elh] synonym: "zygote formation" RELATED [] is_a: GO:0022413 ! reproductive process in single-celled organism relationship: part_of GO:0000747 ! conjugation with cellular fusion [Term] id: GO:0000756 name: response to pheromone involved in conjugation with mutual genetic exchange namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pheromone stimulus during the process of conjugation without cellular fusion." [GOC:clt] synonym: "response to pheromone involved in conjugation without cellular fusion" EXACT [GOC:dph, GOC:tb] is_a: GO:0007154 ! cell communication is_a: GO:0071444 ! cellular response to pheromone intersection_of: GO:0019236 ! response to pheromone intersection_of: part_of GO:0000748 ! conjugation with mutual genetic exchange relationship: part_of GO:0000748 ! conjugation with mutual genetic exchange [Term] id: GO:0000757 name: signal transduction involved in conjugation with mutual genetic exchange namespace: biological_process def: "A signal transduction process resulting in the relay, amplification or dampening of a signal generated in response to pheromone exposure in organisms that undergo conjugation without cellular fusion." [GOC:clt] synonym: "signal transduction involved in conjugation without cellular fusion" EXACT [GOC:dph, GOC:tb] is_a: GO:0007186 ! G-protein coupled receptor signaling pathway intersection_of: GO:0007165 ! signal transduction intersection_of: part_of GO:0000748 ! conjugation with mutual genetic exchange relationship: part_of GO:0000748 ! conjugation with mutual genetic exchange relationship: part_of GO:0000756 ! response to pheromone involved in conjugation with mutual genetic exchange [Term] id: GO:0000758 name: agglutination involved in conjugation with mutual genetic exchange namespace: biological_process def: "During conjugation without cellular fusion, the aggregation or adhesion of compatible mating types via complementary cell-cell interactions." [GOC:elh] synonym: "agglutination involved in conjugation without cellular fusion" EXACT [GOC:dph, GOC:tb] is_a: GO:0000771 ! agglutination involved in conjugation is_a: GO:0098630 ! aggregation of unicellular organisms intersection_of: GO:0098630 ! aggregation of unicellular organisms intersection_of: part_of GO:0000748 ! conjugation with mutual genetic exchange relationship: part_of GO:0000748 ! conjugation with mutual genetic exchange relationship: part_of GO:0000756 ! response to pheromone involved in conjugation with mutual genetic exchange [Term] id: GO:0000759 name: cell morphogenesis involved in conjugation with mutual genetic exchange namespace: biological_process def: "The change in form (cell shape and size) that occurs during sexual reproduction in order to facilitate direct contact between the compatible mating types in organisms that undergo conjugation without cellular fusion." [GOC:clt] synonym: "cellular morphogenesis involved in conjugation without cellular fusion" EXACT [GOC:dph, GOC:tb] is_a: GO:0000767 ! cell morphogenesis involved in conjugation intersection_of: GO:0000902 ! cell morphogenesis intersection_of: part_of GO:0000748 ! conjugation with mutual genetic exchange relationship: part_of GO:0000748 ! conjugation with mutual genetic exchange relationship: part_of GO:0000756 ! response to pheromone involved in conjugation with mutual genetic exchange [Term] id: GO:0000760 name: adaptation to pheromone involved in conjugation with mutual genetic exchange namespace: biological_process def: "In organisms that undergo conjugation without cellular fusion, the process resulting in desensitization following exposure to pheromone stimulus that act to down-regulate further stimulation or block initial conjugation responses." [GOC:clt] synonym: "adaptation to pheromone involved conjugation without cellular fusion" RELATED [GOC:dph, GOC:tb] synonym: "desensitization to pheromone during conjugation without cellular fusion" EXACT [] is_a: GO:0000756 ! response to pheromone involved in conjugation with mutual genetic exchange is_a: GO:0022401 ! negative adaptation of signaling pathway [Term] id: GO:0000761 name: conjugant formation namespace: biological_process def: "During conjugation without cellular fusion, the process that results in pairing complementary mating types. Localized morphological, cytological, and cytoskeletal changes connect the mating types without cytoplasmic mixing." [GOC:elh] is_a: GO:0000771 ! agglutination involved in conjugation relationship: part_of GO:0000748 ! conjugation with mutual genetic exchange [Term] id: GO:0000762 name: pheromone-induced unidirectional conjugation namespace: biological_process def: "The process of unidirectional (polarized) transfer of genetic information in response to a pheromone. It involves direct cellular contact between a donor and recipient cell; the contact is followed by the formation of a cellular bridge that physically connects the cells; some or all of the chromosome(s) of one cell ('male') is then transferred into the other cell ('female'); unidirectional conjugation occurs between cells of different mating types." [GOC:elh] is_a: GO:0009291 ! unidirectional conjugation [Term] id: GO:0000763 name: obsolete cell morphogenesis involved in unidirectional conjugation namespace: biological_process def: "OBSOLETE. The change in form (cell shape and size) that occurs during sexual reproduction in order to facilitate direct contact between the compatible mating types in organisms that undergo unidirectional conjugation." [GOC:clt] comment: This term was made obsolete because unidirectional conjugation occurs only in prokaryotes, which do not undergo morphogenetic changes associated with conjugation. In short, the process described by this term does not occur. synonym: "cell morphogenesis involved in unidirectional conjugation" EXACT [] is_obsolete: true [Term] id: GO:0000764 name: obsolete cellular morphogenesis involved in pheromone-induced unidirectional conjugation namespace: biological_process def: "OBSOLETE. The change in form (cell shape and size) that contributes to sexual reproduction in order to facilitate direct contact between the compatible mating types in organisms that undergo pheromone-induced unidirectional conjugation." [GOC:clt] comment: This term was made obsolete because unidirectional conjugation occurs only in prokaryotes, which do not undergo morphogenetic changes associated with conjugation. In short, the process described by this term does not occur. synonym: "cellular morphogenesis during pheromone-induced unidirectional" RELATED [GOC:dph, GOC:tb] synonym: "cellular morphogenesis involved in pheromone-induced unidirectional conjugation" EXACT [] is_obsolete: true [Term] id: GO:0000765 name: response to pheromone involved in pheromone-induced unidirectional conjugation namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pheromone stimulus that contributes to the process of pheromone-induced unidirectional conjugation." [GOC:clt] synonym: "response to pheromone during pheromone-induced unidirectional" RELATED [GOC:dph, GOC:tb] is_a: GO:0019236 ! response to pheromone intersection_of: GO:0019236 ! response to pheromone intersection_of: part_of GO:0000762 ! pheromone-induced unidirectional conjugation relationship: part_of GO:0000762 ! pheromone-induced unidirectional conjugation [Term] id: GO:0000766 name: negative adaptation of signaling pathway by response to pheromone involved in pheromone-induced unidirectional conjugation namespace: biological_process def: "In organisms that undergo pheromone-induced unidirectional conjugation, the process involved in desensitization following exposure to pheromone stimulus that acts to down-regulate further stimulation or block initial conjugation responses." [GOC:clt] synonym: "adaptation to pheromone during pheromone-induced unidirectional conjugation" RELATED [GOC:dph, GOC:tb] synonym: "desensitization to pheromone during pheromone-induced unidirectional conjugation" EXACT [] synonym: "negative adaptation of signalling pathway by response to pheromone involved in pheromone-induced unidirectional conjugation" EXACT [GOC:mah] is_a: GO:0022401 ! negative adaptation of signaling pathway relationship: part_of GO:0000765 ! response to pheromone involved in pheromone-induced unidirectional conjugation [Term] id: GO:0000767 name: cell morphogenesis involved in conjugation namespace: biological_process def: "The change in form (cell shape and size) that occurs during sexual reproduction in order to facilitate direct contact between the compatible mating types." [GOC:elh] is_a: GO:0000902 ! cell morphogenesis intersection_of: GO:0000902 ! cell morphogenesis intersection_of: part_of GO:0000746 ! conjugation relationship: part_of GO:0000746 ! conjugation [Term] id: GO:0000768 name: syncytium formation by plasma membrane fusion namespace: biological_process def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." [GOC:mtg_muscle, GOC:tb] synonym: "cell fusion" BROAD [] synonym: "cell-cell fusion" EXACT [] is_a: GO:0006949 ! syncytium formation intersection_of: GO:0006949 ! syncytium formation intersection_of: has_part GO:0045026 ! plasma membrane fusion relationship: has_part GO:0045026 ! plasma membrane fusion [Term] id: GO:0000769 name: syncytium formation by mitosis without cytokinesis namespace: biological_process def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by one or more rounds of nuclear division without cytokinesis." [GOC:mah, GOC:tb] synonym: "syncytium formation by mitosis without cell division" RELATED [GOC:mah] is_a: GO:0006949 ! syncytium formation intersection_of: GO:0006949 ! syncytium formation intersection_of: has_part GO:0033301 ! cell cycle comprising mitosis without cytokinesis relationship: has_part GO:0033301 ! cell cycle comprising mitosis without cytokinesis [Term] id: GO:0000770 name: peptide pheromone export namespace: biological_process alt_id: GO:0007325 def: "The directed movement of a peptide pheromone out of a cell by a secretion or export pathway used solely for the export of peptide pheromones." [GOC:elh] synonym: "a-factor export" NARROW [] is_a: GO:0009914 ! hormone transport is_a: GO:0015833 ! peptide transport [Term] id: GO:0000771 name: agglutination involved in conjugation namespace: biological_process def: "The aggregation or adhesion of compatible mating types via complementary cell-cell interactions prior to the formation of irreversible cellular contacts during conjugation." [GOC:elh] is_a: GO:0098610 ! adhesion between unicellular organisms intersection_of: GO:0098610 ! adhesion between unicellular organisms intersection_of: part_of GO:0000746 ! conjugation relationship: part_of GO:0000746 ! conjugation [Term] id: GO:0000772 name: mating pheromone activity namespace: molecular_function def: "The activity of binding to and activating specific cell surface receptors, thereby inducing a behavioral or physiological response(s) from a responding organism or cell that leads to the transfer or union of genetic material between organisms or cells. The mating pheromone can either be retained on the cell surface or secreted." [GOC:clt, GOC:elh] is_a: GO:0005186 ! pheromone activity [Term] id: GO:0000773 name: phosphatidyl-N-methylethanolamine N-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + phosphatidyl-N-methylethanolamine = S-adenosyl-L-homocysteine + phosphatidyl-N-dimethylethanolamine." [EC:2.1.1.71] subset: gosubset_prok synonym: "methyltransferase II" RELATED [EC:2.1.1.71] synonym: "phosphatidyl-N-methylethanolamine methyltransferase activity" EXACT [EC:2.1.1.71] synonym: "phosphatidyl-N-monomethylethanolamine methyltransferase activity" EXACT [EC:2.1.1.71] synonym: "phosphatidylethanolamine methyltransferase I" RELATED [EC:2.1.1.71] synonym: "phosphatidylmonomethylethanolamine methyltransferase activity" EXACT [EC:2.1.1.71] synonym: "phospholipid methyltransferase activity" EXACT [EC:2.1.1.71] synonym: "PLMT" EXACT [] synonym: "S-adenosyl-L-methionine:phosphatidyl-N-methylethanolamine N-methyltransferase activity" EXACT [EC:2.1.1.71] xref: EC:2.1.1.71 xref: MetaCyc:2.1.1.71-RXN is_a: GO:0008170 ! N-methyltransferase activity is_a: GO:0008757 ! S-adenosylmethionine-dependent methyltransferase activity [Term] id: GO:0000774 name: adenyl-nucleotide exchange factor activity namespace: molecular_function def: "Stimulates the hydrolysis and exchange of adenyl nucleotides by other proteins." [GOC:kd] subset: gosubset_prok is_a: GO:0030554 ! adenyl nucleotide binding is_a: GO:0060590 ! ATPase regulator activity [Term] id: GO:0000775 name: chromosome, centromeric region namespace: cellular_component alt_id: GO:0097521 def: "The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome." [GOC:cjm, GOC:elh, GOC:kmv, GOC:pr] comment: Note that this term can be used in place of the obsolete cellular component term 'centromere ; GO:0005698'. synonym: "centromere" RELATED [] synonym: "centromere complex" EXACT [] synonym: "chromosome, centric region" EXACT [] synonym: "chromosome, pericentric region" RELATED [] is_a: GO:0098687 ! chromosomal region [Term] id: GO:0000776 name: kinetochore namespace: cellular_component alt_id: GO:0005699 def: "A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules." [GOC:elh] comment: Note that the kinetochore overlaps the centromeric DNA, but centromeric DNA is not part of the kinetochore. subset: goslim_pir xref: Wikipedia:Kinetochore is_a: GO:0043232 ! intracellular non-membrane-bounded organelle is_a: GO:0043234 ! protein complex is_a: GO:0044427 ! chromosomal part relationship: part_of GO:0000775 ! chromosome, centromeric region [Term] id: GO:0000777 name: condensed chromosome kinetochore namespace: cellular_component def: "A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules." [GOC:elh] is_a: GO:0000776 ! kinetochore intersection_of: GO:0000776 ! kinetochore intersection_of: part_of GO:0000793 ! condensed chromosome relationship: part_of GO:0000779 ! condensed chromosome, centromeric region relationship: part_of GO:0000793 ! condensed chromosome [Term] id: GO:0000778 name: condensed nuclear chromosome kinetochore namespace: cellular_component def: "A multisubunit complex that is located at the centromeric region of a condensed nuclear chromosome and provides an attachment point for the spindle microtubules." [GOC:elh] is_a: GO:0000777 ! condensed chromosome kinetochore is_a: GO:0044454 ! nuclear chromosome part intersection_of: GO:0000776 ! kinetochore intersection_of: part_of GO:0000794 ! condensed nuclear chromosome relationship: part_of GO:0000780 ! condensed nuclear chromosome, centromeric region relationship: part_of GO:0000794 ! condensed nuclear chromosome [Term] id: GO:0000779 name: condensed chromosome, centromeric region namespace: cellular_component def: "The region of a condensed chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome." [GOC:elh, GOC:kmv] comment: Note that this term can be used in place of the obsolete cellular component term 'centromere ; GO:0005698'. Use with caution because this term refers to a specific region of the chromosome and not a protein complex. synonym: "condensed chromosome, centric region" EXACT [] synonym: "condensed chromosome, centromere" RELATED [] synonym: "condensed chromosome, pericentric region" RELATED [] is_a: GO:0000775 ! chromosome, centromeric region intersection_of: GO:0000775 ! chromosome, centromeric region intersection_of: part_of GO:0000793 ! condensed chromosome relationship: part_of GO:0000793 ! condensed chromosome [Term] id: GO:0000780 name: condensed nuclear chromosome, centromeric region namespace: cellular_component def: "The region of a condensed nuclear chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome." [GOC:elh, GOC:kmv] comment: Note that this term can be used in place of the obsolete cellular component term 'centromere ; GO:0005698'. Use with caution because this term refers to a specific region of the chromosome and not a protein complex. synonym: "condensed nuclear chromosome, centric region" EXACT [] synonym: "condensed nuclear chromosome, centromere" RELATED [] synonym: "condensed nuclear chromosome, pericentric region" RELATED [] is_a: GO:0000779 ! condensed chromosome, centromeric region is_a: GO:0044454 ! nuclear chromosome part intersection_of: GO:0000779 ! condensed chromosome, centromeric region intersection_of: part_of GO:0000794 ! condensed nuclear chromosome intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0000794 ! condensed nuclear chromosome relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000781 name: chromosome, telomeric region namespace: cellular_component def: "The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins." [GOC:elh] comment: Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific region of the chromosome and not a protein complex. synonym: "telomere" RELATED [] is_a: GO:0098687 ! chromosomal region [Term] id: GO:0000782 name: telomere cap complex namespace: cellular_component def: "A complex of DNA and protein located at the end of a linear chromosome that protects and stabilizes a linear chromosome." [GOC:elh] comment: Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific protein complex and not a region of the chromosome. subset: goslim_pir subset: gosubset_prok is_a: GO:0032993 ! protein-DNA complex is_a: GO:0044427 ! chromosomal part relationship: part_of GO:0000781 ! chromosome, telomeric region [Term] id: GO:0000783 name: nuclear telomere cap complex namespace: cellular_component def: "A complex of DNA and protein located at the end of a linear chromosome in the nucleus that protects and stabilizes a linear chromosome." [GOC:elh] comment: Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific protein complex and not a region of the chromosome. is_a: GO:0000782 ! telomere cap complex is_a: GO:0044454 ! nuclear chromosome part intersection_of: GO:0000782 ! telomere cap complex intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0000784 ! nuclear chromosome, telomeric region relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000784 name: nuclear chromosome, telomeric region namespace: cellular_component def: "The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins." [GOC:elh] comment: Note that this term can be used in place of the obsolete cellular component term 'telomere ; GO:0005696'. Use with caution because this term refers to a specific region of the chromosome and not a protein complex. synonym: "nuclear chromosome, telomere" EXACT [] is_a: GO:0000781 ! chromosome, telomeric region is_a: GO:0044454 ! nuclear chromosome part intersection_of: GO:0000781 ! chromosome, telomeric region intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000785 name: chromatin namespace: cellular_component alt_id: GO:0005717 def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [GOC:elh, PMID:20404130] comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore. synonym: "chromosome scaffold" RELATED [] xref: NIF_Subcellular:sao1615953555 is_a: GO:0032991 ! macromolecular complex is_a: GO:0044427 ! chromosomal part [Term] id: GO:0000786 name: nucleosome namespace: cellular_component alt_id: GO:0005718 def: "A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures." [GOC:elh] subset: goslim_pir xref: Wikipedia:Nucleosome is_a: GO:0032993 ! protein-DNA complex is_a: GO:0044427 ! chromosomal part is_a: GO:0044815 ! DNA packaging complex relationship: part_of GO:0000785 ! chromatin [Term] id: GO:0000787 name: cytoplasmic nucleosome namespace: cellular_component def: "A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the cytoplasm into higher order structures." [GOC:elh] is_a: GO:0000786 ! nucleosome is_a: GO:0044444 ! cytoplasmic part intersection_of: GO:0000786 ! nucleosome intersection_of: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0000789 ! cytoplasmic chromatin relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0000788 name: nuclear nucleosome namespace: cellular_component def: "A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures." [GOC:elh] is_a: GO:0000786 ! nucleosome is_a: GO:0044454 ! nuclear chromosome part intersection_of: GO:0000786 ! nucleosome intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0000790 ! nuclear chromatin relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000789 name: cytoplasmic chromatin namespace: cellular_component def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the cytoplasm." [GOC:elh, PMID:20404130] is_a: GO:0000785 ! chromatin is_a: GO:0044444 ! cytoplasmic part intersection_of: GO:0000785 ! chromatin intersection_of: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0000229 ! cytoplasmic chromosome relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0000790 name: nuclear chromatin namespace: cellular_component def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus." [GOC:elh, PMID:20404130] is_a: GO:0000785 ! chromatin is_a: GO:0044454 ! nuclear chromosome part intersection_of: GO:0000785 ! chromatin intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000791 name: euchromatin namespace: cellular_component def: "A dispersed and relatively uncompacted form of chromatin." [GOC:elh] xref: NIF_Subcellular:sao445485807 xref: Wikipedia:Euchromatin is_a: GO:0000785 ! chromatin [Term] id: GO:0000792 name: heterochromatin namespace: cellular_component def: "A compact and highly condensed form of chromatin." [GOC:elh] xref: NIF_Subcellular:sao581845896 xref: Wikipedia:Heterochromatin is_a: GO:0000785 ! chromatin [Term] id: GO:0000793 name: condensed chromosome namespace: cellular_component def: "A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure." [GOC:elh] comment: Note that this term can be used to annotate gene products that localize to a mitotic chromosome in an organism that undergoes an 'open mitosis' in which the nuclear envelope breaks down during mitosis. synonym: "cytoplasmic mitotic chromosome" RELATED [] synonym: "metaphase chromosome" RELATED [] synonym: "mitotic chromosome" RELATED [] is_a: GO:0005694 ! chromosome [Term] id: GO:0000794 name: condensed nuclear chromosome namespace: cellular_component def: "A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome." [GOC:elh] comment: Note that this term and its children can be used to annotate gene products that localize to a mitotic chromosome in an organism that undergoes a 'closed mitosis' in which the nuclear envelope does not break down during mitosis and for gene products that localize to a meiotic chromosome. synonym: "meiotic chromosome" RELATED [] synonym: "nuclear mitotic chromosome" RELATED [] is_a: GO:0000228 ! nuclear chromosome is_a: GO:0000793 ! condensed chromosome intersection_of: GO:0000793 ! condensed chromosome intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000795 name: synaptonemal complex namespace: cellular_component alt_id: GO:0005716 def: "A proteinaceous scaffold found between homologous chromosomes during meiosis." [GOC:elh] xref: Wikipedia:Synaptonemal_complex is_a: GO:0044454 ! nuclear chromosome part relationship: part_of GO:0000794 ! condensed nuclear chromosome [Term] id: GO:0000796 name: condensin complex namespace: cellular_component alt_id: GO:0005676 alt_id: GO:0008620 def: "A multisubunit protein complex that plays a central role in chromosome condensation." [GOC:elh] subset: goslim_pir synonym: "13S condensin complex" NARROW [] synonym: "SMC complex" RELATED [] is_a: GO:0044427 ! chromosomal part is_a: GO:0044815 ! DNA packaging complex relationship: part_of GO:0000793 ! condensed chromosome [Term] id: GO:0000797 name: condensin core heterodimer namespace: cellular_component alt_id: GO:0008621 def: "The core heterodimer of a condensin complex, a multisubunit protein complex that plays a central role in chromosome condensation." [GOC:elh] synonym: "8S condensin complex" NARROW [] synonym: "Smc2-Smc4 complex" NARROW [] is_a: GO:0043234 ! protein complex is_a: GO:0044427 ! chromosomal part intersection_of: GO:0043234 ! protein complex intersection_of: part_of GO:0000796 ! condensin complex relationship: part_of GO:0000796 ! condensin complex [Term] id: GO:0000798 name: nuclear cohesin complex namespace: cellular_component def: "A cohesin complex required for cohesion between sister chromatids that remain in the nucleus." [GOC:elh] comment: Note that this term and its children should be used to annotate gene products found in cohesin complexes in organisms that undergo closed mitosis (i.e. where the nuclear envelope does not break down, as in fungi). For organisms in which the nuclear envelope breaks down during mitosis, the parent should be used. is_a: GO:0008278 ! cohesin complex is_a: GO:0044454 ! nuclear chromosome part intersection_of: GO:0008278 ! cohesin complex intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0000794 ! condensed nuclear chromosome relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000799 name: nuclear condensin complex namespace: cellular_component def: "A multisubunit protein complex that plays a central role in the condensation of chromosomes that remain in the nucleus." [GOC:elh] is_a: GO:0000796 ! condensin complex is_a: GO:0044454 ! nuclear chromosome part intersection_of: GO:0000796 ! condensin complex intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0000794 ! condensed nuclear chromosome relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000800 name: lateral element namespace: cellular_component def: "A proteinaceous core found between sister chromatids during meiotic prophase." [GOC:elh] synonym: "axial element" EXACT [GOC:ascb_2009, GOC:dph, GOC:tb] is_a: GO:0044454 ! nuclear chromosome part relationship: part_of GO:0000795 ! synaptonemal complex [Term] id: GO:0000801 name: central element namespace: cellular_component def: "A structural unit of the synaptonemal complex found between the lateral elements." [GOC:elh] is_a: GO:0044454 ! nuclear chromosome part relationship: part_of GO:0000795 ! synaptonemal complex [Term] id: GO:0000802 name: transverse filament namespace: cellular_component def: "A structural unit of the synaptonemal complex that spans the regions between the lateral elements and connects them." [GOC:elh] is_a: GO:0044454 ! nuclear chromosome part relationship: part_of GO:0000795 ! synaptonemal complex [Term] id: GO:0000803 name: sex chromosome namespace: cellular_component def: "A chromosome involved in sex determination." [GOC:elh] is_a: GO:0005694 ! chromosome [Term] id: GO:0000804 name: W chromosome namespace: cellular_component def: "The sex chromosome present in females of species in which the female is the heterogametic sex; generally, the sex chromosome that pairs with the Z chromosome in the heterogametic sex. The W chromosome is absent from the cells of males and present in one copy in the somatic cells of females." [GOC:mah, ISBN:0321000382] xref: Wikipedia:ZW_sex-determination_system is_a: GO:0000803 ! sex chromosome [Term] id: GO:0000805 name: X chromosome namespace: cellular_component def: "The sex chromosome present in both sexes of species in which the male is the heterogametic sex. Two copies of the X chromosome are present in each somatic cell of females and one copy is present in males." [GOC:mah, ISBN:0582227089] xref: Wikipedia:X_chromosome is_a: GO:0000803 ! sex chromosome [Term] id: GO:0000806 name: Y chromosome namespace: cellular_component def: "The sex chromosome present in males of species in which the male is the heterogametic sex; generally, the sex chromosome that pairs with the X chromosome in the heterogametic sex. The Y chromosome is absent from the cells of females and present in one copy in the somatic cells of males." [GOC:mah, ISBN:0582227089] xref: Wikipedia:Y_chromosome is_a: GO:0000803 ! sex chromosome [Term] id: GO:0000807 name: Z chromosome namespace: cellular_component def: "The sex chromosome present in both sexes of species in which the female is the heterogametic sex. Two copies of the Z chromosome are present in each somatic cell of males and one copy is present in females." [GOC:mah, ISBN:0321000382] xref: Wikipedia:ZW_sex-determination_system is_a: GO:0000803 ! sex chromosome [Term] id: GO:0000808 name: origin recognition complex namespace: cellular_component def: "A multisubunit complex that is located at the replication origins of a chromosome." [GOC:elh] subset: goslim_pir subset: gosubset_prok synonym: "ORC" EXACT [] synonym: "origin of replication recognition complex" EXACT [] xref: Wikipedia:Origin_recognition_complex is_a: GO:0043234 ! protein complex is_a: GO:0044427 ! chromosomal part [Term] id: GO:0000809 name: cytoplasmic origin of replication recognition complex namespace: cellular_component def: "A multisubunit complex that is located at the replication origins of a chromosome in the cytoplasm." [GOC:elh] subset: gosubset_prok synonym: "cytoplasmic ORC" EXACT [] synonym: "prokaryotic ORC" RELATED [] is_a: GO:0000808 ! origin recognition complex is_a: GO:0044444 ! cytoplasmic part intersection_of: GO:0000808 ! origin recognition complex intersection_of: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0000229 ! cytoplasmic chromosome relationship: part_of GO:0005737 ! cytoplasm [Term] id: GO:0000810 name: diacylglycerol diphosphate phosphatase activity namespace: molecular_function def: "Catalysis of the reaction: a 1,2-diacyl-sn-glycerol 3-diphosphate + H2O = a 1,2-diacyl-sn-glycerol 3-phosphate + phosphate." [EC:3.1.3.81, GOC:kad, MetaCyc:RXN-11277, PMID:8567632, PMID:9452443] comment: The enzyme entry for EC 3.1.3.81 states that this is a bifunctional enzyme (http://www.chem.qmul.ac.uk/iubmb/enzyme/EC3/1/3/81.html). However, reaction details are only provided for the cumulative enzymatic activity, therefore this term has not been split into two. synonym: "DGPP phosphatase activity" EXACT [] synonym: "DGPP phosphohydrolase activity" EXACT [] synonym: "diacylglycerol pyrophosphate phosphatase activity" EXACT [] xref: EC:3.1.3.81 xref: MetaCyc:RXN-11277 is_a: GO:0016462 ! pyrophosphatase activity [Term] id: GO:0000811 name: GINS complex namespace: cellular_component def: "A heterotetrameric protein complex that associates with replication origins, where it is required for the initiation of DNA replication, and with replication forks." [GOC:rb, GOC:rn, PMID:12730134, PMID:16990792, PMID:17467990] synonym: "Go, Ichi, Ni and San complex" EXACT [] is_a: GO:0031261 ! DNA replication preinitiation complex is_a: GO:0044454 ! nuclear chromosome part [Term] id: GO:0000812 name: Swr1 complex namespace: cellular_component def: "A multisubunit protein complex that is involved in chromatin remodeling. It is required for the incorporation of the histone variant H2AZ into chromatin. In S. cerevisiae, the complex contains Swr1p, a Swi2/Snf2-related ATPase, and 12 additional subunits." [GOC:rb, PMID:14645854, PMID:14690608, PMID:19355820] synonym: "SWR-C" EXACT [] is_a: GO:0044454 ! nuclear chromosome part is_a: GO:0097346 ! INO80-type complex relationship: part_of GO:0000790 ! nuclear chromatin [Term] id: GO:0000813 name: ESCRT I complex namespace: cellular_component def: "An endosomal sorting complex required for transport. It consists of the class E vacuolar protein sorting (Vps) proteins and interacts with ubiquitinated cargoes." [GOC:rb, PMID:12892785, PMID:12900393] synonym: "Endosomal Sorting Complex Required for Transport" BROAD [] is_a: GO:0036452 ! ESCRT complex is_a: GO:0098796 ! membrane protein complex relationship: part_of GO:0010008 ! endosome membrane [Term] id: GO:0000814 name: ESCRT II complex namespace: cellular_component def: "An endosomal sorting complex required for transport and functions downstream of ESCRT I complex. It consists of the class E vacuolar protein sorting (Vps) proteins and is required for the membrane recruitment of ESCRT III complex and binds to ubiquitinated cargoes." [GOC:rb, PMID:12892785, PMID:12900393] synonym: "Endosomal Sorting Complex Required for Transport" BROAD [] is_a: GO:0036452 ! ESCRT complex is_a: GO:0098796 ! membrane protein complex relationship: part_of GO:0010008 ! endosome membrane [Term] id: GO:0000815 name: ESCRT III complex namespace: cellular_component def: "An endosomal sorting complex required for transport. Consists of two soluble subcomplexes of highly charged coiled-coil proteins and is required for sorting and/or concentration of multivesicular body (MVB) cargoes." [GOC:rb, PMID:12892785, PMID:12900393] synonym: "Endosomal Sorting Complex Required for Transport" BROAD [] is_a: GO:0036452 ! ESCRT complex is_a: GO:0098796 ! membrane protein complex relationship: part_of GO:0010008 ! endosome membrane [Term] id: GO:0000817 name: COMA complex namespace: cellular_component def: "A multiprotein complex in yeast consisting of Ctf19p, Okp1p, Mcm21p, and Ame1p. This complex bridges the subunits that are in contact with centromeric DNA and the subunits bound to microtubules during kinetochore assembly." [GOC:se, PMID:14633972] synonym: "Ctf19p-Okp1p-Mcm1p-Ame1p complex" EXACT [] is_a: GO:0043234 ! protein complex is_a: GO:0044454 ! nuclear chromosome part relationship: part_of GO:0000778 ! condensed nuclear chromosome kinetochore [Term] id: GO:0000818 name: nuclear MIS12/MIND complex namespace: cellular_component def: "A multiprotein kinetochore subcomplex that binds to centromeric chromatin and forms part of the inner kinetochore of a chromosome in the nucleus. It helps to recruit outer kinetochore subunits that will bind to microtubules. Nuclear localization arises in some organisms because the nuclear envelope is not broken down during mitosis. In S. cerevisiae, it consists of at least four proteins: Mtw1p, Nnf1p, Nsl1p, and Dsn1." [GOC:krc, GOC:se, PMID:14633972] synonym: "MIND complex" EXACT [] synonym: "Mtw1p Including Nnf1p-Nsl1p-Dsn1p complex" EXACT [] is_a: GO:0000444 ! MIS12/MIND type complex is_a: GO:0044454 ! nuclear chromosome part intersection_of: GO:0000444 ! MIS12/MIND type complex intersection_of: part_of GO:0005634 ! nucleus relationship: part_of GO:0000778 ! condensed nuclear chromosome kinetochore relationship: part_of GO:0005634 ! nucleus [Term] id: GO:0000819 name: sister chromatid segregation namespace: biological_process def: "The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets." [GOC:ai, GOC:elh] is_a: GO:0051276 ! chromosome organization is_a: GO:0098813 ! nuclear chromosome segregation is_a: GO:1902589 ! single-organism organelle organization [Term] id: GO:0000820 name: regulation of glutamine family amino acid metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." [GOC:go_curators] synonym: "regulation of glutamine family amino acid metabolism" EXACT [] is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0051171 ! regulation of nitrogen compound metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0009064 ! glutamine family amino acid metabolic process relationship: regulates GO:0009064 ! glutamine family amino acid metabolic process [Term] id: GO:0000821 name: regulation of arginine metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid." [CHEBI:29016, GOC:go_curators] synonym: "regulation of arginine metabolism" EXACT [] is_a: GO:0000820 ! regulation of glutamine family amino acid metabolic process is_a: GO:0006521 ! regulation of cellular amino acid metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006525 ! arginine metabolic process relationship: regulates GO:0006525 ! arginine metabolic process [Term] id: GO:0000822 name: inositol hexakisphosphate binding namespace: molecular_function def: "Interacting selectively and non-covalently with inositol hexakisphosphate." [GOC:go_curators] synonym: "InsP6 binding" EXACT [] synonym: "IP6 binding" EXACT [] is_a: GO:0043178 ! alcohol binding [Term] id: GO:0000823 name: inositol-1,4,5-trisphosphate 6-kinase activity namespace: molecular_function def: "Catalysis of the reaction: D-myo-inositol 1,4,5-trisphosphate + ATP = D-myo-inositol 1,4,5,6-tetrakisphosphate + ADP + 2 H(+)." [MetaCyc:2.7.1.151-RXN] synonym: "ATP:1D-myo-inositol-1,4,5-trisphosphate 6-phosphotransferase activity" EXACT [] synonym: "inositol polyphosphate multikinase activity" BROAD [] synonym: "inositol trisphosphate 6-kinase activity" BROAD [] synonym: "IpmK" BROAD [] xref: EC:2.7.1.151 xref: KEGG:R05800 xref: MetaCyc:2.7.1.151-RXN is_a: GO:0051766 ! inositol trisphosphate kinase activity [Term] id: GO:0000824 name: inositol tetrakisphosphate 3-kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + 1D-myo-inositol 1,4,5,6-tetrakisphosphate = ADP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate." [GOC:elh] synonym: "1D-myo-inositol-tetrakisphosphate 3-kinase activity" EXACT [] synonym: "EC:2.7.1.151" BROAD [] synonym: "inositol 1,4,5,6-tetrakisphosphate 3-kinase activity" EXACT [] synonym: "inositol polyphosphate multikinase activity" BROAD [] synonym: "IpmK" BROAD [] is_a: GO:0051765 ! inositol tetrakisphosphate kinase activity [Term] id: GO:0000825 name: inositol tetrakisphosphate 6-kinase activity namespace: molecular_function def: "Catalysis of the reaction: 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ATP = 1D-myo-inositol 1,3,4,5,6-pentakisphosphate + ADP." [GOC:elh] synonym: "1D-myo-inositol-tetrakisphosphate 6-kinase activity" EXACT [] synonym: "inositol 1,3,4,5-tetrakisphosphate 6-kinase activity" EXACT [] xref: MetaCyc:RXN-7184 is_a: GO:0051765 ! inositol tetrakisphosphate kinase activity [Term] id: GO:0000826 name: obsolete inositol pyrophosphate synthase activity namespace: molecular_function def: "OBSOLETE. Catalysis of the phosphorylation of inositol phosphates which possess diphosphate bonds." [GOC:elh, PMID:16429326] comment: This term was made obsolete because it is incorrectly defined; 'inositol pyrophosphate' is a inositol derivative to which one (or more) pyrophosphate moieties are attached. 'Inositol pyrophosphate synthase' refers to a class of enzymes that catalyze various different reactions that result in the formation of an IP, so one cannot formulate a general reaction for them. synonym: "inositol diphosphate synthase activity" EXACT [] synonym: "inositol pyrophosphate synthase activity" EXACT [] is_obsolete: true consider: GO:0052746 [Term] id: GO:0000827 name: inositol-1,3,4,5,6-pentakisphosphate kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + 1D-myo-inositol 1,3,4,5,6-pentakisphosphate = ADP + diphospho-1D-myo-inositol tetrakisphosphate. The isomeric configuration of diphospho-1D-myo-inositol tetrakisphosphate is unknown." [GOC:elh, PMID:11311242] synonym: "EC:2.7.4.21" BROAD [] is_a: GO:0016301 ! kinase activity is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor [Term] id: GO:0000828 name: inositol hexakisphosphate kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + 1D-myo-inositol 1,2,3,4,5,6-hexakisphosphate = ADP + diphospho-1D-myo-inositol-pentakisphosphate. The isomeric configuration of diphospho-1D-myo-inositol-pentakisphosphate (PP-IP5) is unknown." [GOC:elh, GOC:vw, PMID:16429326] is_a: GO:0016301 ! kinase activity is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor [Term] id: GO:0000829 name: inositol heptakisphosphate kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + diphospho-1D-myo-inositol-pentakisphosphate = ADP + bis(diphospho)-1D-myo-inositol-tetrakisphosphate. The isomeric configurations of the diphospho-1D-myo-inositol-pentakisphosphate (PP-IP5) and bis(diphospho)-1D-myo-inositol-tetrakisphosphate (bis-PP-IP4) are unknown." [GOC:elh, PMID:16429326] is_a: GO:0016301 ! kinase activity is_a: GO:0016776 ! phosphotransferase activity, phosphate group as acceptor [Term] id: GO:0000830 name: inositol hexakisphosphate 4-kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + 1D-myo-inositol hexakisphosphate = ADP + 4-diphospho-1D-myo-inositol (1,2,3,5,6)pentakisphosphate." [GOC:elh, PMID:16429326] is_a: GO:0000828 ! inositol hexakisphosphate kinase activity [Term] id: GO:0000831 name: inositol hexakisphosphate 6-kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + 1D-myo-inositol hexakisphosphate = ADP + 6-diphospho-1D-myo-inositol (1,2,3,4,5)pentakisphosphate." [GOC:elh, PMID:16429326] is_a: GO:0000828 ! inositol hexakisphosphate kinase activity [Term] id: GO:0000832 name: inositol hexakisphosphate 5-kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + 1D-myo-inositol 1,2,3,4,5,6-hexakisphosphate = ADP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate." [MetaCyc:2.7.1.152-RXN] synonym: "ATP:1D-myo-inositol-hexakisphosphate 5-phosphotransferase activity" EXACT [] xref: EC:2.7.4.21 xref: KEGG:R09087 xref: MetaCyc:2.7.1.152-RXN is_a: GO:0000828 ! inositol hexakisphosphate kinase activity [Term] id: GO:0000833 name: inositol heptakisphosphate 4-kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate = 4,5-bisdiphosphoinositol-1D-myoinositol (1,2,3,6)tetrakisphosphate." [GOC:elh, PMID:16429326] synonym: "diphosphoinositol-pentakisphosphate 4-kinase activity" EXACT [] synonym: "IP7 4-kinase activity" EXACT [] is_a: GO:0000829 ! inositol heptakisphosphate kinase activity [Term] id: GO:0000834 name: inositol heptakisphosphate 6-kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate = 5,6-bisdiphosphoinositol-1D-myoinositol (1,2,3,4)tetrakisphosphate." [GOC:elh, PMID:16429326] is_a: GO:0000829 ! inositol heptakisphosphate kinase activity [Term] id: GO:0000835 name: ER ubiquitin ligase complex namespace: cellular_component def: "A ubiquitin ligase complex found in the ER." [GOC:elh] is_a: GO:0000153 ! cytoplasmic ubiquitin ligase complex is_a: GO:0044432 ! endoplasmic reticulum part is_a: GO:0098796 ! membrane protein complex intersection_of: GO:0000151 ! ubiquitin ligase complex intersection_of: part_of GO:0005783 ! endoplasmic reticulum relationship: part_of GO:0005783 ! endoplasmic reticulum relationship: part_of GO:0005789 ! endoplasmic reticulum membrane [Term] id: GO:0000836 name: Hrd1p ubiquitin ligase complex namespace: cellular_component def: "A multiprotein complex that recognizes and ubiquitinates proteins with misfolded luminal and membrane domains during ER-associated protein degradation (ERAD). In S. cerevisiae, this complex contains the ubiquitin ligase Hrd1p. In mammals, this complex contains the ubiquitin ligase HRD1 (Synoviolin) or AMFR (gp78)." [GOC:bf, GOC:elh, PMID:16619026, PMID:16873066, PMID:21454652] synonym: "HRD1 ubiquitin ligase complex" RELATED [GOC:bf] is_a: GO:0000835 ! ER ubiquitin ligase complex [Term] id: GO:0000837 name: Doa10p ubiquitin ligase complex namespace: cellular_component def: "A multiprotein complex that recognizes and ubiquitinates membrane proteins with misfolded cytosolic domains during ER-associated protein degradation (ERAD). In S. cerevisiae, this complex contains the ubiquitin ligase Ssm4p/Doa10p." [GOC:elh, PMID:16873066] synonym: "Ssm4p ubiquitin ligase complex" EXACT [] is_a: GO:0000835 ! ER ubiquitin ligase complex [Term] id: GO:0000838 name: Hrd1p ubiquitin ligase ERAD-M complex namespace: cellular_component def: "A multiprotein complex that recognizes and ubiquitinates proteins with misfolded membrane domains during ER-associated protein degradation (ERAD). In S. cerevisiae, this complex contains the ubiquitin ligase Hrd1p." [GOC:elh, PMID:16873066] is_a: GO:0000836 ! Hrd1p ubiquitin ligase complex [Term] id: GO:0000839 name: Hrd1p ubiquitin ligase ERAD-L complex namespace: cellular_component def: "A multiprotein complex that recognizes and ubiquitinates proteins with misfolded luminal domains during ER-associated protein degradation (ERAD). In S. cerevisiae, this complex contains the ubiquitin ligase Hrd1p." [GOC:elh, PMID:16873065, PMID:16873066] is_a: GO:0000836 ! Hrd1p ubiquitin ligase complex [Term] id: GO:0000900 name: translation repressor activity, nucleic acid binding namespace: molecular_function def: "Antagonizes the ribosome-mediated translation of mRNA into a polypeptide via direct binding (through a selective and non-covalent interaction) to nucleic acid." [GOC:clt, GOC:vw] is_a: GO:0030371 ! translation repressor activity is_a: GO:0090079 ! translation regulator activity, nucleic acid binding [Term] id: GO:0000901 name: translation repressor activity, non-nucleic acid binding namespace: molecular_function def: "Antagonizes the ribosome-mediated translation of mRNA into a polypeptide but does not bind directly to nucleic acid." [GOC:clt] is_a: GO:0030371 ! translation repressor activity is_a: GO:0045183 ! translation factor activity, non-nucleic acid binding [Term] id: GO:0000902 name: cell morphogenesis namespace: biological_process alt_id: GO:0007148 alt_id: GO:0045790 alt_id: GO:0045791 def: "The developmental process in which the size or shape of a cell is generated and organized." [GOC:clt, GOC:dph, GOC:go_curators, GOC:tb] subset: goslim_chembl subset: goslim_generic subset: goslim_yeast subset: gosubset_prok synonym: "cellular morphogenesis" EXACT [] is_a: GO:0032989 ! cellular component morphogenesis [Term] id: GO:0000903 name: regulation of cell shape during vegetative growth phase namespace: biological_process alt_id: GO:0090061 def: "Any process that modulates the surface configuration of a cell during the vegetative growth phase. The vegetative growth phase is the growth phase during which single celled organisms reproduce by budding or other asexual methods." [GOC:clt, GOC:go_curators, GOC:vw] synonym: "cell morphogenesis during vegetative growth phase" RELATED [GOC:vw] synonym: "cellular morphogenesis during vegetative growth" RELATED [GOC:dph, GOC:tb] synonym: "regulation of cell morphogenesis during vegetative growth phase" RELATED [] is_a: GO:0008360 ! regulation of cell shape intersection_of: GO:0008360 ! regulation of cell shape intersection_of: part_of GO:0072690 ! single-celled organism vegetative growth phase relationship: part_of GO:0072690 ! single-celled organism vegetative growth phase [Term] id: GO:0000904 name: cell morphogenesis involved in differentiation namespace: biological_process def: "The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history." [GOC:go_curators] is_a: GO:0000902 ! cell morphogenesis intersection_of: GO:0000902 ! cell morphogenesis intersection_of: part_of GO:0048468 ! cell development relationship: part_of GO:0048468 ! cell development [Term] id: GO:0000905 name: sporocarp development involved in asexual reproduction namespace: biological_process def: "The formation of a spore-bearing structure by fungus where spores will arise from asexual reproduction." [GOC:clt, GOC:mtg_sensu] synonym: "conidium development" NARROW [] synonym: "fruiting body formation involved in asexual reproduction" BROAD [] synonym: "haploid fruiting" RELATED [] synonym: "homokaryotic fruiting" RELATED [] synonym: "imperfect stage fruiting body development" NARROW [] synonym: "monokaryotic fruiting" RELATED [] is_a: GO:0030584 ! sporocarp development intersection_of: GO:0030584 ! sporocarp development intersection_of: part_of GO:0019954 ! asexual reproduction relationship: part_of GO:0019954 ! asexual reproduction [Term] id: GO:0000906 name: 6,7-dimethyl-8-ribityllumazine synthase activity namespace: molecular_function def: "Catalysis of the reaction: 3,4-dihydroxy-2-butanone-4-phosphate + 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione = 6,7-dimethyl-8-ribityllumazine + phosphate." [EC:5.4.-.-, PMID:7559556] synonym: "lumazine synthase activity" BROAD [MetaCyc:LUMAZINESYN-CPLX] xref: EC:5.4.-.- is_a: GO:0016867 ! intramolecular transferase activity, transferring acyl groups [Term] id: GO:0000907 name: sulfonate dioxygenase activity namespace: molecular_function def: "Catalysis of the reaction: sulfonate + 2-oxoglutarate + O2 = sulfite + aminoacetaldehyde + succinate + CO2." [EC:1.14.11.-, GOC:clt, PMID:10482536] subset: gosubset_prok synonym: "sulfonate/alpha-ketoglutarate dioxygenase activity" EXACT [] synonym: "sulphonate dioxygenase activity" EXACT [] xref: EC:1.14.11.- is_a: GO:0016706 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors [Term] id: GO:0000908 name: taurine dioxygenase activity namespace: molecular_function def: "Catalysis of the reaction: 2-oxoglutarate + O(2) + taurine = aminoacetaldehyde + CO(2) + succinate + sulfite." [EC:1.14.11.17, RHEA:15912] subset: gosubset_prok synonym: "2-aminoethanesulfonate dioxygenase activity" EXACT [EC:1.14.11.17] synonym: "alpha-ketoglutarate-dependent taurine dioxygenase activity" EXACT [EC:1.14.11.17] synonym: "taurine, 2-oxoglutarate:O2 oxidoreductase (sulfite-forming)" EXACT [EC:1.14.11.17] xref: EC:1.14.11.17 xref: KEGG:R05320 xref: MetaCyc:RXN0-299 xref: RHEA:15912 is_a: GO:0016706 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors [Term] id: GO:0000909 name: sporocarp development involved in sexual reproduction namespace: biological_process def: "The process whose specific outcome is the progression of a fruiting body organ over time, from its formation to the mature structure. The fruiting body is a spore bearing structure. In fungi, the sporocarp (also known as fruiting body) is a multicellular structure on which spore-producing structures, such as basidia or asci, are borne. The fruiting body is part of the sexual phase of a fungal life cycle, with the rest of the life cycle being characterized by vegetative mycelial growth. The sporocarp of a basidiomycete is known as a basidiocarp, while the fruiting body of an ascomycete is known as an ascocarp. A significant range of different shapes and morphologies is found in both basidiocarps and ascocarps; these features play an important role in the identification and taxonomy of fungi." [GOC:clt, GOC:mtg_sensu] synonym: "ascus development" NARROW [] synonym: "fruiting body development involved in sexual reproduction" BROAD [] synonym: "fruiting body formation involved in sexual reproduction" BROAD [] synonym: "perfect stage fruiting body development" NARROW [] is_a: GO:0030584 ! sporocarp development intersection_of: GO:0030584 ! sporocarp development intersection_of: part_of GO:0019953 ! sexual reproduction relationship: part_of GO:0019953 ! sexual reproduction [Term] id: GO:0000910 name: cytokinesis namespace: biological_process alt_id: GO:0007104 alt_id: GO:0016288 alt_id: GO:0033205 def: "The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells." [GOC:mtg_cell_cycle] comment: Note that when annotating eukaryotic species, mitotic or meiotic cytokinesis should always be specified for manual annotation and for prokaryotic species use 'FtsZ-dependent cytokinesis ; GO:0043093' or Cdv-dependent cytokinesis ; GO:0061639. Also, note that cytokinesis does not necessarily result in physical separation and detachment of the two daughter cells from each other. subset: gocheck_do_not_manually_annotate subset: goslim_aspergillus subset: goslim_candida subset: goslim_yeast subset: gosubset_prok synonym: "cell cycle cytokinesis" EXACT [] synonym: "cytokinesis involved in cell cycle" EXACT [GOC:dph, GOC:tb] xref: Reactome:REACT_101918 "Mitotic Telophase /Cytokinesis, Mus musculus" xref: Reactome:REACT_108805 "Mitotic Telophase /Cytokinesis, Dictyostelium discoideum" xref: Reactome:REACT_1932 "Mitotic Telophase /Cytokinesis, Homo sapiens" xref: Reactome:REACT_30667 "Mitotic Telophase /Cytokinesis, Schizosaccharomyces pombe" xref: Reactome:REACT_32636 "Mitotic Telophase /Cytokinesis, Bos taurus" xref: Reactome:REACT_78494 "Mitotic Telophase /Cytokinesis, Danio rerio" xref: Reactome:REACT_84722 "Mitotic Telophase /Cytokinesis, Gallus gallus" xref: Reactome:REACT_87726 "Mitotic Telophase /Cytokinesis, Xenopus tropicalis" xref: Reactome:REACT_92849 "Mitotic Telophase /Cytokinesis, Taeniopygia guttata" xref: Reactome:REACT_93374 "Mitotic Telophase /Cytokinesis, Canis familiaris" xref: Reactome:REACT_94382 "Mitotic Telophase /Cytokinesis, Drosophila melanogaster" xref: Reactome:REACT_98952 "Mitotic Telophase /Cytokinesis, Rattus norvegicus" xref: Reactome:REACT_99118 "Mitotic Telophase /Cytokinesis, Caenorhabditis elegans" xref: Wikipedia:Cytokinesis is_a: GO:0022402 ! cell cycle process relationship: has_part GO:0090148 ! membrane fission relationship: part_of GO:0051301 ! cell division [Term] id: GO:0000911 name: cytokinesis by cell plate formation namespace: biological_process def: "The process of dividing the cytoplasm of a parent cell where a structure forms in the cytoplasm and grows until reaching the plasma membrane, thereby completely separating the cytoplasms of adjacent progeny cells. An example of this is found in Arabidopsis thaliana." [GOC:clt] is_a: GO:1902410 ! mitotic cytokinetic process [Term] id: GO:0000912 name: assembly of actomyosin apparatus involved in cytokinesis namespace: biological_process def: "The assembly and arrangement of an apparatus composed of actin, myosin, and associated proteins that will function in cytokinesis." [GOC:mtg_cell_cycle] synonym: "actomyosin apparatus assembly involved in cytokinesis" EXACT [GOC:mah] synonym: "cytokinesis, formation of actomyosin apparatus" EXACT [GOC:dph, GOC:tb] synonym: "formation of actomyosin apparatus involved in cytokinesis" RELATED [GOC:dph] is_a: GO:0022607 ! cellular component assembly is_a: GO:0032506 ! cytokinetic process relationship: part_of GO:0061640 ! cytoskeleton-dependent cytokinesis [Term] id: GO:0000913 name: preprophase band assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a set of components to form the preprophase band, a dense band of microtubules that marks the position in the cell where cytokinesis will occur in cells that perform cytokinesis by cell plate formation." [GOC:clt, GOC:mah] synonym: "preprophase band formation" RELATED [GOC:mah] is_a: GO:0022607 ! cellular component assembly is_a: GO:1903047 ! mitotic cell cycle process relationship: part_of GO:0000911 ! cytokinesis by cell plate formation [Term] id: GO:0000914 name: phragmoplast assembly namespace: biological_process def: "The formation of a structure composed of actin, myosin, and associated proteins that will function in cytokinesis in cells that perform cytokinesis by cell plate formation. The structure usually contains antiparallel microtubules and membrane (often visible as vesicles)." [GOC:clt] synonym: "phragmoplast formation" RELATED [goc:dph] is_a: GO:1902407 ! assembly of actomyosin apparatus involved in mitotic cytokinesis relationship: part_of GO:0000911 ! cytokinesis by cell plate formation [Term] id: GO:0000915 name: actomyosin contractile ring assembly namespace: biological_process alt_id: GO:0045573 def: "The process of assembly of a ring composed of actin, myosin, and associated proteins that will function in cytokinesis." [GOC:clt, GOC:dph, GOC:tb] synonym: "constriction ring assembly" NARROW [] synonym: "contractile ring assembly" EXACT [GOC:ascb_2009, GOC:dph, GOC:tb] synonym: "cytokinesis, actomyosin contractile ring assembly" EXACT [] synonym: "cytokinesis, actomyosin contractile ring formation" RELATED [GOC:ascb_2009, GOC:dph, GOC:tb] synonym: "cytokinesis, actomyosin ring biosynthesis" RELATED [] synonym: "cytokinesis, actomyosin ring formation" RELATED [] synonym: "cytokinesis, contractile ring assembly" RELATED [GOC:mah] is_a: GO:0000912 ! assembly of actomyosin apparatus involved in cytokinesis is_a: GO:0044837 ! actomyosin contractile ring organization [Term] id: GO:0000916 name: actomyosin contractile ring contraction namespace: biological_process def: "The process of an actomyosin ring getting smaller in diameter, in the context of cytokinesis that takes place as part of a cell cycle." [GOC:clt, GOC:dph, GOC:mah, GOC:tb] synonym: "contractile ring constriction" BROAD [GOC:ascb_2009, GOC:dph, GOC:tb] synonym: "contractile ring contraction involved in cell cycle cytokinesis" EXACT [GOC:mah, GOC:vw] synonym: "cytokinesis, actomyosin ring contraction" EXACT [] synonym: "cytokinesis, contractile ring contraction" BROAD [GOC:dph, GOC:tb] is_a: GO:0036213 ! contractile ring contraction relationship: part_of GO:0061640 ! cytoskeleton-dependent cytokinesis [Term] id: GO:0000917 name: barrier septum assembly namespace: biological_process alt_id: GO:0071937 alt_id: GO:1902411 def: "The assembly and arrangement of a septum that spans the plasma membrane interface between progeny cells following cytokinesis. The progeny cells that form a barrier septum are not able to exchange intracellular material." [GOC:mtg_cell_cycle] synonym: "barrier septum assembly involved in cell cycle cytokinesis" EXACT [] synonym: "barrier septum assembly involved in cell cycle cytokinesis involved in mitotic cell cycle" EXACT [GOC:TermGenie] synonym: "barrier septum formation" EXACT [GOC:mah] synonym: "barrier septum formation involved in cell cycle cytokinesis" EXACT [] synonym: "barrier septum formation involved in cell cycle cytokinesis involved in mitotic cell cycle" EXACT [GOC:TermGenie] synonym: "barrier septum formation involved in mitotic cell cycle" EXACT [GOC:TermGenie] synonym: "formation of barrier septum" EXACT [] synonym: "formation of barrier septum involved in mitotic cell cycle" EXACT [GOC:TermGenie] synonym: "mitotic barrier septum assembly" EXACT [] synonym: "septation" BROAD [] synonym: "septin assembly and septum biosynthesis" RELATED [] synonym: "septin assembly and septum biosynthesis involved in mitotic cell cycle" RELATED [GOC:TermGenie] synonym: "septin assembly and septum formation" RELATED [] synonym: "septin assembly and septum formation involved in mitotic cell cycle" RELATED [GOC:TermGenie] is_a: GO:0090529 ! cell septum assembly is_a: GO:1902410 ! mitotic cytokinetic process relationship: part_of GO:0000278 ! mitotic cell cycle relationship: part_of GO:0000281 ! mitotic cytokinesis relationship: part_of GO:0061640 ! cytoskeleton-dependent cytokinesis [Term] id: GO:0000918 name: barrier septum site selection namespace: biological_process def: "The process of marking the site where a barrier septum will form." [GOC:clt] synonym: "selection of site for barrier cell septum biosynthesis" EXACT [] synonym: "selection of site for barrier cell septum formation" EXACT [] synonym: "selection of site for barrier septum formation" EXACT [GOC:curators] synonym: "septin assembly and septum biosynthesis" BROAD [] synonym: "septin assembly and septum formation" BROAD [] synonym: "septum positioning" EXACT [] is_a: GO:1902410 ! mitotic cytokinetic process relationship: part_of GO:0000917 ! barrier septum assembly [Term] id: GO:0000919 name: cell plate assembly namespace: biological_process def: "The process of assembly, maturation, and growth of the cell plate to the cell periphery in cells that divide by cell plate formation; often involves deposition of cell wall material in and around the phragmoplast." [GOC:clt] synonym: "cell plate formation" RELATED [GOC:mah] is_a: GO:0022607 ! cellular component assembly is_a: GO:1903047 ! mitotic cell cycle process relationship: part_of GO:0000911 ! cytokinesis by cell plate formation [Term] id: GO:0000920 name: cell separation after cytokinesis namespace: biological_process alt_id: GO:1902409 alt_id: GO:2000695 def: "The process of physically separating progeny cells after cytokinesis; this may involve enzymatic digestion of septum or cell wall components." [GOC:mtg_cell_cycle, GOC:TermGenie] synonym: "cell separation following cytokinesis" EXACT [GOC:dph, GOC:tb] synonym: "cytokinetic cell separation" RELATED [] synonym: "mitotic cytokinetic cell separation" EXACT [] synonym: "rotokinesis" NARROW [] is_a: GO:0009987 ! cellular process relationship: part_of GO:0051301 ! cell division [Term] id: GO:0000921 name: septin ring assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of septins and associated proteins to form an organized structure resembling a ring at the cell cortex." [GOC:clt] subset: gosubset_prok synonym: "septin assembly and septum biosynthesis" BROAD [] synonym: "septin assembly and septum formation" BROAD [] is_a: GO:0031106 ! septin ring organization is_a: GO:0043623 ! cellular protein complex assembly is_a: GO:0070925 ! organelle assembly [Term] id: GO:0000922 name: spindle pole namespace: cellular_component alt_id: GO:0030615 def: "Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules." [GOC:clt] is_a: GO:0044430 ! cytoskeletal part relationship: part_of GO:0005819 ! spindle [Term] id: GO:0000923 name: equatorial microtubule organizing center namespace: cellular_component def: "A microtubule organizing center formed by a band of gamma-tubulin that is recruited to a circumferential band of F-actin at the midpoint of a cell and which nucleates microtubules from the cell division site at the end of mitosis." [PMID:11792817] synonym: "EMTOC" EXACT [] synonym: "equatorial microtubule organising centre" EXACT [] is_a: GO:0005815 ! microtubule organizing center is_a: GO:0032155 ! cell division site part intersection_of: GO:0005815 ! microtubule organizing center intersection_of: part_of GO:0032153 ! cell division site relationship: part_of GO:0032153 ! cell division site [Term] id: GO:0000924 name: gamma-tubulin ring complex, centrosomal namespace: cellular_component alt_id: GO:0000925 alt_id: GO:0000926 def: "A centrosome-localized multiprotein complex composed of gamma-tubulin and other non-tubulin proteins assembled into a ring structure that is thought to be the unit of nucleation at the minus end of a microtubule. Gamma-tubulin small complexes are thought to be the core repeating units of the ring." [GOC:clt, GOC:mtg_sensu, PMID:12134075, PMID:17021256] synonym: "gamma-tubulin large complex, centrosomal" EXACT [] is_a: GO:0008274 ! gamma-tubulin ring complex intersection_of: GO:0008274 ! gamma-tubulin ring complex intersection_of: part_of GO:0000242 ! pericentriolar material relationship: part_of GO:0000242 ! pericentriolar material [Term] id: GO:0000927 name: gamma-tubulin small complex, centrosomal namespace: cellular_component def: "A centrosomal complex usually comprising two gamma-tubulin molecules, at least two conserved non-tubulin proteins that multimerize along with additional non-tubulin proteins in animal cells into larger functional complexes. Gamma-tubulin small complexes are thought to be the repeating unit making up the core of the gamma-tubulin ring complex. An example of this structure is found in Mus musculus." [GOC:mtg_sensu, PMID:12134075] is_a: GO:0008275 ! gamma-tubulin small complex [Term] id: GO:0000928 name: gamma-tubulin small complex, spindle pole body namespace: cellular_component def: "A complex composed of two gamma-tubulin molecules and conserved non-tubulin proteins located in the spindle pole body and isolated by fractionation from cells. The complex, approximately 6S-9S, is analogous to the small complex in animal cells but contains fewer subunits, and is not thought to multimerize into larger functional units, like complexes in those organisms. An example of this structure is found in Saccharomyces cerevisiae." [GOC:mtg_sensu, PMID:12134075] synonym: "Tub4 complex" EXACT [] is_a: GO:0008275 ! gamma-tubulin small complex intersection_of: GO:0008275 ! gamma-tubulin small complex intersection_of: part_of GO:0005816 ! spindle pole body relationship: part_of GO:0005816 ! spindle pole body [Term] id: GO:0000930 name: gamma-tubulin complex namespace: cellular_component def: "A multiprotein complex composed of gamma-tubulin and other non-tubulin proteins. Gamma-tubulin complexes are localized to microtubule organizing centers, and play an important role in the nucleation of microtubules. The number and complexity of non-tubulin proteins associated with these complexes varies between species." [GOC:clt, PMID:12134075] subset: goslim_pir is_a: GO:0043234 ! protein complex is_a: GO:0044450 ! microtubule organizing center part [Term] id: GO:0000931 name: gamma-tubulin large complex namespace: cellular_component alt_id: GO:0000929 def: "A complex of gamma tubulin and associated proteins thought to be formed by multimerization of gamma-tubulin small complexes. An example of this structure is found in Schizosaccharomyces pombe." [GOC:mtg_sensu, PMID:12134075] is_a: GO:0000930 ! gamma-tubulin complex [Term] id: GO:0000932 name: cytoplasmic mRNA processing body namespace: cellular_component def: "A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. mRNA processing and binding proteins are localized to these foci." [GOC:clt, PMID:12730603] synonym: "cytoplasmic foci" RELATED [] synonym: "P body" EXACT [] synonym: "P-body" EXACT [] xref: Wikipedia:P_body is_a: GO:0036464 ! cytoplasmic ribonucleoprotein granule [Term] id: GO:0000933 name: adventitious septum namespace: cellular_component def: "A cell septum whose formation is independent of nuclear division." [GOC:clt, ISBN:0471940526] is_a: GO:0030428 ! cell septum [Term] id: GO:0000934 name: porous cell septum namespace: cellular_component def: "A septum or cross wall which does not entirely span the space between two portions of cell wall and may contain a specialized central pore structure. A porous septum allows the movement of organelles and/or cytoplasm between compartments." [GOC:clt] synonym: "porous septum" BROAD [] is_a: GO:0030428 ! cell septum [Term] id: GO:0000935 name: barrier septum namespace: cellular_component def: "A septum which spans a cell and does not allow exchange of organelles or cytoplasm between compartments." [GOC:clt] synonym: "complete septum" EXACT [] is_a: GO:0030428 ! cell septum [Term] id: GO:0000936 name: primary cell septum namespace: cellular_component def: "A cell septum that forms following nuclear division." [GOC:clt, ISBN:0471940526] synonym: "primary septum" BROAD [] is_a: GO:0030428 ! cell septum [Term] id: GO:0000937 name: dolipore septum namespace: cellular_component def: "A septum, or cross-wall, between two portions of a cell or hypha; contains a central pore around which the septum is swollen to form a barrel-shaped structure; pore is covered on each side of the septum by a septal pore cap (parenthosome)." [GOC:clt] is_a: GO:0000934 ! porous cell septum [Term] id: GO:0000938 name: GARP complex namespace: cellular_component def: "A quatrefoil tethering complex required for retrograde traffic from the early endosome back to the late Golgi and biogenesis of cytoplasmic vesicles." [GOC:clt, GOC:rn, PMID:10637310, PMID:12077354, PMID:12446664] synonym: "Golgi associated retrograde protein complex" EXACT [] synonym: "VFT tethering complex" EXACT [] synonym: "Vps fifty three tethering complex" EXACT [] is_a: GO:0044431 ! Golgi apparatus part is_a: GO:0044433 ! cytoplasmic vesicle part is_a: GO:0099023 ! tethring complex relationship: part_of GO:0016023 ! cytoplasmic, membrane-bounded vesicle [Term] id: GO:0000939 name: condensed chromosome inner kinetochore namespace: cellular_component def: "The region of a condensed chromosome kinetochore closest to centromeric DNA; in mammals the CREST antigens (CENP proteins) are found in this layer; this layer may help define underlying centromeric chromatin structure and position of the kinetochore on the chromosome." [GOC:clt, PMID:10619130, PMID:11483983] synonym: "inner centromere core complex" RELATED [] synonym: "inner kinetochore of condensed chromosome" EXACT [GOC:curators] synonym: "inner kinetochore plate" NARROW [] is_a: GO:0043234 ! protein complex is_a: GO:0044427 ! chromosomal part relationship: part_of GO:0000777 ! condensed chromosome kinetochore [Term] id: GO:0000940 name: condensed chromosome outer kinetochore namespace: cellular_component def: "The region of a condensed chromosome kinetochore most external to centromeric DNA; this outer region mediates kinetochore-microtubule interactions." [GOC:clt, PMID:11483983] synonym: "outer kinetochore of condensed chromosome" EXACT [GOC:curators] synonym: "outer kinetochore plate" NARROW [] is_a: GO:0043234 ! protein complex is_a: GO:0044427 ! chromosomal part relationship: part_of GO:0000777 ! condensed chromosome kinetochore [Term] id: GO:0000941 name: condensed nuclear chromosome inner kinetochore namespace: cellular_component def: "The region of a condensed nuclear chromosome kinetochore closest to centromeric DNA; this layer may help define underlying centromeric chromatin structure and position of the kinetochore on the chromosome." [GOC:clt, PMID:10619130, PMID:1148398] synonym: "inner kinetochore of condensed nuclear chromosome" EXACT [GOC:curators] is_a: GO:0000939 ! condensed chromosome inner kinetochore is_a: GO:0044454 ! nuclear chromosome part intersection_of: GO:0000939 ! condensed chromosome inner kinetochore intersection_of: part_of GO:0000778 ! condensed nuclear chromosome kinetochore relationship: part_of GO:0000778 ! condensed nuclear chromosome kinetochore [Term] id: GO:0000942 name: condensed nuclear chromosome outer kinetochore namespace: cellular_component def: "The region of a condensed nuclear chromosome kinetochore most external to centromeric DNA; this outer region mediates kinetochore-microtubule interactions." [GOC:clt, PMID:1148398] synonym: "outer kinetochore of condensed nuclear chromosome" EXACT [GOC:curators] is_a: GO:0000940 ! condensed chromosome outer kinetochore is_a: GO:0044454 ! nuclear chromosome part intersection_of: GO:0000940 ! condensed chromosome outer kinetochore intersection_of: part_of GO:0000778 ! condensed nuclear chromosome kinetochore relationship: part_of GO:0000778 ! condensed nuclear chromosome kinetochore [Term] id: GO:0000943 name: retrotransposon nucleocapsid namespace: cellular_component def: "A complex of the retrotransposon RNA genome, reverse transcriptase, integrase, and associated molecules required for reproduction and integration of the retrotransposon into the host genome; the main structural molecule of the nucleocapsid is often a gag protein homolog." [GOC:clt, PMID:10861903] synonym: "Virus-like particle" EXACT [] synonym: "VLP" EXACT [] xref: Wikipedia:Virus-like_particle is_a: GO:0044428 ! nuclear part [Term] id: GO:0000944 name: base pairing with rRNA namespace: molecular_function def: "Interacting selectively and non-covalently with ribosomal ribonucleic acid (rRNA) via hydrogen bonds between the bases of a gene product molecule and the bases of a target rRNA molecule." [GOC:krc] comment: Note that with respect to annotation, "base pairing with RNA" and its child terms are intended to be used to annotate the activity of gene products composed of nucleic acid, presumably RNA, to interact with other RNA molecules via base pairing. Internal base pairing with itself is considered part of the secondary structure of the molecule and is not within the scope of GO function. is_a: GO:0000498 ! base pairing with RNA is_a: GO:0019843 ! rRNA binding [Term] id: GO:0000945 name: base pairing with snRNA namespace: molecular_function def: "Interacting selectively and non-covalently with small nuclear ribonucleic acid (snRNA) via hydrogen bonds between the bases of a gene product molecule and the bases of a target snRNA molecule." [GOC:krc] comment: Note that with respect to annotation, "base pairing with RNA" and its child terms are intended to be used to annotate the activity of gene products composed of nucleic acid, presumably RNA, to interact with other RNA molecules via base pairing. Internal base pairing with itself is considered part of the secondary structure of the molecule and is not within the scope of GO function. is_a: GO:0000498 ! base pairing with RNA is_a: GO:0017069 ! snRNA binding [Term] id: GO:0000946 name: base pairing with tRNA namespace: molecular_function def: "Interacting selectively and non-covalently with transfer ribonucleic acid (mRNA) via hydrogen bonds between the bases of a gene product molecule and the bases of a target tRNA molecule." [GOC:krc] comment: Note that with respect to annotation, "base pairing with RNA" and its child terms are intended to be used to annotate the activity of gene products composed of nucleic acid, presumably RNA, to interact with other RNA molecules via base pairing. Internal base pairing with itself is considered part of the secondary structure of the molecule and is not within the scope of GO function. is_a: GO:0000049 ! tRNA binding is_a: GO:0000498 ! base pairing with RNA [Term] id: GO:0000947 name: amino acid catabolic process to alcohol via Ehrlich pathway namespace: biological_process def: "The chemical reactions and pathways involving the catabolism of amino acids to produce alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols." [GOC:krc, PMID:18281432] is_a: GO:0000955 ! amino acid catabolic process via Ehrlich pathway is_a: GO:0046165 ! alcohol biosynthetic process [Term] id: GO:0000948 name: amino acid catabolic process to carboxylic acid via Ehrlich pathway namespace: biological_process def: "The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids." [GOC:krc, PMID:18281432] is_a: GO:0000955 ! amino acid catabolic process via Ehrlich pathway is_a: GO:0046394 ! carboxylic acid biosynthetic process [Term] id: GO:0000949 name: aromatic amino acid family catabolic process to alcohol via Ehrlich pathway namespace: biological_process def: "The chemical reactions and pathways involving the catabolism of aromatic amino acids to produce aromatic alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When an aromatic family amino acid, phenylalanine, tyrosine, or tryptophan, is used as the substrate, 2-phenylethanol, 4-hydroxyphenylethanol, or tryptophol, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols." [GOC:krc, PMID:18281432] is_a: GO:0000947 ! amino acid catabolic process to alcohol via Ehrlich pathway is_a: GO:0009074 ! aromatic amino acid family catabolic process [Term] id: GO:0000950 name: branched-chain amino acid catabolic process to alcohol via Ehrlich pathway namespace: biological_process def: "The chemical reactions and pathways involving the catabolism of branched chain amino acids to produce branched chain alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When a branched chain family amino acid, leucine, isoleucine, or valine, is used as the substrate, 3-methylbutanol, 2-methylbutanol, or 2-methylpropanol, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols." [GOC:krc, PMID:18281432] synonym: "branched chain family amino acid catabolic process to alcohol via Ehrlich pathway" EXACT [GOC:krc] is_a: GO:0000947 ! amino acid catabolic process to alcohol via Ehrlich pathway is_a: GO:0009083 ! branched-chain amino acid catabolic process [Term] id: GO:0000951 name: methionine catabolic process to 3-methylthiopropanol namespace: biological_process def: "The chemical reactions and pathways involving the catabolism of branched chain amino acids to produce branched chain alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When methionine is used as the substrate, 3-methylthiopropanol is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols." [GOC:krc, PMID:18281432] is_a: GO:0000947 ! amino acid catabolic process to alcohol via Ehrlich pathway is_a: GO:0009087 ! methionine catabolic process is_a: GO:0044272 ! sulfur compound biosynthetic process [Term] id: GO:0000952 name: aromatic amino acid family catabolic process to carboxylic acid via Ehrlich pathway namespace: biological_process def: "The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When an aromatic family amino acid, phenylalanine, tyrosine, or tryptophan, is used as the substrate, 2-phenylethanoate, 4-hydroxyphenylethanoate, or 2-(Indol-3-yl)-ethanoate, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids." [GOC:krc, PMID:18281432] is_a: GO:0000948 ! amino acid catabolic process to carboxylic acid via Ehrlich pathway is_a: GO:0009074 ! aromatic amino acid family catabolic process [Term] id: GO:0000953 name: branched-chain amino acid catabolic process to carboxylic acid via Ehrlich pathway namespace: biological_process def: "The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When a branched chain family amino acid, leucine, isoleucine, or valine, is used as the substrate, 3-methylbutanoate, 2-methylbutanoate, or 2-methylpropanoate, respectively, is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids." [GOC:krc, PMID:18281432] synonym: "branched chain family amino acid catabolic process to carboxylic acid via Ehrlich pathway" EXACT [GOC:krc] is_a: GO:0000948 ! amino acid catabolic process to carboxylic acid via Ehrlich pathway is_a: GO:0009083 ! branched-chain amino acid catabolic process [Term] id: GO:0000954 name: methionine catabolic process to 3-methylthiopropanoate namespace: biological_process def: "The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When methionine is used as the substrate, 3-methylthiopropanoate is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids." [GOC:krc, PMID:18281432] is_a: GO:0000948 ! amino acid catabolic process to carboxylic acid via Ehrlich pathway is_a: GO:0006633 ! fatty acid biosynthetic process is_a: GO:0009087 ! methionine catabolic process [Term] id: GO:0000955 name: amino acid catabolic process via Ehrlich pathway namespace: biological_process def: "The chemical reactions and pathways involving the catabolism of amino acids to produce alcohols or carboxylic acids containing one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives, sometimes referred to as fusel acids, may be produced instead of alcohols." [GOC:krc, PMID:18281432] is_a: GO:0009063 ! cellular amino acid catabolic process [Term] id: GO:0000956 name: nuclear-transcribed mRNA catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of nuclear-transcribed mRNAs in eukaryotic cells." [GOC:krc] synonym: "nuclear mRNA breakdown" EXACT [] synonym: "nuclear mRNA catabolism" EXACT [] synonym: "nuclear mRNA degradation" EXACT [] is_a: GO:0006402 ! mRNA catabolic process [Term] id: GO:0000957 name: mitochondrial RNA catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of RNA transcribed from the mitochondrial genome and occurring in the mitochondrion." [GOC:krc, GOC:mah] is_a: GO:0000959 ! mitochondrial RNA metabolic process is_a: GO:0006401 ! RNA catabolic process intersection_of: GO:0006401 ! RNA catabolic process intersection_of: occurs_in GO:0005739 ! mitochondrion relationship: occurs_in GO:0005739 ! mitochondrion [Term] id: GO:0000958 name: mitochondrial mRNA catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of mRNA transcribed from the mitochondrial genome and occurring in the mitochondrion." [GOC:krc, GOC:mah] is_a: GO:0000957 ! mitochondrial RNA catabolic process is_a: GO:0006402 ! mRNA catabolic process intersection_of: GO:0006402 ! mRNA catabolic process intersection_of: occurs_in GO:0005739 ! mitochondrion relationship: occurs_in GO:0005739 ! mitochondrion [Term] id: GO:0000959 name: mitochondrial RNA metabolic process namespace: biological_process def: "The chemical reactions and pathways involving RNA transcribed from the mitochondrial genome and occurring in the mitochondrion." [GOC:krc, GOC:mah] is_a: GO:0016070 ! RNA metabolic process intersection_of: GO:0016070 ! RNA metabolic process intersection_of: occurs_in GO:0005739 ! mitochondrion relationship: occurs_in GO:0005739 ! mitochondrion [Term] id: GO:0000960 name: regulation of mitochondrial RNA catabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome." [GOC:krc, GOC:mah] is_a: GO:0031329 ! regulation of cellular catabolic process is_a: GO:0051252 ! regulation of RNA metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0000957 ! mitochondrial RNA catabolic process relationship: regulates GO:0000957 ! mitochondrial RNA catabolic process [Term] id: GO:0000961 name: negative regulation of mitochondrial RNA catabolic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome." [GOC:krc, GOC:mah] is_a: GO:0000960 ! regulation of mitochondrial RNA catabolic process is_a: GO:1902369 ! negative regulation of RNA catabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0000957 ! mitochondrial RNA catabolic process relationship: negatively_regulates GO:0000957 ! mitochondrial RNA catabolic process [Term] id: GO:0000962 name: positive regulation of mitochondrial RNA catabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome." [GOC:krc, GOC:mah] is_a: GO:0000960 ! regulation of mitochondrial RNA catabolic process is_a: GO:0031331 ! positive regulation of cellular catabolic process is_a: GO:0051254 ! positive regulation of RNA metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0000957 ! mitochondrial RNA catabolic process relationship: positively_regulates GO:0000957 ! mitochondrial RNA catabolic process [Term] id: GO:0000963 name: mitochondrial RNA processing namespace: biological_process def: "The conversion of a primary RNA molecule transcribed from a mitochondrial genome into one or more mature RNA molecules; occurs in the mitochondrion." [GOC:krc, GOC:mah] is_a: GO:0000959 ! mitochondrial RNA metabolic process is_a: GO:0006396 ! RNA processing is_a: GO:0007005 ! mitochondrion organization intersection_of: GO:0006396 ! RNA processing intersection_of: occurs_in GO:0005739 ! mitochondrion relationship: occurs_in GO:0005739 ! mitochondrion [Term] id: GO:0000964 name: mitochondrial RNA 5'-end processing namespace: biological_process def: "Any process involved in forming the mature 5' end of an RNA molecule transcribed from a mitochondrial genome; occurs in the mitochondrion." [GOC:krc, GOC:mah] synonym: "mitochondrial RNA 5' end processing" RELATED [] is_a: GO:0000963 ! mitochondrial RNA processing is_a: GO:0000966 ! RNA 5'-end processing intersection_of: GO:0000966 ! RNA 5'-end processing intersection_of: occurs_in GO:0005739 ! mitochondrion relationship: occurs_in GO:0005739 ! mitochondrion [Term] id: GO:0000965 name: mitochondrial RNA 3'-end processing namespace: biological_process def: "Any process involved in forming the mature 3' end of an RNA molecule transcribed from a mitochondrial genome; occurs in the mitochondrion." [GOC:krc, GOC:mah] synonym: "mitochondrial RNA 3' end processing" RELATED [] is_a: GO:0000963 ! mitochondrial RNA processing is_a: GO:0031123 ! RNA 3'-end processing intersection_of: GO:0031123 ! RNA 3'-end processing intersection_of: occurs_in GO:0005739 ! mitochondrion relationship: occurs_in GO:0005739 ! mitochondrion [Term] id: GO:0000966 name: RNA 5'-end processing namespace: biological_process def: "Any process involved in forming the mature 5' end of an RNA molecule." [GOC:krc] synonym: "RNA 5' end processing" EXACT [] is_a: GO:0006396 ! RNA processing [Term] id: GO:0000967 name: rRNA 5'-end processing namespace: biological_process def: "Any process involved in forming the mature 5' end of an rRNA molecule." [GOC:krc] synonym: "rRNA 5' end processing" EXACT [] is_a: GO:0006364 ! rRNA processing is_a: GO:0034471 ! ncRNA 5'-end processing [Term] id: GO:0000968 name: tRNA exon ligation namespace: biological_process def: "An RNA exon ligation process that rejoins two exons of a pre-tRNA which has had the intron removed." [GOC:krc] is_a: GO:0000378 ! RNA exon ligation relationship: part_of GO:0006388 ! tRNA splicing, via endonucleolytic cleavage and ligation created_by: kchris creation_date: 2009-04-28T10:22:40Z [Term] id: GO:0000969 name: tRNA exon ligation utilizing ATP as source of linkage phosphate namespace: biological_process def: "A tRNA exon ligation process in which the splice junction phosphate is derived from exogenous ATP. This type of ligation to rejoin the 5' and 3' exons of a tRNA is observed in vertebrate species." [GOC:krc, PMID:17786051] is_a: GO:0000968 ! tRNA exon ligation created_by: kchris creation_date: 2009-04-28T10:29:37Z [Term] id: GO:0000970 name: tRNA exon ligation utilizing GTP as source of linkage phosphate namespace: biological_process def: "A tRNA exon ligation process in which the splice junction phosphate is derived from exogenous GTP. This type of ligation to rejoin the 5' and 3' exons of a tRNA is observed in the yeast Saccharomyces cerevisiae where the ligation reaction also produces a 2'-phosphate at the splice junction which is subsequently removed as part of the ligation process." [GOC:krc, PMID:18217203, PMID:9299409] is_a: GO:0000968 ! tRNA exon ligation created_by: kchris creation_date: 2009-04-28T10:33:25Z [Term] id: GO:0000971 name: tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate namespace: biological_process def: "A tRNA exon ligation process in which the splice junction phosphate is derived from the 2',3' cyclic phosphate at the 3'-end of the 5'-exon. This type of ligation to rejoin the 5' and 3' exons of a tRNA is observed in wheat, Chlamydomonas, and vertebrate species including humans." [GOC:krc, PMID:17786051, PMID:18217203, PMID:9299409] is_a: GO:0000968 ! tRNA exon ligation created_by: kchris creation_date: 2009-04-28T10:36:17Z [Term] id: GO:0000972 name: transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery namespace: biological_process def: "The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery. In S. cerevisiae, this process involves cis-acting DNA sequences such as the TATA box and upstream activating sequence (UAS) elements, trans-acting transcriptional activators, and also the 3'-UTR of the transcript." [GOC:krc, PMID:18614049] is_a: GO:0051276 ! chromosome organization created_by: kchris creation_date: 2009-09-10T12:25:11Z [Term] id: GO:0000973 name: posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery namespace: biological_process def: "The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery even after transcription has been repressed." [GOC:krc, PMID:17373856, PMID:18614049] is_a: GO:0000972 ! transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery created_by: kchris creation_date: 2009-09-10T12:28:04Z [Term] id: GO:0000974 name: Prp19 complex namespace: cellular_component def: "A protein complex consisting of Prp19 and associated proteins that is involved in the transition from the precatalytic spliceosome to the activated form that catalyzes step 1 of splicing, and which remains associated with the spliceosome through the second catalytic step. It is widely conserved, found in both yeast and mammals, though the exact composition varies. In S. cerevisiae, it contains Prp19p, Ntc20p, Snt309p, Isy1p, Syf2p, Cwc2p, Prp46p, Clf1p, Cef1p, and Syf1p." [GOC:krc, PMID:16540691, PMID:19239890] synonym: "nineteen complex" NARROW [] synonym: "NTC" RELATED [] synonym: "Prp19/CDC5 complex" NARROW [] is_a: GO:0043234 ! protein complex created_by: kchris creation_date: 2009-10-12T10:01:30Z [Term] id: GO:0000975 name: regulatory region DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a DNA region that regulates a DNA-based process. Such processes include transcription, DNA replication, and DNA repair." [GOC:txnOH] is_a: GO:0001067 ! regulatory region nucleic acid binding is_a: GO:0003677 ! DNA binding created_by: kchris creation_date: 2010-08-10T10:56:24Z [Term] id: GO:0000976 name: transcription regulatory region sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH] comment: The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". is_a: GO:0044212 ! transcription regulatory region DNA binding is_a: GO:1990837 ! sequence-specific double-stranded DNA binding created_by: kchris creation_date: 2010-08-10T11:00:02Z [Term] id: GO:0000977 name: RNA polymerase II regulatory region sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II." [GOC:txnOH] comment: The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". is_a: GO:0000976 ! transcription regulatory region sequence-specific DNA binding is_a: GO:0001012 ! RNA polymerase II regulatory region DNA binding created_by: kchris creation_date: 2010-08-10T11:05:36Z [Term] id: GO:0000978 name: RNA polymerase II core promoter proximal region sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II." [GOC:txnOH] comment: Note that the phrase "upstream activating sequence", or UAS is often used in S. cerevisiae literature to refer to regulatory sequences that occur in the region upstream and proximal to the core promoter. In contrast, in bacteria such as E. coli, the phrase "upstream activating sequence", or UAS is a synonym for "enhancer". synonym: "RNA polymerase II upstream activating sequence (UAS) sequence-specific DNA binding" RELATED [] is_a: GO:0000977 ! RNA polymerase II regulatory region sequence-specific DNA binding is_a: GO:0000987 ! core promoter proximal region sequence-specific DNA binding created_by: kchris creation_date: 2010-08-10T02:17:19Z [Term] id: GO:0000979 name: RNA polymerase II core promoter sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase II basal transcription machinery." [GOC:txnOH] is_a: GO:0000977 ! RNA polymerase II regulatory region sequence-specific DNA binding is_a: GO:0001046 ! core promoter sequence-specific DNA binding created_by: kchris creation_date: 2010-08-10T02:17:28Z [Term] id: GO:0000980 name: RNA polymerase II distal enhancer sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter." [GOC:txnOH] comment: Note that distal enhancers of the type found in mammalian cells are not known to occur in either Saccharomyces cerevisiae or Schizosaccharomyces pombe. While some S. cerevisiae literature does refer to sequences distal to the initiation site, these distal sites do not seem to function independently of position or orientation as mammalian distal enhancers do and are not considered to be enhancers. is_a: GO:0000977 ! RNA polymerase II regulatory region sequence-specific DNA binding is_a: GO:0001158 ! enhancer sequence-specific DNA binding created_by: kchris creation_date: 2010-08-10T02:29:25Z [Term] id: GO:0000981 name: RNA polymerase II transcription factor activity, sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] synonym: "sequence-specific DNA binding RNA polymerase II transcription factor activity" EXACT [] is_a: GO:0003700 ! transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0000977 ! RNA polymerase II regulatory region sequence-specific DNA binding relationship: part_of GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: kchris creation_date: 2010-08-10T02:37:21Z [Term] id: GO:0000982 name: transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II." [GOC:txnOH] synonym: "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity" EXACT [] synonym: "transcription factor" BROAD [GOC:vw] is_a: GO:0000981 ! RNA polymerase II transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0000978 ! RNA polymerase II core promoter proximal region sequence-specific DNA binding created_by: kchris creation_date: 2010-08-10T02:39:46Z [Term] id: GO:0000983 name: transcription factor activity, RNA polymerase II core promoter sequence-specific namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in an RNA polymerase II (Pol II) core promoter, the region composed of the transcription start site and binding sites for transcription factors of the Pol II basal transcription machinery, in order to modulate transcription by Pol II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] synonym: "RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity" EXACT [] is_a: GO:0000981 ! RNA polymerase II transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0000979 ! RNA polymerase II core promoter sequence-specific DNA binding created_by: kchris creation_date: 2010-08-10T02:47:56Z [Term] id: GO:0000984 name: bacterial-type RNA polymerase regulatory region sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is part of a regulatory region that controls the transcription of a gene or operon by a bacterial-type RNA polymerase." [GOC:txnOH] comment: The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". subset: gosubset_prok synonym: "eubacterial-type RNA polymerase regulatory region sequence-specific DNA binding" RELATED [] is_a: GO:0000976 ! transcription regulatory region sequence-specific DNA binding is_a: GO:0001017 ! bacterial-type RNA polymerase regulatory region DNA binding created_by: kchris creation_date: 2010-08-10T02:58:18Z [Term] id: GO:0000985 name: bacterial-type RNA polymerase core promoter sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in a bacterial-type RNA polymerase core promoter, the region composed of the transcription start site and binding sites for transcription factors of the basal transcription machinery, in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] subset: gosubset_prok synonym: "eubacterial-type RNA polymerase core promoter sequence-specific DNA binding" EXACT [] is_a: GO:0000984 ! bacterial-type RNA polymerase regulatory region sequence-specific DNA binding is_a: GO:0001046 ! core promoter sequence-specific DNA binding created_by: kchris creation_date: 2010-08-10T03:01:38Z [Term] id: GO:0000986 name: bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase." [GOC:txnOH] subset: gosubset_prok synonym: "eubacterial-type RNA polymerase regulatory transcription factor sequence-specific DNA binding" EXACT [] is_a: GO:0000984 ! bacterial-type RNA polymerase regulatory region sequence-specific DNA binding is_a: GO:0000987 ! core promoter proximal region sequence-specific DNA binding created_by: kchris creation_date: 2010-08-10T03:02:31Z [Term] id: GO:0000987 name: core promoter proximal region sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH] comment: The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". is_a: GO:0000976 ! transcription regulatory region sequence-specific DNA binding is_a: GO:0001159 ! core promoter proximal region DNA binding created_by: kchris creation_date: 2010-08-10T03:40:16Z [Term] id: GO:0000988 name: transcription factor activity, protein binding namespace: molecular_function def: "Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. This term does not provide specificity with respect to the type of protein binding, e.g. transcription factor binding or RNA polymerase binding. Please use a child term that provides that specificity or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_generic subset: goslim_yeast synonym: "protein binding transcription factor activity" EXACT [] synonym: "transcription factor activity" BROAD [] is_a: GO:0003674 ! molecular_function intersection_of: GO:0003674 ! molecular_function intersection_of: has_part GO:0005515 ! protein binding intersection_of: part_of GO:1903506 ! regulation of nucleic acid-templated transcription relationship: has_part GO:0005515 ! protein binding relationship: part_of GO:1903506 ! regulation of nucleic acid-templated transcription created_by: kchris creation_date: 2010-08-10T04:03:22Z [Term] id: GO:0000989 name: transcription factor activity, transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] synonym: "transcription factor binding transcription factor activity" EXACT [] is_a: GO:0000988 ! transcription factor activity, protein binding intersection_of: GO:0003674 ! molecular_function intersection_of: has_part GO:0008134 ! transcription factor binding intersection_of: regulates GO:0097659 ! nucleic acid-templated transcription relationship: has_part GO:0008134 ! transcription factor binding relationship: regulates GO:0097659 ! nucleic acid-templated transcription created_by: kchris creation_date: 2010-08-10T04:57:43Z [Term] id: GO:0000990 name: transcription factor activity, core RNA polymerase binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] synonym: "core RNA polymerase binding transcription factor activity" EXACT [] is_a: GO:0000988 ! transcription factor activity, protein binding intersection_of: GO:0003674 ! molecular_function intersection_of: has_part GO:0043175 ! RNA polymerase core enzyme binding intersection_of: part_of GO:1903506 ! regulation of nucleic acid-templated transcription relationship: has_part GO:0043175 ! RNA polymerase core enzyme binding relationship: part_of GO:1903506 ! regulation of nucleic acid-templated transcription created_by: kchris creation_date: 2010-08-10T05:01:03Z [Term] id: GO:0000991 name: transcription factor activity, core RNA polymerase II binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] synonym: "core RNA polymerase II binding transcription factor activity" EXACT [] is_a: GO:0000990 ! transcription factor activity, core RNA polymerase binding intersection_of: GO:0003674 ! molecular_function intersection_of: has_part GO:0000993 ! RNA polymerase II core binding intersection_of: part_of GO:0006357 ! regulation of transcription from RNA polymerase II promoter relationship: has_part GO:0000993 ! RNA polymerase II core binding relationship: part_of GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: kchris creation_date: 2010-08-10T05:03:45Z [Term] id: GO:0000992 name: polymerase III regulatory region sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is part of a regulatory region that controls transcription by RNA polymerase III. The transcribed region might be contain a single gene or a cistron containing multiple genes." [GOC:txnOH, PMID:12381659] comment: The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". is_a: GO:0000976 ! transcription regulatory region sequence-specific DNA binding is_a: GO:0001016 ! RNA polymerase III regulatory region DNA binding created_by: kchris creation_date: 2010-08-11T03:49:28Z [Term] id: GO:0000993 name: RNA polymerase II core binding namespace: molecular_function def: "Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits." [GOC:txnOH] is_a: GO:0001099 ! basal RNA polymerase II transcription machinery binding is_a: GO:0032403 ! protein complex binding is_a: GO:0043175 ! RNA polymerase core enzyme binding created_by: kchris creation_date: 2010-08-11T03:57:27Z [Term] id: GO:0000994 name: RNA polymerase III core binding namespace: molecular_function def: "Interacting selectively and non-covalently with RNA polymerase III core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of seventeen subunits." [GOC:txnOH] is_a: GO:0043175 ! RNA polymerase core enzyme binding created_by: kchris creation_date: 2010-08-11T03:58:58Z [Term] id: GO:0000995 name: transcription factor activity, core RNA polymerase III binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH, PMID:12381659] synonym: "core RNA polymerase III binding transcription factor activity" EXACT [] is_a: GO:0000990 ! transcription factor activity, core RNA polymerase binding intersection_of: GO:0003674 ! molecular_function intersection_of: has_part GO:0000994 ! RNA polymerase III core binding intersection_of: part_of GO:0006359 ! regulation of transcription from RNA polymerase III promoter relationship: has_part GO:0000994 ! RNA polymerase III core binding relationship: part_of GO:0006359 ! regulation of transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-08-11T03:59:13Z [Term] id: GO:0000996 name: core DNA-dependent RNA polymerase binding promoter specificity activity namespace: molecular_function def: "Interacting selectively and non-covalently with a DNA-dependent core RNA polymerase to form a holoenzyme complex and also, while present in the holoenzyme, interacting with promoter sequences in order to confer sequence specific recognition of promoter DNA sequence motifs." [GOC:txnOH] is_a: GO:0000990 ! transcription factor activity, core RNA polymerase binding intersection_of: GO:0003674 ! molecular_function intersection_of: has_part GO:0000976 ! transcription regulatory region sequence-specific DNA binding intersection_of: has_part GO:0043175 ! RNA polymerase core enzyme binding intersection_of: part_of GO:0006355 ! regulation of transcription, DNA-templated relationship: has_part GO:0000976 ! transcription regulatory region sequence-specific DNA binding relationship: has_part GO:0043175 ! RNA polymerase core enzyme binding relationship: part_of GO:0006355 ! regulation of transcription, DNA-templated created_by: kchris creation_date: 2010-08-11T04:12:24Z [Term] id: GO:0000997 name: mitochondrial RNA polymerase core promoter sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is part of the core promoter for the mitochondrial RNA polymerase." [GOC:txnOH] is_a: GO:0001044 ! mitochondrial RNA polymerase regulatory region sequence-specific DNA binding is_a: GO:0001046 ! core promoter sequence-specific DNA binding created_by: kchris creation_date: 2010-08-17T04:48:40Z [Term] id: GO:0000999 name: RNA polymerase III type 1 promoter transcriptional preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on a type 1 RNA polymerase III (Pol III) promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is the first step of transcription. Type 1 promoters require TFIIIA for promoter recognition, which then recruits TFIIIC. TFIIIC in turn recruits TFIIIB, which recruits Pol III to the promoter." [GOC:txnOH, PMID:12381659] is_a: GO:0070898 ! RNA polymerase III transcriptional preinitiation complex assembly relationship: part_of GO:0001022 ! transcription initiation from RNA polymerase III type 1 promoter created_by: kchris creation_date: 2010-08-19T04:16:04Z [Term] id: GO:0001000 name: bacterial-type RNA polymerase core enzyme binding namespace: molecular_function def: "Interacting selectively and non-covalently with the bacterial-type RNA polymerase core enzyme, typically consisting of two alpha, one beta, one beta prime, and one omega subunit." [GOC:txnOH] comment: Should omega be included here? subset: gosubset_prok synonym: "eubacterial-type RNA polymerase core enzyme binding" EXACT [] is_a: GO:0043175 ! RNA polymerase core enzyme binding created_by: kchris creation_date: 2010-08-17T04:59:00Z [Term] id: GO:0001001 name: mitochondrial single-subunit type RNA polymerase binding namespace: molecular_function def: "Interacting selectively and non-covalently with a single subunit mitochondrial RNA polymerase enzyme, which is composed of a single catalytic subunit similar to the RNA polymerase enzymes from phages T3, T7, and SP6." [GOC:txnOH, PMID:20701995, PMID:2088182] is_a: GO:0001050 ! single-subunit type RNA polymerase binding created_by: kchris creation_date: 2010-08-17T05:01:28Z [Term] id: GO:0001002 name: RNA polymerase III type 1 promoter sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is a part of a type 1 promoter that controls transcription by RNA polymerase III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition." [GOC:txnOH, PMID:12381659] is_a: GO:0000992 ! polymerase III regulatory region sequence-specific DNA binding is_a: GO:0001030 ! RNA polymerase III type 1 promoter DNA binding created_by: kchris creation_date: 2010-08-18T05:38:20Z [Term] id: GO:0001003 name: RNA polymerase III type 2 promoter sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is a part of a type 2 promoter that controls transcription by RNA polymerase III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs." [GOC:txnOH, PMID:12381659] is_a: GO:0000992 ! polymerase III regulatory region sequence-specific DNA binding is_a: GO:0001031 ! RNA polymerase III type 2 promoter DNA binding created_by: kchris creation_date: 2010-08-18T05:51:18Z [Term] id: GO:0001004 name: transcription factor activity, RNA polymerase III promoter sequence-specific binding, TFIIIB recruiting namespace: molecular_function def: "The function of binding to a specific DNA sequence motif in an RNA polymerase III (Pol III) promoter in order to recruit the Pol III recruiting factor TFIIIB to the promoter." [GOC:txnOH, PMID:12381659] synonym: "RNA polymerase III promoter sequence-specific DNA binding TFIIIB recruiting transcription factor activity" EXACT [] is_a: GO:0001010 ! transcription factor activity, sequence-specific DNA binding transcription factor recruiting is_a: GO:0001034 ! RNA polymerase III transcription factor activity, sequence-specific DNA binding is_a: GO:0001153 ! transcription factor activity, RNA polymerase III transcription factor recruiting relationship: has_part GO:0000992 ! polymerase III regulatory region sequence-specific DNA binding relationship: has_part GO:0001154 ! TFIIIB-class transcription factor binding created_by: kchris creation_date: 2010-08-18T05:53:32Z [Term] id: GO:0001005 name: transcription factor activity, RNA polymerase III type 1 promoter sequence-specific binding, TFIIIB recruiting namespace: molecular_function def: "The function of binding to a specific DNA sequence motif in a type 1 RNA polymerase III (Pol III) promoter in order to recruit the Pol III recruiting factor TFIIIB to the promoter. For type 1 Pol III promoters, this requires both TFIIIA and TFIIIC." [GOC:txnOH, PMID:12381659] comment: This represents TFIIIA. synonym: "RNA polymerase III type 1 promoter sequence-specific DNA binding TFIIIB recruiting transcription factor activity" EXACT [] synonym: "TFIIIA activity" RELATED [] synonym: "TFIIIC-type activity" RELATED [] is_a: GO:0001004 ! transcription factor activity, RNA polymerase III promoter sequence-specific binding, TFIIIB recruiting relationship: has_part GO:0001002 ! RNA polymerase III type 1 promoter sequence-specific DNA binding relationship: part_of GO:0000999 ! RNA polymerase III type 1 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-18T05:57:29Z [Term] id: GO:0001006 name: RNA polymerase III type 3 promoter sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is a part of a type 3 promoter that controls transcription by RNA polymerase III (Pol III). A type 3 Pol III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae." [GOC:txnOH, PMID:12381659] is_a: GO:0000992 ! polymerase III regulatory region sequence-specific DNA binding is_a: GO:0001032 ! RNA polymerase III type 3 promoter DNA binding created_by: kchris creation_date: 2010-08-18T06:02:26Z [Term] id: GO:0001007 name: transcription factor activity, RNA polymerase III transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] synonym: "RNA polymerase III transcription factor binding transcription factor activity" EXACT [] is_a: GO:0000989 ! transcription factor activity, transcription factor binding relationship: has_part GO:0001025 ! RNA polymerase III transcription factor binding relationship: part_of GO:0006359 ! regulation of transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-08-18T06:24:07Z [Term] id: GO:0001008 name: transcription factor activity, RNA polymerase III type 2 promoter sequence-specific binding, TFIIIB recruiting namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence motif in a type 2 RNA polymerase III (Pol III) promoter in order to recruit TFIIIB to the promoter. For type 2 Pol III promoters, this requires TFIIIC activity." [GOC:txnOH, PMID:12381659] synonym: "RNA polymerase III type 2 promoter sequence-specific DNA binding TFIIIB recruiting transcription factor activity" EXACT [] synonym: "TFIIIC-type activity" RELATED [] synonym: "type 2 RNA polymerase III promoter recognition" EXACT [] is_a: GO:0001004 ! transcription factor activity, RNA polymerase III promoter sequence-specific binding, TFIIIB recruiting relationship: has_part GO:0001003 ! RNA polymerase III type 2 promoter sequence-specific DNA binding relationship: part_of GO:0001021 ! RNA polymerase III type 2 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-18T06:30:45Z [Term] id: GO:0001009 name: transcription from RNA polymerase III type 2 promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by RNA polymerase III (RNAP III), originating at a type 2 RNAP III promoter. Type 2 RNAP III promoters consist of an A box and a B box downstream of the transcription start site within the sequence of the mature RNA and the process of initiation is different than from other promoter types. Type 2 promoters are found in many tRNA genes as well as in other small RNAs." [GOC:txnOH, PMID:12381659] is_a: GO:0006383 ! transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-08-18T06:37:56Z [Term] id: GO:0001010 name: transcription factor activity, sequence-specific DNA binding transcription factor recruiting namespace: molecular_function def: "The function of binding to a specific DNA sequence and recruiting another transcription factor to the DNA in order to modulate transcription. The recruited factor may bind DNA directly, or may be colocalized via protein-protein interactions." [GOC:txnOH] synonym: "sequence-specific DNA binding transcription factor recruiting transcription factor activity" EXACT [] is_a: GO:0001134 ! transcription factor activity, transcription factor recruiting is_a: GO:0003700 ! transcription factor activity, sequence-specific DNA binding created_by: kchris creation_date: 2010-08-18T06:46:33Z [Term] id: GO:0001011 name: transcription factor activity, sequence-specific DNA binding, RNA polymerase recruiting namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence and recruiting RNA polymerase to the DNA in order to form the preinitiation complex (PIC)." [GOC:txnOH] synonym: "sequence-specific DNA binding RNA polymerase recruiting transcription factor activity" EXACT [] is_a: GO:0003700 ! transcription factor activity, sequence-specific DNA binding created_by: kchris creation_date: 2010-08-18T06:49:16Z [Term] id: GO:0001012 name: RNA polymerase II regulatory region DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase II. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw] is_a: GO:0044212 ! transcription regulatory region DNA binding created_by: kchris creation_date: 2010-08-19T09:43:58Z [Term] id: GO:0001013 name: RNA polymerase I regulatory region DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by RNA polymerase I. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw] is_a: GO:0044212 ! transcription regulatory region DNA binding created_by: kchris creation_date: 2010-08-19T09:44:02Z [Term] id: GO:0001014 name: snoRNA transcription from a type 2 RNA polymerase III promoter namespace: biological_process def: "The synthesis of small nucleolar RNA (snoRNA) from a DNA template by RNA polymerase III, originating at a type 2 RNA polymerase III promoter." [GOC:txnOH] is_a: GO:0001009 ! transcription from RNA polymerase III type 2 promoter is_a: GO:0009302 ! snoRNA transcription created_by: kchris creation_date: 2010-08-18T07:13:45Z [Term] id: GO:0001015 name: snoRNA transcription from an RNA polymerase II promoter namespace: biological_process def: "The synthesis of small nucleolar RNA (snoRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter." [GOC:txnOH] is_a: GO:0006366 ! transcription from RNA polymerase II promoter is_a: GO:0009302 ! snoRNA transcription created_by: kchris creation_date: 2010-08-18T07:21:18Z [Term] id: GO:0001016 name: RNA polymerase III regulatory region DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a DNA region that controls the transcription of a gene by RNA polymerase III. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw, PMID:12381659] is_a: GO:0044212 ! transcription regulatory region DNA binding created_by: kchris creation_date: 2010-08-19T09:36:17Z [Term] id: GO:0001017 name: bacterial-type RNA polymerase regulatory region DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a DNA region that controls the transcription of a gene or operon by a bacterial-type RNA polymerase. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH] subset: gosubset_prok synonym: "eubacterial-type RNA polymerase regulatory region DNA binding" EXACT [] is_a: GO:0044212 ! transcription regulatory region DNA binding created_by: kchris creation_date: 2010-08-19T09:45:42Z [Term] id: GO:0001018 name: mitochondrial RNA polymerase regulatory region DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by mitochondrial RNA polymerase. Binding may occur as a high affinity and sequence specific interaction or as a lower affinity interaction observed once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw, PMID:20056105] is_a: GO:0044212 ! transcription regulatory region DNA binding created_by: kchris creation_date: 2010-08-19T09:46:22Z [Term] id: GO:0001019 name: plastid RNA polymerase regulatory region DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a DNA region that controls the transcription of a region of DNA by a plastid RNA polymerase. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH, GOC:vw] is_a: GO:0044212 ! transcription regulatory region DNA binding created_by: kchris creation_date: 2010-08-19T09:46:27Z [Term] id: GO:0001020 name: RNA polymerase III type 3 promoter transcriptional preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on a type 1 RNA polymerase III (Pol III) promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is the first step of transcription." [GOC:txnOH, PMID:12381659] is_a: GO:0070898 ! RNA polymerase III transcriptional preinitiation complex assembly relationship: part_of GO:0001024 ! transcription initiation from RNA polymerase III type 3 promoter created_by: kchris creation_date: 2010-08-19T04:18:46Z [Term] id: GO:0001021 name: RNA polymerase III type 2 promoter transcriptional preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on a type 2 RNA polymerase III (Pol III) promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is the first step of transcription. Type 2 promoters require TFIIIC for promoter recognition, which then recruits TFIIIB, which in turn which recruits Pol III to the promoter." [GOC:txnOH, PMID:12381659] is_a: GO:0070898 ! RNA polymerase III transcriptional preinitiation complex assembly relationship: part_of GO:0001023 ! transcription initiation from RNA polymerase III type 2 promoter created_by: kchris creation_date: 2010-08-19T04:18:53Z [Term] id: GO:0001022 name: transcription initiation from RNA polymerase III type 1 promoter namespace: biological_process def: "A transcription initiation process on a type 1 RNA polymerase III (Pol III) that results in RNA synthesis by Pol III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition." [GOC:txnOH, PMID:12381659] is_a: GO:0006384 ! transcription initiation from RNA polymerase III promoter relationship: part_of GO:0042791 ! 5S class rRNA transcription from RNA polymerase III type 1 promoter created_by: kchris creation_date: 2010-08-19T04:33:52Z [Term] id: GO:0001023 name: transcription initiation from RNA polymerase III type 2 promoter namespace: biological_process def: "A transcription initiation process on a type 2 RNA polymerase III (Pol III) that results in RNA synthesis by Pol III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs." [GOC:txnOH, PMID:12381659] is_a: GO:0006384 ! transcription initiation from RNA polymerase III promoter relationship: part_of GO:0001009 ! transcription from RNA polymerase III type 2 promoter created_by: kchris creation_date: 2010-08-19T04:35:09Z [Term] id: GO:0001024 name: transcription initiation from RNA polymerase III type 3 promoter namespace: biological_process def: "A transcription initiation process on a type 3 RNA polymerase III (Pol III) that results in RNA synthesis by Pol III. A type 3 Pol III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae." [GOC:txnOH, PMID:12381659] is_a: GO:0006384 ! transcription initiation from RNA polymerase III promoter relationship: part_of GO:0001035 ! transcription from RNA polymerase III type 3 promoter created_by: kchris creation_date: 2010-08-19T04:35:14Z [Term] id: GO:0001025 name: RNA polymerase III transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III transcription factor, any protein required to initiate or regulate transcription by RNA polymerase III." [GOC:txnOH] is_a: GO:0008134 ! transcription factor binding created_by: kchris creation_date: 2010-08-20T03:26:50Z [Term] id: GO:0001026 name: TFIIIB-type transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way, Once recruited to an RNA polymerase III promoter by one or more other transcription factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH] synonym: "RNA polymerase III recruiting transcription factor activity" EXACT [] is_a: GO:0000995 ! transcription factor activity, core RNA polymerase III binding is_a: GO:0001007 ! transcription factor activity, RNA polymerase III transcription factor binding relationship: has_part GO:0001016 ! RNA polymerase III regulatory region DNA binding created_by: kchris creation_date: 2010-08-23T12:24:31Z [Term] id: GO:0001027 name: RNA polymerase III type 1 promoter TFIIIB-type transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 1 promoter by TFIIIA-type and TFIIIC-type factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH, PMID:12381659] synonym: "RNA polymerase III type 1 promoter polymerase recruiting transcription factor activity" RELATED [] is_a: GO:0001026 ! TFIIIB-type transcription factor activity relationship: has_part GO:0001030 ! RNA polymerase III type 1 promoter DNA binding relationship: part_of GO:0000999 ! RNA polymerase III type 1 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-23T12:50:20Z [Term] id: GO:0001028 name: RNA polymerase III type 2 promoter TFIIIB-type transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 2 promoter by a TFIIIC-type factor, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH, PMID:12381659] synonym: "RNA polymerase III type 2 promoter polymerase recruiting transcription factor activity" RELATED [] is_a: GO:0001026 ! TFIIIB-type transcription factor activity relationship: has_part GO:0001031 ! RNA polymerase III type 2 promoter DNA binding relationship: part_of GO:0001021 ! RNA polymerase III type 2 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-23T12:52:01Z [Term] id: GO:0001029 name: RNA polymerase III type 3 promoter TFIIIB-type transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III type 3 promoter by SNAP-type and TFIIIC-type factors, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH, PMID:12381659] synonym: "RNA polymerase III type 3 promoter polymerase recruiting transcription factor activity" RELATED [] is_a: GO:0001026 ! TFIIIB-type transcription factor activity relationship: has_part GO:0001032 ! RNA polymerase III type 3 promoter DNA binding relationship: part_of GO:0001020 ! RNA polymerase III type 3 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-23T12:52:40Z [Term] id: GO:0001030 name: RNA polymerase III type 1 promoter DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a region of DNA that is a part of a type 1 promoter that controls transcription by RNA polymerase III. Type 1 promoters are found in 5S rRNA genes, downstream of the transcription start site within the sequence of the mature RNA, and require TFIIIA for recognition." [GOC:txnOH, PMID:12381659] is_a: GO:0001016 ! RNA polymerase III regulatory region DNA binding is_a: GO:0080084 ! 5S rDNA binding created_by: kchris creation_date: 2010-08-23T12:58:54Z [Term] id: GO:0001031 name: RNA polymerase III type 2 promoter DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a region of DNA that is a part of a type 2 promoter that controls transcription by RNA polymerase III. Type 2 promoters consist of an A box and a B box downstream of the transcription start site within the sequence within the sequence of the mature RNA. Type 2 promoters are found in many tRNA genes as well as in other small RNAs." [GOC:txnOH, PMID:12381659] is_a: GO:0001016 ! RNA polymerase III regulatory region DNA binding created_by: kchris creation_date: 2010-08-23T01:14:56Z [Term] id: GO:0001032 name: RNA polymerase III type 3 promoter DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a region of DNA that is a part of a type 3 promoter that controls transcription by RNA polymerase III. A type 3 Pol III promoter is composed of elements upstream of the transcription start site, including a TATA box. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae." [GOC:txnOH, PMID:12381659] is_a: GO:0001016 ! RNA polymerase III regulatory region DNA binding created_by: kchris creation_date: 2010-08-23T01:15:14Z [Term] id: GO:0001033 name: transcription factor activity, RNA polymerase III type 3 promoter TFIIIB recruiting namespace: molecular_function def: "The function of binding to a specific DNA sequence motif in a type 3 RNA polymerase III (Pol III) promoter in order to recruit TFIIIB to the promoter. For type 3 Pol III promoters, this requires SNAPc activity." [GOC:txnOH, PMID:12381659] comment: This represents TFIIIC. synonym: "RNA polymerase III type 3 promoter TFIIIB recruiting transcription factor activity" EXACT [] synonym: "SNAPc-type activity" RELATED [] synonym: "type 3 RNA polymerase III promoter recognition" EXACT [] is_a: GO:0001004 ! transcription factor activity, RNA polymerase III promoter sequence-specific binding, TFIIIB recruiting relationship: has_part GO:0001006 ! RNA polymerase III type 3 promoter sequence-specific DNA binding relationship: part_of GO:0001020 ! RNA polymerase III type 3 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-23T03:04:17Z [Term] id: GO:0001034 name: RNA polymerase III transcription factor activity, sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase III. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH, PMID:12381659] synonym: "sequence-specific DNA binding RNA polymerase III transcription factor activity" EXACT [] is_a: GO:0003700 ! transcription factor activity, sequence-specific DNA binding relationship: part_of GO:0006359 ! regulation of transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-08-23T03:41:48Z [Term] id: GO:0001035 name: transcription from RNA polymerase III type 3 promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by RNA polymerase III (RNAP III), originating at a type 3 RNAP III promoter. A type 3 RNAP III promoter is composed of elements upstream of the transcription start site, including a TATA box and the process of initiation is different than from other promoter types. The human U6 snRNA gene has a type 3 promoter. Type 3 Pol III promoters have not been observed in S. cerevisiae." [GOC:txnOH, PMID:12381659] synonym: "U6 snRNA transcription (mammalian)" NARROW [] is_a: GO:0006383 ! transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-08-23T04:17:41Z [Term] id: GO:0001036 name: transcription initiation from RNA polymerase III hybrid type promoter namespace: biological_process def: "A transcription initiation process on a hybrid type RNA polymerase III (Pol III) that results in RNA synthesis by Pol III (Pol III). A hybrid Pol III promoter contains both regulatory elements both upstream and downstream of the transcription initiation site. An example gene with such a promoter is the S. cerevisiae U6 gene." [GOC:txnOH, PMID:12381659] is_a: GO:0006384 ! transcription initiation from RNA polymerase III promoter relationship: part_of GO:0001041 ! transcription from a RNA polymerase III hybrid type promoter created_by: kchris creation_date: 2010-08-23T06:08:55Z [Term] id: GO:0001037 name: RNA polymerase III hybrid type promoter DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a region of DNA that is a part of a hybrid promoter that controls transcription by RNA polymerase III (Pol III). A hybrid Pol III promoter contains both regulatory elements both upstream and downstream of the transcription initiation site. An example gene with such a promoter is the S. cerevisiae U6 gene." [GOC:txnOH, PMID:12381659] is_a: GO:0001016 ! RNA polymerase III regulatory region DNA binding created_by: kchris creation_date: 2010-08-24T02:51:34Z [Term] id: GO:0001038 name: RNA polymerase III hybrid type promoter TFIIIB recruiting transcription factor activity namespace: molecular_function def: "Once recruited to an RNA polymerase III hybrid type promoter by sequence-specific DNA binding transcription factors, direct DNA binding, or a combination of both, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH, PMID:12381659] is_a: GO:0001004 ! transcription factor activity, RNA polymerase III promoter sequence-specific binding, TFIIIB recruiting relationship: has_part GO:0001039 ! RNA polymerase III hybrid type promoter sequence-specific DNA binding relationship: part_of GO:0001043 ! RNA polymerase III hybrid type promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-23T06:17:33Z [Term] id: GO:0001039 name: RNA polymerase III hybrid type promoter sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is a part of a hybrid type promoter that controls transcription by RNA polymerase III (Pol III). A hybrid Pol III promoter contains both regulatory elements both upstream and downstream of the transcription initiation site. An example gene with such a promoter is the S. cerevisiae U6 gene." [GOC:txnOH, PMID:12381659] is_a: GO:0000992 ! polymerase III regulatory region sequence-specific DNA binding is_a: GO:0001037 ! RNA polymerase III hybrid type promoter DNA binding created_by: kchris creation_date: 2010-08-23T06:21:24Z [Term] id: GO:0001040 name: RNA polymerase III hybrid type promoter TFIIIB-type transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III (Pol III) complex, typically composed of seventeen subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way. Once recruited to an RNA polymerase III hybrid type promoter, binds to DNA, recruits RNA polymerase III and facilitates the transition from the closed to the open complex." [GOC:txnOH, PMID:12381659] is_a: GO:0001026 ! TFIIIB-type transcription factor activity relationship: has_part GO:0001037 ! RNA polymerase III hybrid type promoter DNA binding relationship: part_of GO:0001043 ! RNA polymerase III hybrid type promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-23T06:28:23Z [Term] id: GO:0001041 name: transcription from a RNA polymerase III hybrid type promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by RNA polymerase III, originating at a hybrid type RNA polymerase III (RNAP III) promoter. A hybrid RNAP III promoter contains both regulatory elements both upstream and downstream of the transcription initiation site. An example gene with such a promoter is the S. cerevisiae U6 gene." [GOC:txnOH, PMID:12381659] synonym: "U2 snRNA transcription (S. cerevisiae)" NARROW [] is_a: GO:0006383 ! transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-08-24T02:11:52Z [Term] id: GO:0001042 name: RNA polymerase I core binding namespace: molecular_function def: "Interacting selectively and non-covalently with RNA polymerase I core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of seventeen subunits." [GOC:txnOH] is_a: GO:0043175 ! RNA polymerase core enzyme binding created_by: kchris creation_date: 2010-09-23T01:39:23Z [Term] id: GO:0001043 name: RNA polymerase III hybrid type promoter transcriptional preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on a hybrid type RNA polymerase III (Pol III) promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is the first step of transcription. Hybrid type promoters contain both gene-internal and upstream elements. An example of a hybrid promoter is the U6 snRNA gene." [GOC:txnOH, PMID:12381659] is_a: GO:0070898 ! RNA polymerase III transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-08-24T02:19:52Z [Term] id: GO:0001044 name: mitochondrial RNA polymerase regulatory region sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific sequence of DNA that controls the transcription of a region of DNA by mitochondrial RNA polymerase." [GOC:txnOH] comment: The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". is_a: GO:0000976 ! transcription regulatory region sequence-specific DNA binding is_a: GO:0001018 ! mitochondrial RNA polymerase regulatory region DNA binding created_by: kchris creation_date: 2010-08-25T04:11:49Z [Term] id: GO:0001045 name: mitochondrial RNA polymerase core promoter proximal region sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a mitochondrial RNA polymerase." [GOC:txnOH, PMID:20670382] is_a: GO:0000987 ! core promoter proximal region sequence-specific DNA binding is_a: GO:0001044 ! mitochondrial RNA polymerase regulatory region sequence-specific DNA binding created_by: kchris creation_date: 2010-08-25T04:13:36Z [Term] id: GO:0001046 name: core promoter sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region composed of the transcription start site and binding sites for the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH] comment: The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". is_a: GO:0000976 ! transcription regulatory region sequence-specific DNA binding is_a: GO:0001047 ! core promoter binding created_by: kchris creation_date: 2010-08-25T04:17:44Z [Term] id: GO:0001047 name: core promoter binding namespace: molecular_function def: "Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH] is_a: GO:0044212 ! transcription regulatory region DNA binding created_by: kchris creation_date: 2010-08-27T03:00:52Z [Term] id: GO:0001048 name: RNA polymerase IV core binding namespace: molecular_function def: "Interacting selectively and non-covalently with RNA polymerase IV core enzyme, a multisubunit eukaryotic nuclear RNA polymerase found in plants and involved in siRNA production." [GOC:txnOH, PMID:19110459] is_a: GO:0043175 ! RNA polymerase core enzyme binding created_by: kchris creation_date: 2010-09-23T01:41:03Z [Term] id: GO:0001049 name: RNA polymerase V core binding namespace: molecular_function def: "Interacting selectively and non-covalently with RNA polymerase V core enzyme, a multisubunit eukaryotic nuclear RNA polymerase found in plants and involved in production of noncoding transcripts at target loci for silencing." [GOC:txnOH, PMID:19110459] is_a: GO:0043175 ! RNA polymerase core enzyme binding created_by: kchris creation_date: 2010-09-23T01:41:08Z [Term] id: GO:0001050 name: single-subunit type RNA polymerase binding namespace: molecular_function def: "Interacting selectively and non-covalently with a single subunit RNA polymerase enzyme, which is composed of a single catalytic subunit similar to the RNA polymerase enzymes from phages T3, T7, and SP6." [GOC:txnOH, PMID:20701995] synonym: "SP6-type RNA polymerase binding" EXACT [] synonym: "T3-type RNA polymerase binding" EXACT [] synonym: "T3/T7 type RNA polymerase binding" EXACT [] synonym: "T7-type RNA polymerase binding" EXACT [] is_a: GO:0070063 ! RNA polymerase binding created_by: kchris creation_date: 2010-09-23T02:33:45Z [Term] id: GO:0001051 name: plastid single-subunit type RNA polymerase binding namespace: molecular_function def: "Interacting selectively and non-covalently with a single subunit plastid RNA polymerase enzyme, which is composed of a single catalytic subunit similar to the RNA polymerase enzymes from phages T3, T7, and SP6." [GOC:txnOH, PMID:20701995] is_a: GO:0001050 ! single-subunit type RNA polymerase binding created_by: kchris creation_date: 2010-09-23T02:42:57Z [Term] id: GO:0001052 name: plastid PEP RNA polymerase core enzyme binding namespace: molecular_function def: "Interacting selectively and non-covalently with the bacterial-type plastid PEP RNA polymerase core enzyme, typically consisting of two alpha, one beta, one beta prime, and one double prime subunit." [GOC:txnOH, PMID:20701995] is_a: GO:0001000 ! bacterial-type RNA polymerase core enzyme binding created_by: kchris creation_date: 2010-09-23T02:49:31Z [Term] id: GO:0001053 name: plastid sigma factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a plastid PEP core RNA polymerase to form a holoenzyme complex and also, while present in the holoenzyme, interacting with promoter sequences in order to confer sequence specific recognition of plastid PEP core promoter DNA sequence motifs." [GOC:txnOH, PMID:20701995] subset: gosubset_prok synonym: "sigma transcription factor" RELATED [] is_a: GO:0016987 ! sigma factor activity relationship: has_part GO:0001052 ! plastid PEP RNA polymerase core enzyme binding created_by: kchris creation_date: 2010-09-23T03:03:00Z [Term] id: GO:0001054 name: RNA polymerase I activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase I specific promoter to direct initiation and catalyzes DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase I promoter" EXACT [] is_a: GO:0003899 ! DNA-directed RNA polymerase activity intersection_of: GO:0003899 ! DNA-directed RNA polymerase activity intersection_of: part_of GO:0006360 ! transcription from RNA polymerase I promoter relationship: part_of GO:0006360 ! transcription from RNA polymerase I promoter created_by: kchris creation_date: 2010-09-23T03:36:11Z [Term] id: GO:0001055 name: RNA polymerase II activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase II promoter" EXACT [] is_a: GO:0003899 ! DNA-directed RNA polymerase activity intersection_of: GO:0003899 ! DNA-directed RNA polymerase activity intersection_of: part_of GO:0006366 ! transcription from RNA polymerase II promoter relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter created_by: kchris creation_date: 2010-09-23T03:44:23Z [Term] id: GO:0001056 name: RNA polymerase III activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase III specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase III promoter" EXACT [] is_a: GO:0003899 ! DNA-directed RNA polymerase activity intersection_of: GO:0003899 ! DNA-directed RNA polymerase activity intersection_of: part_of GO:0006383 ! transcription from RNA polymerase III promoter relationship: part_of GO:0006383 ! transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-09-23T03:44:47Z [Term] id: GO:0001057 name: RNA polymerase IV activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase IV specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase IV promoter" EXACT [] is_a: GO:0003899 ! DNA-directed RNA polymerase activity intersection_of: GO:0003899 ! DNA-directed RNA polymerase activity intersection_of: part_of GO:0001059 ! transcription from RNA polymerase IV promoter relationship: part_of GO:0001059 ! transcription from RNA polymerase IV promoter created_by: kchris creation_date: 2010-09-23T03:44:55Z [Term] id: GO:0001058 name: RNA polymerase V activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains an RNA polymerase V specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] synonym: "DNA-directed RNA polymerase activity involved in transcription from RNA polymerase V promoter" EXACT [] is_a: GO:0003899 ! DNA-directed RNA polymerase activity intersection_of: GO:0003899 ! DNA-directed RNA polymerase activity intersection_of: part_of GO:0001060 ! transcription from RNA polymerase V promoter relationship: part_of GO:0001060 ! transcription from RNA polymerase V promoter created_by: kchris creation_date: 2010-09-23T03:45:01Z [Term] id: GO:0001059 name: transcription from RNA polymerase IV promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by RNA polymerase IV (Pol III), originating at a Pol IV-specific promoter." [GOC:txnOH, PMID:19110459] synonym: "transcription from RNA pol IV promoter" EXACT [] is_a: GO:0006351 ! transcription, DNA-templated created_by: kchris creation_date: 2010-09-23T03:51:35Z [Term] id: GO:0001060 name: transcription from RNA polymerase V promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by RNA polymerase V (Pol III), originating at a Pol V-specific promoter." [GOC:txnOH, PMID:19110459] synonym: "transcription from RNA pol V promoter" EXACT [] is_a: GO:0006351 ! transcription, DNA-templated created_by: kchris creation_date: 2010-09-23T03:54:04Z [Term] id: GO:0001061 name: bacterial-type RNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a bacterial-type specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] is_a: GO:0003899 ! DNA-directed RNA polymerase activity relationship: part_of GO:0001121 ! transcription from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2010-10-19T03:36:01Z [Term] id: GO:0001062 name: plastid PEP-A RNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a plastid PEP-A RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH, PMID:20701995] is_a: GO:0001061 ! bacterial-type RNA polymerase activity relationship: part_of GO:0042793 ! transcription from plastid promoter created_by: kchris creation_date: 2010-10-19T03:38:49Z [Term] id: GO:0001063 name: plastid PEP-B RNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a plastid PEP-B RNA polymerase II specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH, PMID:20701995] is_a: GO:0001061 ! bacterial-type RNA polymerase activity relationship: part_of GO:0042793 ! transcription from plastid promoter created_by: kchris creation_date: 2010-10-19T03:46:46Z [Term] id: GO:0001064 name: single subunit type RNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a single-subunit-type RNA polymerase-specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] synonym: "T3/T7 type RNA polymerase activity" EXACT [] is_a: GO:0003899 ! DNA-directed RNA polymerase activity created_by: kchris creation_date: 2010-10-19T03:47:56Z [Term] id: GO:0001065 name: mitochondrial single subunit type RNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a single-subunit-type mitochondrial RNA polymerase-specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH] is_a: GO:0001064 ! single subunit type RNA polymerase activity relationship: part_of GO:0006390 ! transcription from mitochondrial promoter created_by: kchris creation_date: 2010-10-19T03:50:51Z [Term] id: GO:0001066 name: plastid single subunit type RNA polymerase activity namespace: molecular_function def: "Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template that contains a single subunit type plastid RNA polymerase specific promoter to direct initiation and catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'." [GOC:txnOH, PMID:20701995] is_a: GO:0001064 ! single subunit type RNA polymerase activity relationship: part_of GO:0042793 ! transcription from plastid promoter created_by: kchris creation_date: 2010-10-19T03:54:57Z [Term] id: GO:0001067 name: regulatory region nucleic acid binding namespace: molecular_function def: "Interacting selectively and non-covalently with a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair." [GOC:txnOH] is_a: GO:0003676 ! nucleic acid binding created_by: kchris creation_date: 2010-10-21T04:08:56Z [Term] id: GO:0001068 name: transcription regulatory region RNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a RNA region within the transcript that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon." [GOC:txnOH] is_a: GO:0001069 ! regulatory region RNA binding created_by: kchris creation_date: 2010-10-21T04:15:32Z [Term] id: GO:0001069 name: regulatory region RNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a RNA region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair." [GOC:txnOH] is_a: GO:0001067 ! regulatory region nucleic acid binding is_a: GO:0003723 ! RNA binding created_by: kchris creation_date: 2010-10-21T04:17:01Z [Term] id: GO:0001070 name: RNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH, PMID:8332211] synonym: "transcription factor activity" BROAD [] is_a: GO:0001071 ! nucleic acid binding transcription factor activity relationship: has_part GO:0001068 ! transcription regulatory region RNA binding created_by: kchris creation_date: 2010-10-21T04:19:17Z [Term] id: GO:0001071 name: nucleic acid binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a DNA or RNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. This term does not provide specificity with respect to the type of nucleic acid binding, e.g. RNA or DNA. Please use a child term that provides that specificity or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate subset: goslim_chembl subset: goslim_generic subset: goslim_yeast synonym: "transcription factor activity" BROAD [] is_a: GO:0003674 ! molecular_function relationship: has_part GO:0003676 ! nucleic acid binding relationship: part_of GO:2001141 ! regulation of RNA biosynthetic process created_by: kchris creation_date: 2010-10-21T04:37:54Z [Term] id: GO:0001072 name: transcription antitermination factor activity, RNA binding namespace: molecular_function def: "Binds to RNA, typically within the nascent RNA transcript, to promote readthrough of a transcription termination site and thus extending the length of the RNA transcript produced. Examples of antitermination factors which bind the nascent RNA include the lambda N protein and the HIV-1 tat protein." [GOC:txnOH, PMID:8332211] subset: gosubset_prok synonym: "RNA binding transcription antitermination factor activity" EXACT [] is_a: GO:0001070 ! RNA binding transcription factor activity relationship: part_of GO:0031564 ! transcription antitermination created_by: kchris creation_date: 2010-10-21T04:48:17Z [Term] id: GO:0001073 name: transcription antitermination factor activity, DNA binding namespace: molecular_function def: "Binds to DNA, typically within region of the promoter and transcribed region, to promote readthrough of a transcription termination site and thus extending the length of the RNA transcript produced. Examples of antitermination factors which bind DNA include the lambda Q protein." [GOC:txnOH, PMID:8332211] subset: gosubset_prok synonym: "DNA binding transcription antitermination factor activity" EXACT [] is_a: GO:0003700 ! transcription factor activity, sequence-specific DNA binding relationship: part_of GO:0031564 ! transcription antitermination created_by: kchris creation_date: 2010-10-21T05:18:52Z [Term] id: GO:0001074 name: transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding involved in preinitiation complex assembly namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to promote assembly of the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase II promoter." [GOC:txnOH] synonym: "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly" EXACT [] is_a: GO:0000982 ! transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-10-22T02:30:43Z [Term] id: GO:0001075 name: transcription factor activity, RNA polymerase II core promoter sequence-specific binding involved in preinitiation complex assembly namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in an RNA polymerase II (Pol II) core promoter, the region composed of the transcription start site and binding sites for transcription factors of the Pol II basal transcription machinery, in order to promote assembly of the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase II promoter." [GOC:txnOH] synonym: "RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity involved in preinitiation complex assembly" EXACT [] synonym: "sequence-specific core promoter binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly" EXACT [] is_a: GO:0000983 ! transcription factor activity, RNA polymerase II core promoter sequence-specific relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2010-10-22T02:35:51Z [Term] id: GO:0001076 name: transcription factor activity, RNA polymerase II transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] synonym: "RNA polymerase II transcription factor binding transcription factor activity" EXACT [] is_a: GO:0000989 ! transcription factor activity, transcription factor binding intersection_of: GO:0000988 ! transcription factor activity, protein binding intersection_of: has_part GO:0001085 ! RNA polymerase II transcription factor binding relationship: has_part GO:0001085 ! RNA polymerase II transcription factor binding relationship: part_of GO:0006357 ! regulation of transcription from RNA polymerase II promoter created_by: kchris creation_date: 2010-10-22T02:49:32Z [Term] id: GO:0001077 name: transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:txnOH] synonym: "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" EXACT [] is_a: GO:0000982 ! transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding is_a: GO:0001228 ! transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding created_by: kchris creation_date: 2010-10-26T03:40:43Z [Term] id: GO:0001078 name: transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:txnOH] synonym: "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" EXACT [] is_a: GO:0000982 ! transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding is_a: GO:0001227 ! transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding created_by: kchris creation_date: 2010-10-26T03:56:48Z [Term] id: GO:0001079 name: nitrogen catabolite regulation of transcription from RNA polymerase II promoter namespace: biological_process def: "A transcription regulation process in which the presence of one nitrogen source leads to the modulation of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources." [GOC:mah, GOC:txnOH, PMID:19104072] synonym: "regulation of transcription from RNA polymerase II promoter by nitrogen catabolites" EXACT [GOC:mah] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0090293 ! nitrogen catabolite regulation of transcription created_by: kchris creation_date: 2010-10-27T03:29:01Z [Term] id: GO:0001080 name: nitrogen catabolite activation of transcription from RNA polymerase II promoter namespace: biological_process def: "A transcription regulation process in which the presence of one nitrogen source leads to an increase in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources." [GOC:mah, GOC:txnOH, PMID:19104072] synonym: "positive regulation of transcription from RNA polymerase II promoter by nitrogen catabolites" EXACT [GOC:mah] is_a: GO:0001079 ! nitrogen catabolite regulation of transcription from RNA polymerase II promoter is_a: GO:0090294 ! nitrogen catabolite activation of transcription created_by: kchris creation_date: 2010-10-27T03:32:34Z [Term] id: GO:0001081 name: nitrogen catabolite repression of transcription from RNA polymerase II promoter namespace: biological_process def: "A transcription regulation process in which the presence of one nitrogen source leads to a decrease in the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources." [GOC:mah, GOC:txnOH, PMID:19104072] synonym: "negative regulation of transcription from RNA polymerase II promoter by nitrogen catabolites" EXACT [GOC:mah] is_a: GO:0001079 ! nitrogen catabolite regulation of transcription from RNA polymerase II promoter is_a: GO:0090295 ! nitrogen catabolite repression of transcription created_by: kchris creation_date: 2010-10-27T03:38:05Z [Term] id: GO:0001082 name: transcription factor activity, RNA polymerase I transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase I transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] synonym: "RNA polymerase I transcription factor binding transcription factor activity" EXACT [] is_a: GO:0000989 ! transcription factor activity, transcription factor binding relationship: has_part GO:0001179 ! RNA polymerase I transcription factor binding relationship: part_of GO:0006356 ! regulation of transcription from RNA polymerase I promoter created_by: kchris creation_date: 2010-10-27T04:03:47Z [Term] id: GO:0001083 name: transcription factor activity, RNA polymerase II basal transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] synonym: "RNA polymerase II basal transcription factor binding transcription factor activity" EXACT [] is_a: GO:0001076 ! transcription factor activity, RNA polymerase II transcription factor binding intersection_of: GO:0000988 ! transcription factor activity, protein binding intersection_of: has_part GO:0001091 ! RNA polymerase II basal transcription factor binding relationship: has_part GO:0001091 ! RNA polymerase II basal transcription factor binding created_by: kchris creation_date: 2010-10-27T04:12:55Z [Term] id: GO:0001084 name: transcription factor activity, TFIID-class binding namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH] synonym: "TFIID-class binding transcription factor activity" EXACT [] is_a: GO:0001083 ! transcription factor activity, RNA polymerase II basal transcription factor binding intersection_of: GO:0000988 ! transcription factor activity, protein binding intersection_of: has_part GO:0001094 ! TFIID-class transcription factor binding relationship: has_part GO:0001094 ! TFIID-class transcription factor binding created_by: kchris creation_date: 2010-10-27T04:15:22Z [Term] id: GO:0001085 name: RNA polymerase II transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II." [GOC:txnOH] is_a: GO:0008134 ! transcription factor binding created_by: kchris creation_date: 2010-10-28T02:08:59Z [Term] id: GO:0001086 name: transcription factor activity, TFIIA-class binding namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIA class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH] synonym: "TFIIA-class binding transcription factor activity" EXACT [] is_a: GO:0001083 ! transcription factor activity, RNA polymerase II basal transcription factor binding intersection_of: GO:0000988 ! transcription factor activity, protein binding intersection_of: has_part GO:0001092 ! TFIIA-class transcription factor binding relationship: has_part GO:0001092 ! TFIIA-class transcription factor binding created_by: kchris creation_date: 2010-10-28T02:14:59Z [Term] id: GO:0001087 name: transcription factor activity, TFIIB-class binding namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIB class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH] synonym: "TFIIB-class binding transcription factor activity" EXACT [] is_a: GO:0001083 ! transcription factor activity, RNA polymerase II basal transcription factor binding intersection_of: GO:0000988 ! transcription factor activity, protein binding intersection_of: has_part GO:0001093 ! TFIIB-class transcription factor binding relationship: has_part GO:0001093 ! TFIIB-class transcription factor binding created_by: kchris creation_date: 2010-10-28T02:18:00Z [Term] id: GO:0001088 name: transcription factor activity, TFIIE-class binding namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIE class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH] synonym: "TFIIE-class binding transcription factor activity" EXACT [] is_a: GO:0001083 ! transcription factor activity, RNA polymerase II basal transcription factor binding intersection_of: GO:0000988 ! transcription factor activity, protein binding intersection_of: has_part GO:0001095 ! TFIIE-class transcription factor binding relationship: has_part GO:0001095 ! TFIIE-class transcription factor binding created_by: kchris creation_date: 2010-10-28T02:25:22Z [Term] id: GO:0001089 name: transcription factor activity, TFIIF-class transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIF class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH] synonym: "TFIIF-class binding transcription factor activity" EXACT [] is_a: GO:0001083 ! transcription factor activity, RNA polymerase II basal transcription factor binding intersection_of: GO:0000988 ! transcription factor activity, protein binding intersection_of: has_part GO:0001096 ! TFIIF-class transcription factor binding relationship: has_part GO:0001096 ! TFIIF-class transcription factor binding created_by: kchris creation_date: 2010-10-28T02:27:12Z [Term] id: GO:0001090 name: transcription factor activity, TFIIH-class binding namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIH class in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH] synonym: "TFIIH-class binding transcription factor activity" EXACT [] is_a: GO:0001083 ! transcription factor activity, RNA polymerase II basal transcription factor binding intersection_of: GO:0000988 ! transcription factor activity, protein binding intersection_of: has_part GO:0001097 ! TFIIH-class transcription factor binding relationship: has_part GO:0001097 ! TFIIH-class transcription factor binding created_by: kchris creation_date: 2010-10-28T02:28:01Z [Term] id: GO:0001091 name: RNA polymerase II basal transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor, any of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor." [GOC:txnOH, PMID:16858867] is_a: GO:0001085 ! RNA polymerase II transcription factor binding is_a: GO:0001099 ! basal RNA polymerase II transcription machinery binding created_by: kchris creation_date: 2010-10-28T02:30:02Z [Term] id: GO:0001092 name: TFIIA-class transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIA class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor." [GOC:krc, PMID:16858867] is_a: GO:0001091 ! RNA polymerase II basal transcription factor binding created_by: kchris creation_date: 2010-10-28T02:37:19Z [Term] id: GO:0001093 name: TFIIB-class transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIB class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor." [GOC:krc, PMID:16858867] is_a: GO:0001091 ! RNA polymerase II basal transcription factor binding created_by: kchris creation_date: 2010-10-28T02:46:15Z [Term] id: GO:0001094 name: TFIID-class transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIID class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor." [GOC:krc, PMID:16858867] is_a: GO:0001091 ! RNA polymerase II basal transcription factor binding created_by: kchris creation_date: 2010-10-28T02:48:33Z [Term] id: GO:0001095 name: TFIIE-class transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIE class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor." [GOC:krc, PMID:16858867] is_a: GO:0001091 ! RNA polymerase II basal transcription factor binding created_by: kchris creation_date: 2010-10-28T02:49:20Z [Term] id: GO:0001096 name: TFIIF-class transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIF class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor." [GOC:krc, PMID:16858867] is_a: GO:0001091 ! RNA polymerase II basal transcription factor binding created_by: kchris creation_date: 2010-10-28T02:51:20Z [Term] id: GO:0001097 name: TFIIH-class transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II transcription factor of the TFIIH class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II and defined as a basal or general transcription factor." [GOC:krc, PMID:16858867] is_a: GO:0001091 ! RNA polymerase II basal transcription factor binding created_by: kchris creation_date: 2010-10-28T02:51:41Z [Term] id: GO:0001098 name: basal transcription machinery binding namespace: molecular_function def: "Interacting selectively and non-covalently with the basal transcription machinery which is composed of the RNA polymerase core enzyme and the basal transcription factor(s), the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase." [GOC:txnOH] comment: Note that the definition of basal, or general, transcription factors has typically been done at a small number of well characterized activator-independent promoters. At an activator-dependent promoter, one or more additional factors are generally required in addition to the basal factors. is_a: GO:0005515 ! protein binding created_by: kchris creation_date: 2010-11-24T12:50:49Z [Term] id: GO:0001099 name: basal RNA polymerase II transcription machinery binding namespace: molecular_function def: "Interacting selectively and non-covalently with the basal transcription machinery for RNA polymerase II which is composed of the RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits, and the basal RNA polymerase II transcription factors, the minimal set of factors required for formation of the preinitiation complex (PIC) by the RNA polymerase." [GOC:txnOH] comment: Note that the definition of basal, or general, transcription factors has typically been done at a small number of well characterized activator-independent promoters. At an activator-dependent promoter, one or more additional factors are generally required in addition to the basal factors. is_a: GO:0001098 ! basal transcription machinery binding created_by: kchris creation_date: 2010-11-24T12:54:33Z [Term] id: GO:0001100 name: negative regulation of exit from mitosis namespace: biological_process def: "Any process involved in the inhibition of progression from anaphase/telophase (high mitotic CDK activity) to G1 (low mitotic CDK activity)." [GOC:rn] synonym: "down regulation of exit from mitosis" EXACT [] synonym: "down-regulation of exit from mitosis" EXACT [] synonym: "downregulation of exit from mitosis" EXACT [] synonym: "inhibition of exit from mitosis" NARROW [] is_a: GO:0007096 ! regulation of exit from mitosis is_a: GO:0045839 ! negative regulation of mitotic nuclear division is_a: GO:1901991 ! negative regulation of mitotic cell cycle phase transition intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0010458 ! exit from mitosis relationship: negatively_regulates GO:0010458 ! exit from mitosis [Term] id: GO:0001101 name: response to acid chemical namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form." [GOC:go_curators, GOC:rn, http://en.wikipedia.org/wiki/Acid] comment: This term should be used to describe a response to a specific acid as a chemical. E.g., if an organism were responding to glutamate, then the response would be glutamate-specific; the organism is actually responding to the chemical structure of the anion portion of the dissociated acid. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. If annotating experiments where an acid is playing a role as a proton donor, please annotate to GO:0010447 'response to acidic pH' instead. subset: gocheck_do_not_manually_annotate synonym: "response to acid" BROAD [] synonym: "response to acid anion" RELATED [] synonym: "response to oxoanion" RELATED [] is_a: GO:0042221 ! response to chemical [Term] id: GO:0001102 name: RNA polymerase II activating transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription." [GOC:txnOH] is_a: GO:0001085 ! RNA polymerase II transcription factor binding is_a: GO:0033613 ! activating transcription factor binding created_by: kchris creation_date: 2010-11-24T02:17:08Z [Term] id: GO:0001103 name: RNA polymerase II repressing transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription." [GOC:txnOH] is_a: GO:0001085 ! RNA polymerase II transcription factor binding is_a: GO:0070491 ! repressing transcription factor binding created_by: kchris creation_date: 2010-11-24T02:34:55Z [Term] id: GO:0001104 name: RNA polymerase II transcription cofactor activity namespace: molecular_function alt_id: GO:0016455 def: "Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to modulate transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between regulatory transcription factors and the basal RNAP II transcription machinery." [GOC:txnOH, PMID:10213677, PMID:16858867] subset: gosubset_prok synonym: "RNA polymerase II transcription cofactor activity" EXACT [] synonym: "RNA polymerase II transcription mediator activity" RELATED [] synonym: "RNA polymerase II transcriptional co-regulator" EXACT [] synonym: "RNA polymerase II transcriptional cofactor activity" EXACT [] synonym: "thyroid receptor-associated protein" RELATED [] synonym: "TRAP protein" RELATED [] is_a: GO:0001076 ! transcription factor activity, RNA polymerase II transcription factor binding is_a: GO:0003712 ! transcription cofactor activity relationship: has_part GO:0001099 ! basal RNA polymerase II transcription machinery binding created_by: kchris creation_date: 2010-11-24T03:02:15Z [Term] id: GO:0001105 name: RNA polymerase II transcription coactivator activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery." [GOC:txnOH, PMID:10213677, PMID:16858867] comment: Note that some basal transcription factors are themselves considered to have coactivator activity, in that they mediate interactions between an activator and either RNA polymerase II itself or another basal transcription factor. subset: gosubset_prok synonym: "RNA polymerase II transcription co-activator activity" EXACT [] synonym: "RNA polymerase II transcription coactivator activity" EXACT [] is_a: GO:0001104 ! RNA polymerase II transcription cofactor activity is_a: GO:0001190 ! transcriptional activator activity, RNA polymerase II transcription factor binding is_a: GO:0003713 ! transcription coactivator activity relationship: has_part GO:0001102 ! RNA polymerase II activating transcription factor binding relationship: part_of GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: kchris creation_date: 2010-11-24T03:08:19Z [Term] id: GO:0001106 name: RNA polymerase II transcription corepressor activity namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II repressing transcription factor and also with the RNA polymerase II basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery." [GOC:txnOH, PMID:10213677, PMID:16858867] synonym: "RNA polymerase II transcription co-repressor activity" EXACT [] synonym: "RNA polymerase II transcription corepressor activity" EXACT [] is_a: GO:0001104 ! RNA polymerase II transcription cofactor activity is_a: GO:0001191 ! transcriptional repressor activity, RNA polymerase II transcription factor binding is_a: GO:0003714 ! transcription corepressor activity relationship: has_part GO:0001103 ! RNA polymerase II repressing transcription factor binding relationship: part_of GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: kchris creation_date: 2010-11-24T03:14:44Z [Term] id: GO:0001108 name: bacterial-type RNA polymerase holo enzyme binding namespace: molecular_function def: "Interacting selectively and non-covalently with the basal transcription machinery which is composed of a bacterial-type RNA polymerase core enzyme and a sigma factor, the minimal set of factors required for formation of the preinitiation complex (PIC) by a bacterial-type RNA polymerase." [GOC:txnOH] subset: gosubset_prok synonym: "basal bacterial-type RNA polymerase transcription machinery binding" EXACT [] is_a: GO:0001098 ! basal transcription machinery binding created_by: kchris creation_date: 2010-11-30T04:26:04Z [Term] id: GO:0001109 name: promoter clearance during DNA-templated transcription namespace: biological_process def: "Any process involved in the transition from the initiation to the elongation phases of transcription by a DNA-dependent RNA polymerase, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors." [GOC:txnOH, PMID:15020047, PMID:18280161] synonym: "promoter clearance during DNA-dependent transcription" EXACT [GOC:txnOH] synonym: "promoter escape" BROAD [] is_a: GO:0032774 ! RNA biosynthetic process relationship: has_part GO:0001119 ! protein-DNA-RNA complex remodeling relationship: part_of GO:0006351 ! transcription, DNA-templated created_by: kchris creation_date: 2010-12-01T02:13:09Z [Term] id: GO:0001110 name: promoter clearance from RNA polymerase III promoter namespace: biological_process def: "Any process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase III, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase." [GOC:txnOH] is_a: GO:0001109 ! promoter clearance during DNA-templated transcription relationship: part_of GO:0006383 ! transcription from RNA polymerase III promoter created_by: kchris creation_date: 2010-12-01T03:08:29Z [Term] id: GO:0001111 name: promoter clearance from RNA polymerase II promoter namespace: biological_process def: "Any process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase II, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors." [GOC:txnOH, PMID:15020047] synonym: "promoter escape from RNA polymerase II promoter" EXACT [] is_a: GO:0001109 ! promoter clearance during DNA-templated transcription relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter created_by: kchris creation_date: 2010-12-01T03:09:31Z [Term] id: GO:0001112 name: DNA-templated transcriptional open complex formation namespace: biological_process def: "Any process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble." [GOC:txnOH, PMID:15020047, PMID:18280161] synonym: "DNA-dependent transcriptional open complex formation" EXACT [GOC:txnOH] synonym: "promoter melting" BROAD [] is_a: GO:0001120 ! protein-DNA complex remodeling relationship: part_of GO:0006352 ! DNA-templated transcription, initiation created_by: kchris creation_date: 2010-12-02T02:15:04Z [Term] id: GO:0001113 name: transcriptional open complex formation at RNA polymerase II promoter namespace: biological_process def: "Any process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase II preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble." [GOC:txnOH, PMID:15020047, PMID:18280161] synonym: "RNA polymerase II promoter melting" EXACT [] is_a: GO:0001112 ! DNA-templated transcriptional open complex formation relationship: part_of GO:0006367 ! transcription initiation from RNA polymerase II promoter created_by: kchris creation_date: 2010-12-02T02:27:19Z [Term] id: GO:0001114 name: protein-DNA-RNA complex namespace: cellular_component def: "A macromolecular complex containing protein, DNA, and RNA molecules." [GOC:txnOH] is_a: GO:0032991 ! macromolecular complex created_by: kchris creation_date: 2010-12-03T02:09:38Z [Term] id: GO:0001115 name: protein-DNA-RNA complex subunit organization namespace: biological_process def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA-RNA complex." [GOC:txnOH] synonym: "protein-DNA-RNA complex subunit organisation" EXACT [GOC:mah] is_a: GO:0043933 ! macromolecular complex subunit organization created_by: kchris creation_date: 2010-12-03T04:00:02Z [Term] id: GO:0001116 name: protein-DNA-RNA complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex." [GOC:txnOH] is_a: GO:0001115 ! protein-DNA-RNA complex subunit organization is_a: GO:0034622 ! cellular macromolecular complex assembly created_by: kchris creation_date: 2010-12-03T04:01:38Z [Term] id: GO:0001117 name: protein-DNA-RNA complex disassembly namespace: biological_process def: "The disaggregation of a protein-DNA-RNA complex into its constituent components." [GOC:txnOH] is_a: GO:0001115 ! protein-DNA-RNA complex subunit organization is_a: GO:0032984 ! macromolecular complex disassembly created_by: kchris creation_date: 2010-12-03T04:04:07Z [Term] id: GO:0001118 name: transcription ternary complex disassembly namespace: biological_process def: "The disaggregation of a transcription ternary complex, composed of RNA polymerase, template DNA, and an RNA transcript, into its constituent components." [GOC:txnOH] synonym: "transcription protein-DNA-RNA complex disassembly" EXACT [] is_a: GO:0001117 ! protein-DNA-RNA complex disassembly relationship: part_of GO:0006353 ! DNA-templated transcription, termination created_by: kchris creation_date: 2010-12-03T04:11:34Z [Term] id: GO:0001119 name: protein-DNA-RNA complex remodeling namespace: biological_process def: "The acquisition, loss, or modification of macromolecules within a complex, resulting in the alteration of an existing complex." [GOC:txnOH] is_a: GO:0001115 ! protein-DNA-RNA complex subunit organization is_a: GO:0034367 ! macromolecular complex remodeling created_by: kchris creation_date: 2010-12-03T04:15:52Z [Term] id: GO:0001120 name: protein-DNA complex remodeling namespace: biological_process def: "The acquisition, loss, or modification of macromolecules within a complex, resulting in the alteration of an existing complex." [GOC:txnOH] is_a: GO:0034367 ! macromolecular complex remodeling is_a: GO:0071824 ! protein-DNA complex subunit organization created_by: kchris creation_date: 2010-12-03T04:17:15Z [Term] id: GO:0001121 name: transcription from bacterial-type RNA polymerase promoter namespace: biological_process def: "The synthesis of RNA from a DNA template by a bacterial-type RNA polymerase, originating at a bacterial-type promoter." [GOC:txnOH] is_a: GO:0006351 ! transcription, DNA-templated created_by: kchris creation_date: 2010-12-06T03:32:13Z [Term] id: GO:0001122 name: promoter clearance from bacterial-type RNA polymerase promoter namespace: biological_process def: "Any process involved in the transition from the initiation to the elongation phase of transcription by a bacterial-type RNA polymerase, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance generally involves dissociation of the sigma initiation factor." [GOC:txnOH, PMID:18280161] is_a: GO:0001109 ! promoter clearance during DNA-templated transcription relationship: part_of GO:0001121 ! transcription from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2010-12-06T03:38:10Z [Term] id: GO:0001123 name: transcription initiation from bacterial-type RNA polymerase promoter namespace: biological_process def: "Any process involved in the assembly of bacterial-type RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription." [GOC:txnOH, PMID:18280161] is_a: GO:0006352 ! DNA-templated transcription, initiation relationship: part_of GO:0001121 ! transcription from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2010-12-06T03:40:12Z [Term] id: GO:0001124 name: transcription elongation from bacterial-type RNA polymerase promoter namespace: biological_process def: "The extension of an RNA molecule after transcription initiation and promoter clearance at a bacterial-type RNA polymerase promoter by the addition of ribonucleotides catalyzed by a bacterial-type RNA polymerase." [GOC:txnOH, PMID:18280161] synonym: "RNA elongation from bacterial-type RNA polymerase promoter" EXACT [] is_a: GO:0006354 ! DNA-templated transcription, elongation relationship: part_of GO:0001121 ! transcription from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2010-12-06T03:46:27Z [Term] id: GO:0001125 name: transcription termination from bacterial-type RNA polymerase promoter namespace: biological_process def: "The process in which the synthesis of an RNA molecule by a bacterial-type RNA polymerase using a DNA template is completed." [GOC:txnOH, PMID:18280161] is_a: GO:0006353 ! DNA-templated transcription, termination relationship: part_of GO:0001121 ! transcription from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2010-12-06T03:47:43Z [Term] id: GO:0001126 name: bacterial-type RNA polymerase preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on a bacterial-type RNA polymerase promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase." [GOC:txnOH, PMID:18280161] synonym: "bacterial-type RNA polymerase transcription PIC biosynthesis" EXACT [] synonym: "bacterial-type RNA polymerase transcription PIC formation" EXACT [] synonym: "bacterial-type RNA polymerase transcriptional preinitiation complex formation" EXACT [] is_a: GO:0070897 ! DNA-templated transcriptional preinitiation complex assembly relationship: part_of GO:0001123 ! transcription initiation from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2010-12-06T03:54:45Z [Term] id: GO:0001127 name: transcriptional open complex formation at bacterial-type RNA polymerase promoter namespace: biological_process def: "Any process involved in the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase II preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble." [GOC:txnOH, PMID:18280161] is_a: GO:0001112 ! DNA-templated transcriptional open complex formation relationship: part_of GO:0001123 ! transcription initiation from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2010-12-06T04:04:16Z [Term] id: GO:0001128 name: RNA polymerase II transcription coactivator activity involved in preinitiation complex assembly namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or stability of the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC). Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery." [GOC:txnOH, PMID:16858867] comment: Note that some basal transcription factors are themselves considered to have coactivator activity, in that they mediate interactions between an activator and either RNA polymerase II itself or another basal transcription factor. synonym: "RNA polymerase II transcription coactivator activity involved in preinitiation complex assembly" EXACT [] is_a: GO:0001105 ! RNA polymerase II transcription coactivator activity relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-20T02:13:36Z [Term] id: GO:0001129 name: RNA polymerase II transcription factor activity, TBP-class protein binding, involved in preinitiation complex assembly namespace: molecular_function def: "Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), to facilitate the aggregation, arrangement and bonding together of proteins on RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase." [GOC:txnOH, PMID:16858867] comment: For example, both TFIIA as well as TFIIB interact with TBP bound to DNA to stabilize formation of the preinitiation complex. synonym: "TATA-binding protein binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly" NARROW [] synonym: "TBP-class protein binding RNA polymerase II transcription factor activity involved in preinitiation complex assembly" EXACT [] is_a: GO:0001132 ! RNA polymerase II transcription factor activity, TBP-class protein binding relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-20T02:53:35Z [Term] id: GO:0001130 name: bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] synonym: "sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity" EXACT [] is_a: GO:0003700 ! transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0000984 ! bacterial-type RNA polymerase regulatory region sequence-specific DNA binding created_by: kchris creation_date: 2011-01-26T10:36:02Z [Term] id: GO:0001131 name: transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] synonym: "bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity" EXACT [] is_a: GO:0001130 ! bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0000986 ! bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding created_by: kchris creation_date: 2011-01-26T10:50:37Z [Term] id: GO:0001132 name: RNA polymerase II transcription factor activity, TBP-class protein binding namespace: molecular_function def: "Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs), in order to modulate transcription. The transcription factor may or may not also interact selectively with DNA as well." [GOC:txnOH, PMID:16858867] synonym: "TATA-binding protein binding RNA polymerase II transcription factor activity" NARROW [] synonym: "TBP-class protein binding RNA polymerase II transcription factor activity" EXACT [] synonym: "TRF protein binding RNA polymerase II transcription factor activity" NARROW [] is_a: GO:0001083 ! transcription factor activity, RNA polymerase II basal transcription factor binding relationship: has_part GO:0017025 ! TBP-class protein binding created_by: kchris creation_date: 2011-01-20T04:15:44Z [Term] id: GO:0001133 name: RNA polymerase II transcription factor activity, sequence-specific transcription regulatory region DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA by RNA polymerase II and recruiting another transcription factor to the DNA in order to modulate transcription by RNAP II." [GOC:txnOH, PMID:16858867] synonym: "sequence-specific transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity" EXACT [] is_a: GO:0001010 ! transcription factor activity, sequence-specific DNA binding transcription factor recruiting created_by: kchris creation_date: 2011-01-20T04:40:20Z [Term] id: GO:0001134 name: transcription factor activity, transcription factor recruiting namespace: molecular_function def: "Interacting selectively and non-covalently with a specific transcription factor, which may be a single protein or a complex, and with another protein, macromolecule, or complex, recruiting that specific transcription factor to the transcription machinery complex and thus permitting those molecules to function in a coordinated way, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH, PMID:16858867] synonym: "transcription factor recruiting transcription factor activity" EXACT [] is_a: GO:0000989 ! transcription factor activity, transcription factor binding created_by: kchris creation_date: 2011-01-20T04:57:59Z [Term] id: GO:0001135 name: transcription factor activity, RNA polymerase II transcription factor recruiting namespace: molecular_function def: "The function of binding to an RNA polymerase II (RNAP II) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP II." [GOC:txnOH, PMID:16858867] synonym: "RNA polymerase II transcription factor recruiting transcription factor activity" EXACT [] is_a: GO:0001076 ! transcription factor activity, RNA polymerase II transcription factor binding is_a: GO:0001134 ! transcription factor activity, transcription factor recruiting created_by: kchris creation_date: 2011-01-20T05:13:12Z [Term] id: GO:0001136 name: transcription factor activity, TFIIE-class transcription factor recruiting namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II (RNAP II) transcription factor of the TFIIE-class in order to recruit it to the RNAP II preinitiation complex (PIC) in order to modulate transcription by RNAP II." [GOC:txnOH, PMID:16858867] synonym: "TFIIE-class transcription factor recruiting transcription factor activity" EXACT [] is_a: GO:0001088 ! transcription factor activity, TFIIE-class binding is_a: GO:0001135 ! transcription factor activity, RNA polymerase II transcription factor recruiting relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-20T05:24:07Z [Term] id: GO:0001137 name: transcription factor activity, TFIIF-class transcription factor recruiting namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II (RNAP II) transcription factor of the TFIIF-class in order to recruit it to the RNAP II preinitiation complex (PIC) in order to modulate transcription by RNAP II." [GOC:txnOH, PMID:16858867] synonym: "TFIIF-class transcription factor recruiting transcription factor activity" EXACT [] is_a: GO:0001089 ! transcription factor activity, TFIIF-class transcription factor binding is_a: GO:0001135 ! transcription factor activity, RNA polymerase II transcription factor recruiting relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-20T05:35:02Z [Term] id: GO:0001138 name: transcription factor activity, TFIIH-class transcription factor recruiting namespace: molecular_function def: "Interacting selectively and non-covalently with a basal RNA polymerase II (RNAP II) transcription factor of the TFIIH-class in order to recruit it to the RNAP II preinitiation complex (PIC) in order to modulate transcription by RNAP II." [GOC:txnOH, PMID:16858867] synonym: "TFIIH-class transcription factor recruiting transcription factor activity" EXACT [] is_a: GO:0001090 ! transcription factor activity, TFIIH-class binding is_a: GO:0001135 ! transcription factor activity, RNA polymerase II transcription factor recruiting relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-20T05:39:10Z [Term] id: GO:0001139 name: transcription factor activity, core RNA polymerase II recruiting namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II (Pol II) complex, typically composed of twelve subunits, and with another protein, macromolecule, or complex, permitting those molecules to function in a coordinated way in order to facilitate the aggregation, arrangement and bonding together of proteins on an RNA polymerase II promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription by RNA polymerase." [GOC:txnOH, PMID:16858867] synonym: "core RNA polymerase II recruiting transcription factor activity" EXACT [] is_a: GO:0000991 ! transcription factor activity, core RNA polymerase II binding relationship: part_of GO:0051123 ! RNA polymerase II transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-20T05:55:01Z [Term] id: GO:0001140 name: transcriptional activator activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH, PMID:20491932, PMID:20629756] synonym: "bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" EXACT [] is_a: GO:0001131 ! transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding is_a: GO:0001216 ! bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding relationship: part_of GO:0001121 ! transcription from bacterial-type RNA polymerase promoter relationship: part_of GO:0045893 ! positive regulation of transcription, DNA-templated created_by: kchris creation_date: 2011-01-26T03:09:27Z [Term] id: GO:0001141 name: transcriptional repressor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to stop, prevent, or reduce the frequency, rate or extent of transcription from a bacterial-type RNA polymerase promoter." [GOC:txnOH, PMID:20491932, PMID:20629756] synonym: "bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" EXACT [] is_a: GO:0001131 ! transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding is_a: GO:0001217 ! bacterial-type RNA polymerase transcriptional repressor activity, sequence-specific DNA binding created_by: kchris creation_date: 2011-01-26T03:15:45Z [Term] id: GO:0001142 name: mitochondrial RNA polymerase transcription factor activity, sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by mitochondrial RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH, PMID:18391175] synonym: "sequence-specific DNA binding mitochondrial RNA polymerase transcription factor activity" EXACT [] is_a: GO:0003700 ! transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0001044 ! mitochondrial RNA polymerase regulatory region sequence-specific DNA binding relationship: part_of GO:0006390 ! transcription from mitochondrial promoter created_by: kchris creation_date: 2011-01-27T01:55:21Z [Term] id: GO:0001143 name: mitochondrial RNA polymerase core promoter sequence-specific DNA binding transcription factor activity namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence that is part of the core promoter for mitochondrial RNA polymerase in order to modulate transcription by mitochondrial RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH, PMID:18391175] is_a: GO:0001142 ! mitochondrial RNA polymerase transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0000997 ! mitochondrial RNA polymerase core promoter sequence-specific DNA binding created_by: kchris creation_date: 2011-01-27T02:08:44Z [Term] id: GO:0001144 name: transcription factor activity, mitochondrial RNA polymerase core promoter proximal region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a mitochondrial RNA polymerase in order to modulate transcription by mitochondrial RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH, PMID:18391175] synonym: "mitochondrial RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity" EXACT [] is_a: GO:0001142 ! mitochondrial RNA polymerase transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0001045 ! mitochondrial RNA polymerase core promoter proximal region sequence-specific DNA binding created_by: kchris creation_date: 2011-01-27T02:11:59Z [Term] id: GO:0001145 name: mitochondrial RNA polymerase termination site sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is a terminator for mitochondrial RNA polymerase." [GOC:txnOH, PMID:18391175] is_a: GO:0001044 ! mitochondrial RNA polymerase regulatory region sequence-specific DNA binding is_a: GO:0001147 ! transcription termination site sequence-specific DNA binding created_by: kchris creation_date: 2011-01-27T02:34:53Z [Term] id: GO:0001146 name: transcription factor activity, mitochondrial RNA polymerase terminator site sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is a terminator for mitochondrial RNA polymerase in order to promote transcription termination by mitochondrial RNA polymerase." [GOC:txnOH, PMID:18391175] synonym: "mitochondrial RNA polymerase terminator site sequence-specific DNA binding transcription factor activity" EXACT [] is_a: GO:0001142 ! mitochondrial RNA polymerase transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0001145 ! mitochondrial RNA polymerase termination site sequence-specific DNA binding relationship: part_of GO:0006393 ! termination of mitochondrial transcription created_by: kchris creation_date: 2011-01-27T02:42:23Z [Term] id: GO:0001147 name: transcription termination site sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that promotes termination by RNA polymerase. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH, PMID:18280161, PMID:18391175] comment: Transcription termination sites can be recognized by the RNA polymerase (RNAP) itself or by another protein which interacts with the RNAP to promote transcription termination. Note that not all genes have a specific sequence that functions as a termination site; for most mRNAs transcribed by RNAP II termination is not mediated by a specific termination sequence, but is coupled to polyadenylation. is_a: GO:0000976 ! transcription regulatory region sequence-specific DNA binding is_a: GO:0001160 ! transcription termination site DNA binding created_by: kchris creation_date: 2011-01-27T02:48:26Z [Term] id: GO:0001148 name: bacterial-type RNA polymerase termination site sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is a terminator for bacterial-type RNA polymerase." [GOC:txnOH, PMID:18280161] is_a: GO:0000984 ! bacterial-type RNA polymerase regulatory region sequence-specific DNA binding is_a: GO:0001147 ! transcription termination site sequence-specific DNA binding created_by: kchris creation_date: 2011-01-27T03:04:07Z [Term] id: GO:0001149 name: transcription factor activity, bacterial-type RNA polymerase termination site sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is a termination site for bacterial-type RNA polymerase in order to promote transcription termination by bacterial-type RNA polymerase." [GOC:txnOH, PMID:18280161] synonym: "bacterial-type RNA polymerase termination site sequence-specific DNA binding transcription factor activity" EXACT [] is_a: GO:0001130 ! bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0001148 ! bacterial-type RNA polymerase termination site sequence-specific DNA binding created_by: kchris creation_date: 2011-01-27T03:08:41Z [Term] id: GO:0001150 name: bacterial-type RNA polymerase enhancer sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is an enhancer region that helps activate transcription of a gene or operon by a bacterial-type RNA polymerase. Enhancers for sigma-54 holoenzymes are typically located 80 to 150 base pairs upstream from the transcription start site, although they can be further away or may be downstream of the promoter. Some transcription units dependent on sigma-70 holoenzymes may also include enhancer sequences." [GOC:txnOH, PMID:11282468, PMID:20629756] comment: Note that the phrase "upstream activating sequence", or UAS is often used in S. cerevisiae literature to refer to regulatory sequences that occur in the region upstream and proximal to the core promoter. In contrast, in bacteria such as E. coli, the phrase "upstream activating sequence", or UAS is a synonym for "enhancer". synonym: "bacterial-type RNA polymerase upstream activating sequence (UAS) sequence-specific DNA binding" EXACT [] is_a: GO:0000984 ! bacterial-type RNA polymerase regulatory region sequence-specific DNA binding is_a: GO:0001158 ! enhancer sequence-specific DNA binding created_by: kchris creation_date: 2011-01-27T03:42:53Z [Term] id: GO:0001151 name: transcription factor activity, bacterial-type RNA polymerase transcription enhancer sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is a bacterial-type enhancer region in order to activate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex. Enhancers for sigma-54 holoenzymes are typically located 80 to 150 base pairs upstream from the transcription start site. Some transcription units dependent on sigma-70 holoenzymes may also include enhancer sequences." [GOC:txnOH, PMID:20629756] synonym: "bacterial-type RNA polymerase transcription enhancer sequence-specific DNA binding transcription factor activity" EXACT [] is_a: GO:0001130 ! bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0001150 ! bacterial-type RNA polymerase enhancer sequence-specific DNA binding created_by: kchris creation_date: 2011-01-27T03:47:54Z [Term] id: GO:0001152 name: transcription factor activity, RNA polymerase III type 1 promoter sequence-specific binding, TFIIIC recruiting namespace: molecular_function def: "The function of binding to a specific DNA sequence motif in a type 1 RNA polymerase III (Pol III) promoter in order to recruit the transcription factor TFIIIC to the promoter." [GOC:txnOH, PMID:12381659] comment: This represents TFIIIA. synonym: "RNA polymerase III type 1 promoter sequence-specific DNA binding TFIIIC recruiting transcription factor activity" EXACT [] synonym: "TFIIIA activity" RELATED [] synonym: "type 1 RNA polymerase III promoter recognition" EXACT [] is_a: GO:0001010 ! transcription factor activity, sequence-specific DNA binding transcription factor recruiting is_a: GO:0001153 ! transcription factor activity, RNA polymerase III transcription factor recruiting relationship: has_part GO:0001002 ! RNA polymerase III type 1 promoter sequence-specific DNA binding relationship: has_part GO:0001156 ! TFIIIC-class transcription factor binding relationship: part_of GO:0000999 ! RNA polymerase III type 1 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-27T04:18:21Z [Term] id: GO:0001153 name: transcription factor activity, RNA polymerase III transcription factor recruiting namespace: molecular_function def: "The function of binding to an RNA polymerase III (RNAP III) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP III." [GOC:txnOH] synonym: "RNA polymerase III transcription factor recruiting transcription factor activity" EXACT [] is_a: GO:0001007 ! transcription factor activity, RNA polymerase III transcription factor binding is_a: GO:0001134 ! transcription factor activity, transcription factor recruiting created_by: kchris creation_date: 2011-01-27T04:45:37Z [Term] id: GO:0001154 name: TFIIIB-class transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III transcription factor of the TFIIIB class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase III." [GOC:txnOH, PMID:12381659] is_a: GO:0001025 ! RNA polymerase III transcription factor binding created_by: kchris creation_date: 2011-01-27T04:53:50Z [Term] id: GO:0001155 name: TFIIIA-class transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III transcription factor of the TFIIIA class, one of the factors involved in formation of the preinitiation complex (PIC) at type 1 promoters (5S genes) by RNA polymerase III." [GOC:txnOH, PMID:12381659] is_a: GO:0001025 ! RNA polymerase III transcription factor binding created_by: kchris creation_date: 2011-01-27T04:57:49Z [Term] id: GO:0001156 name: TFIIIC-class transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase III transcription factor of the TFIIIC class, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase III." [GOC:txnOH, PMID:12381659] is_a: GO:0001025 ! RNA polymerase III transcription factor binding created_by: kchris creation_date: 2011-01-27T05:02:22Z [Term] id: GO:0001157 name: transcription factor activity, RNA polymerase III type 1 promoter TFIIIB namespace: molecular_function def: "The function of binding to a specific DNA sequence motif in a type 1 RNA polymerase III (Pol III) promoter in order to recruit the Pol III recruiting factor TFIIIB to the promoter. For type 1 Pol III promoters, this requires both TFIIIA and TFIIIC." [GOC:txnOH, PMID:12381659] comment: This represents TFIIIA. synonym: "RNA polymerase III type 1 promoter TFIIIB recruiting transcription factor activity" EXACT [] synonym: "TFIIIC-type activity" RELATED [] is_a: GO:0001153 ! transcription factor activity, RNA polymerase III transcription factor recruiting relationship: has_part GO:0001154 ! TFIIIB-class transcription factor binding relationship: has_part GO:0001155 ! TFIIIA-class transcription factor binding relationship: part_of GO:0000999 ! RNA polymerase III type 1 promoter transcriptional preinitiation complex assembly created_by: kchris creation_date: 2011-01-27T05:27:28Z [Term] id: GO:0001158 name: enhancer sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter." [GOC:txnOH] is_a: GO:0000976 ! transcription regulatory region sequence-specific DNA binding is_a: GO:0035326 ! enhancer binding created_by: kchris creation_date: 2011-01-28T03:29:40Z [Term] id: GO:0001159 name: core promoter proximal region DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a region of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH] is_a: GO:0044212 ! transcription regulatory region DNA binding created_by: kchris creation_date: 2011-01-28T03:37:52Z [Term] id: GO:0001160 name: transcription termination site DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a region of DNA that promotes termination by RNA polymerase. The transcribed region might be described as a gene, cistron, or operon." [GOC:txnOH] is_a: GO:0044212 ! transcription regulatory region DNA binding created_by: kchris creation_date: 2011-01-28T03:39:44Z [Term] id: GO:0001161 name: intronic transcription regulatory region sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with an intronic DNA sequence that regulates the transcription of the transcript it is contained within." [GOC:txnOH] is_a: GO:0044213 ! intronic transcription regulatory region DNA binding created_by: kchris creation_date: 2011-01-28T03:44:02Z [Term] id: GO:0001162 name: RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II intronic DNA sequence that regulates the transcription of the transcript it is contained within." [GOC:txnOH] is_a: GO:0000977 ! RNA polymerase II regulatory region sequence-specific DNA binding is_a: GO:0001161 ! intronic transcription regulatory region sequence-specific DNA binding created_by: kchris creation_date: 2011-01-28T03:46:19Z [Term] id: GO:0001163 name: RNA polymerase I regulatory region sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase I." [GOC:txnOH] is_a: GO:0001013 ! RNA polymerase I regulatory region DNA binding created_by: kchris creation_date: 2011-01-31T04:12:06Z [Term] id: GO:0001164 name: RNA polymerase I CORE element sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery. This site is often referred to as the CORE element. In mammalian cells, the CORE element functions in conjunction with the Upstream Control Element (UCE), while in fungi, protozoa, and plants, the CORE element functions without a UCE." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] synonym: "RNA polymerase I core element sequence-specific DNA binding" EXACT [] synonym: "RNA polymerase I core promoter sequence-specific DNA binding" EXACT [] is_a: GO:0001046 ! core promoter sequence-specific DNA binding is_a: GO:0001163 ! RNA polymerase I regulatory region sequence-specific DNA binding created_by: kchris creation_date: 2011-01-31T04:47:48Z [Term] id: GO:0001165 name: RNA polymerase I upstream control element sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with the upstream control element (UCE, or alternately referred to as the upstream element), a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase I." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] synonym: "RNA polymerase I upstream element sequence-specific DNA binding" RELATED [] is_a: GO:0000987 ! core promoter proximal region sequence-specific DNA binding is_a: GO:0001163 ! RNA polymerase I regulatory region sequence-specific DNA binding created_by: kchris creation_date: 2011-01-31T05:09:10Z [Term] id: GO:0001166 name: RNA polymerase I enhancer sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a RNA polymerase I (Pol I) enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] is_a: GO:0001158 ! enhancer sequence-specific DNA binding is_a: GO:0001163 ! RNA polymerase I regulatory region sequence-specific DNA binding created_by: kchris creation_date: 2011-01-31T05:29:59Z [Term] id: GO:0001167 name: RNA polymerase I transcription factor activity, sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase I. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:txnOH] synonym: "sequence-specific DNA binding RNA polymerase I transcription factor activity" EXACT [] is_a: GO:0003700 ! transcription factor activity, sequence-specific DNA binding relationship: part_of GO:0006356 ! regulation of transcription from RNA polymerase I promoter created_by: kchris creation_date: 2011-02-03T04:07:46Z [Term] id: GO:0001168 name: transcription factor activity, RNA polymerase I upstream control element sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with the upstream control element (UCE, or alternately referred to as the upstream element, UE), a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase I in order to modulate transcription by RNA polymerase I." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] synonym: "RNA polymerase I upstream control element sequence-specific DNA binding transcription factor activity" EXACT [] is_a: GO:0001167 ! RNA polymerase I transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0001165 ! RNA polymerase I upstream control element sequence-specific DNA binding created_by: kchris creation_date: 2011-02-03T04:10:23Z [Term] id: GO:0001169 name: transcription factor activity, RNA polymerase I CORE element sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with CORE element, a regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery in order to modulate transcription by RNA polymerase I." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] synonym: "RNA polymerase I CORE element sequence-specific DNA binding transcription factor activity" EXACT [] synonym: "RNA polymerase I core promoter sequence-specific DNA binding transcription factor" EXACT [] is_a: GO:0001167 ! RNA polymerase I transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0001164 ! RNA polymerase I CORE element sequence-specific DNA binding created_by: kchris creation_date: 2011-02-03T04:10:42Z [Term] id: GO:0001170 name: transcription factor activity, RNA polymerase I enhancer sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a RNA polymerase I (Pol I) enhancer in order to modulate transcription by RNA polymerase I." [GOC:txnOH, PMID:12865296, PMID:14969726, PMID:8057832] synonym: "RNA polymerase I enhancer sequence-specific DNA binding transcription factor activity" EXACT [] is_a: GO:0001167 ! RNA polymerase I transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0001166 ! RNA polymerase I enhancer sequence-specific DNA binding created_by: kchris creation_date: 2011-02-03T04:10:59Z [Term] id: GO:0001171 name: reverse transcription namespace: biological_process def: "A DNA synthesis process that uses RNA as the initial template for synthesis of DNA, but which also includes an RNase activity to remove the RNA strand of an RNA-DNA heteroduplex produced by the RNA-dependent synthesis step and use of the initial DNA strand as a template for DNA synthesis." [GOC:txnOH, PMID:20358252] xref: Wikipedia:Reverse_transcription is_a: GO:0006278 ! RNA-dependent DNA biosynthetic process relationship: has_part GO:0003964 ! RNA-directed DNA polymerase activity relationship: has_part GO:0004533 ! exoribonuclease H activity created_by: kchris creation_date: 2011-03-14T03:51:08Z [Term] id: GO:0001172 name: transcription, RNA-templated namespace: biological_process def: "The cellular synthesis of RNA on a template of RNA." [GOC:txnOH] subset: gosubset_prok synonym: "transcription, RNA-dependent" EXACT [GOC:txnOH] is_a: GO:0097659 ! nucleic acid-templated transcription created_by: kchris creation_date: 2011-03-14T03:54:46Z [Term] id: GO:0001173 name: DNA-templated transcriptional start site selection namespace: biological_process def: "Any process involved in the selection of the specific location within the template strand of a DNA-dependent RNA polymerase promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH, PMID:16826228, PMID:18846104] synonym: "DNA-dependent transcriptional start site selection" EXACT [GOC:txnOH] is_a: GO:0032774 ! RNA biosynthetic process relationship: part_of GO:0006352 ! DNA-templated transcription, initiation created_by: kchris creation_date: 2011-06-20T12:44:11Z [Term] id: GO:0001174 name: transcriptional start site selection at RNA polymerase II promoter namespace: biological_process def: "Any process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH, PMID:16826228, PMID:18846104] is_a: GO:0001173 ! DNA-templated transcriptional start site selection relationship: part_of GO:0006367 ! transcription initiation from RNA polymerase II promoter created_by: kchris creation_date: 2011-06-20T01:35:28Z [Term] id: GO:0001175 name: transcriptional start site selection at RNA polymerase III promoter namespace: biological_process def: "Any process involved in the selection of the specific location within the template strand of an RNA polymerase III promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH] is_a: GO:0001173 ! DNA-templated transcriptional start site selection relationship: part_of GO:0006384 ! transcription initiation from RNA polymerase III promoter created_by: kchris creation_date: 2011-06-20T01:47:38Z [Term] id: GO:0001176 name: transcriptional start site selection at bacterial-type RNA polymerase promoter namespace: biological_process def: "Any process involved in the selection of the specific location within the template strand of a bacterial-type RNA polymerase promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH] is_a: GO:0001173 ! DNA-templated transcriptional start site selection relationship: part_of GO:0001123 ! transcription initiation from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2011-06-20T01:48:56Z [Term] id: GO:0001177 name: regulation of transcriptional open complex formation at RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the rate, frequency or extent of a process involved the melting of the DNA hybrid of the core promoter region within the transcriptional closed complex of an RNA polymerase II preinitiation complex (PIC) to produce an open complex where the DNA duplex around the transcription initiation site is unwound to form the transcription bubble." [GOC:txnOH] is_a: GO:0060260 ! regulation of transcription initiation from RNA polymerase II promoter intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001113 ! transcriptional open complex formation at RNA polymerase II promoter relationship: regulates GO:0001113 ! transcriptional open complex formation at RNA polymerase II promoter created_by: kchris creation_date: 2011-06-20T02:01:18Z [Term] id: GO:0001178 name: regulation of transcriptional start site selection at RNA polymerase II promoter namespace: biological_process def: "Any process that modulates the rate, frequency or extent of a process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript." [GOC:txnOH] is_a: GO:0060260 ! regulation of transcription initiation from RNA polymerase II promoter intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001174 ! transcriptional start site selection at RNA polymerase II promoter relationship: regulates GO:0001174 ! transcriptional start site selection at RNA polymerase II promoter created_by: kchris creation_date: 2011-06-20T02:06:00Z [Term] id: GO:0001179 name: RNA polymerase I transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase I transcription factor, any protein required to initiate or regulate transcription by RNA polymerase I." [GOC:txnOH] is_a: GO:0008134 ! transcription factor binding created_by: kchris creation_date: 2011-08-12T03:03:03Z [Term] id: GO:0001180 name: transcription initiation from RNA polymerase I promoter for nuclear large rRNA transcript namespace: biological_process def: "Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an polymerase I promoter for the nuclear large ribosomal RNA (rRNA) transcript, resulting in the subsequent synthesis of rRNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription." [GOC:txnOH] is_a: GO:0006361 ! transcription initiation from RNA polymerase I promoter relationship: part_of GO:0042790 ! transcription of nuclear large rRNA transcript from RNA polymerase I promoter created_by: kchris creation_date: 2011-08-15T03:45:49Z [Term] id: GO:0001181 name: transcription factor activity, core RNA polymerase I binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase I (RNAP I) complex, typically composed of fourteen subunits, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] synonym: "core RNA polymerase I binding transcription factor activity" EXACT [] is_a: GO:0000990 ! transcription factor activity, core RNA polymerase binding intersection_of: GO:0003674 ! molecular_function intersection_of: has_part GO:0001042 ! RNA polymerase I core binding intersection_of: part_of GO:0006356 ! regulation of transcription from RNA polymerase I promoter relationship: has_part GO:0001042 ! RNA polymerase I core binding relationship: part_of GO:0006356 ! regulation of transcription from RNA polymerase I promoter created_by: kchris creation_date: 2011-08-12T04:13:30Z [Term] id: GO:0001182 name: promoter clearance from RNA polymerase I promoter namespace: biological_process def: "Any process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase I, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors." [GOC:txnOH] is_a: GO:0001109 ! promoter clearance during DNA-templated transcription relationship: part_of GO:0006360 ! transcription from RNA polymerase I promoter created_by: kchris creation_date: 2011-08-15T03:49:28Z [Term] id: GO:0001183 name: transcription elongation from RNA polymerase I promoter for nuclear large rRNA transcript namespace: biological_process def: "The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I promoter for the nuclear large ribosomal RNA (rRNA) transcript by the addition of ribonucleotides catalyzed by RNA polymerase I." [GOC:txnOH] is_a: GO:0006362 ! transcription elongation from RNA polymerase I promoter relationship: part_of GO:0042790 ! transcription of nuclear large rRNA transcript from RNA polymerase I promoter created_by: kchris creation_date: 2011-08-15T03:57:25Z [Term] id: GO:0001184 name: promoter clearance from RNA polymerase I promoter for nuclear large rRNA transcript namespace: biological_process def: "Any process involved in the transition from the initiation to the elongation phases of transcription by RNA polymerase I at a promoter for the nuclear large ribosomal RNA (rRNA) transcript, generally including a conformational change from the initiation conformation to the elongation conformation. Promoter clearance often involves breaking contact with transcription factors involved only in the initiation phase and making contacts with elongation specific factors." [GOC:txnOH] is_a: GO:0001182 ! promoter clearance from RNA polymerase I promoter relationship: part_of GO:0042790 ! transcription of nuclear large rRNA transcript from RNA polymerase I promoter created_by: kchris creation_date: 2011-08-15T04:03:52Z [Term] id: GO:0001185 name: termination of RNA polymerase I transcription from promoter for nuclear large rRNA transcript namespace: biological_process def: "The process in which the synthesis of an rRNA molecule from a promoter for the nuclear large ribosomal RNA (rRNA) transcript by RNA polymerase I using a DNA template is completed. RNAP I termination requires binding of a terminator protein so specific sequences downstream of the transcription unit." [GOC:txnOH] is_a: GO:0006363 ! termination of RNA polymerase I transcription relationship: part_of GO:0042790 ! transcription of nuclear large rRNA transcript from RNA polymerase I promoter created_by: kchris creation_date: 2011-08-15T04:07:43Z [Term] id: GO:0001186 name: transcription factor activity, RNA polymerase I transcription factor recruiting namespace: molecular_function def: "The function of binding to an RNA polymerase I (RNAP I) transcription factor and recruiting it to the transcription machinery complex in order to modulate transcription by RNAP I." [GOC:txnOH, PMID:12381659, PMID:14969726, PMID:8057832] synonym: "RNA polymerase I transcription factor recruiting transcription factor activity" EXACT [] is_a: GO:0001082 ! transcription factor activity, RNA polymerase I transcription factor binding is_a: GO:0001134 ! transcription factor activity, transcription factor recruiting created_by: kchris creation_date: 2011-08-24T04:00:18Z [Term] id: GO:0001187 name: transcription factor activity, RNA polymerase I CORE element binding transcription factor recruiting namespace: molecular_function def: "Interacting selectively and non-covalently with the CORE element, a regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery and also binding to an RNA polymerase I (RNAP I) transcription factor to recruit it to the transcription machinery complex in order to modulate transcription by RNA polymerase I." [GOC:txnOH, PMID:12381659, PMID:14969726, PMID:8057832] synonym: "RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity" EXACT [] is_a: GO:0001169 ! transcription factor activity, RNA polymerase I CORE element sequence-specific binding is_a: GO:0001186 ! transcription factor activity, RNA polymerase I transcription factor recruiting relationship: part_of GO:0001189 ! RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript created_by: kchris creation_date: 2011-08-24T04:07:50Z [Term] id: GO:0001188 name: RNA polymerase I transcriptional preinitiation complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on promoter DNA to form the transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from an RNA polymerase I promoter." [GOC:txnOH, PMID:12381659, PMID:14969726, PMID:8057832] is_a: GO:0070897 ! DNA-templated transcriptional preinitiation complex assembly relationship: part_of GO:0006361 ! transcription initiation from RNA polymerase I promoter created_by: kchris creation_date: 2011-08-24T04:16:28Z [Term] id: GO:0001189 name: RNA polymerase I transcriptional preinitiation complex assembly at the promoter for the nuclear large rRNA transcript namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins on CORE promoter element DNA of the nuclear large ribosomal RNA (rRNA) transcript to form a transcriptional preinitiation complex (PIC), the formation of which is a prerequisite for transcription from the large rRNA promoter, resulting in the subsequent synthesis of the large rRNA transcript." [GOC:txnOH, PMID:12381659, PMID:14969726, PMID:8057832] is_a: GO:0001188 ! RNA polymerase I transcriptional preinitiation complex assembly relationship: part_of GO:0001180 ! transcription initiation from RNA polymerase I promoter for nuclear large rRNA transcript created_by: kchris creation_date: 2011-08-24T04:20:43Z [Term] id: GO:0001190 name: transcriptional activator activity, RNA polymerase II transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to increase the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH] synonym: "RNA polymerase II transcription factor binding transcription activator activity" EXACT [] synonym: "RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription" EXACT [] is_a: GO:0098811 ! transcriptional repressor activity, RNA polymerase II activating transcription factor binding intersection_of: GO:0000988 ! transcription factor activity, protein binding intersection_of: has_part GO:0001085 ! RNA polymerase II transcription factor binding intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter relationship: has_part GO:0001085 ! RNA polymerase II transcription factor binding relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter relationship: part_of GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter relationship: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: kchris creation_date: 2011-08-25T02:07:14Z [Term] id: GO:0001191 name: transcriptional repressor activity, RNA polymerase II transcription factor binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well." [GOC:txnOH, PMID:9811836] synonym: "RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription" EXACT [] synonym: "RNA polymerase II transcription factor binding transcription repressor activity" EXACT [] synonym: "RNA polymerase II transcription repressor activity" BROAD [] is_a: GO:0001076 ! transcription factor activity, RNA polymerase II transcription factor binding intersection_of: GO:0000988 ! transcription factor activity, protein binding intersection_of: has_part GO:0001085 ! RNA polymerase II transcription factor binding intersection_of: part_of GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter relationship: has_part GO:0001085 ! RNA polymerase II transcription factor binding relationship: part_of GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: kchris creation_date: 2011-08-25T02:12:30Z [Term] id: GO:0001192 name: maintenance of transcriptional fidelity during DNA-templated transcription elongation namespace: biological_process def: "Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation on a DNA template." [GOC:txnOH] synonym: "maintenance of transcriptional fidelity during DNA-dependent transcription elongation" EXACT [GOC:txnOH] is_a: GO:0032774 ! RNA biosynthetic process relationship: part_of GO:0006354 ! DNA-templated transcription, elongation created_by: kchris creation_date: 2011-09-02T02:25:30Z [Term] id: GO:0001193 name: maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter namespace: biological_process def: "Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from an RNA polymerase II promoter." [GOC:txnOH, PMID:14531857, PMID:16492753, PMID:17535246] synonym: "maintenance of transcriptional fidelity during DNA-dependent transcription elongation from RNA polymerase II promoter" EXACT [GOC:txnOH] is_a: GO:0001192 ! maintenance of transcriptional fidelity during DNA-templated transcription elongation relationship: part_of GO:0006368 ! transcription elongation from RNA polymerase II promoter created_by: kchris creation_date: 2011-09-02T02:31:00Z [Term] id: GO:0001194 name: maintenance of transcriptional fidelity during DNA-templated transcription elongation from bacterial-type RNA polymerase promoter namespace: biological_process def: "Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from a bacterial-type RNA polymerase promoter." [GOC:txnOH] synonym: "maintenance of transcriptional fidelity during DNA-dependent transcription elongation from bacterial-type RNA polymerase promoter" EXACT [GOC:txnOH] is_a: GO:0001192 ! maintenance of transcriptional fidelity during DNA-templated transcription elongation relationship: part_of GO:0001124 ! transcription elongation from bacterial-type RNA polymerase promoter created_by: kchris creation_date: 2011-09-02T02:37:59Z [Term] id: GO:0001195 name: maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase III promoter namespace: biological_process def: "Suppression of the occurrence of transcriptional errors, such as substitutions and/or insertions of nucleotides that do not correctly match the template base, during the process of transcription elongation from a RNA polymerase III promoter." [GOC:txnOH] synonym: "maintenance of transcriptional fidelity during DNA-dependent transcription elongation from RNA polymerase III promoter" EXACT [GOC:txnOH] is_a: GO:0001192 ! maintenance of transcriptional fidelity during DNA-templated transcription elongation relationship: part_of GO:0006385 ! transcription elongation from RNA polymerase III promoter created_by: kchris creation_date: 2011-09-02T02:41:29Z [Term] id: GO:0001196 name: regulation of mating-type specific transcription from RNA polymerase II promoter namespace: biological_process def: "Any mating-type specific process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:txnOH] is_a: GO:0006357 ! regulation of transcription from RNA polymerase II promoter is_a: GO:0007532 ! regulation of mating-type specific transcription, DNA-templated intersection_of: GO:0007532 ! regulation of mating-type specific transcription, DNA-templated intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter relationship: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: kchris creation_date: 2011-11-23T09:25:32Z [Term] id: GO:0001197 name: positive regulation of mating-type specific transcription from RNA polymerase II promoter namespace: biological_process def: "Any mating-type specific process that activates or increases the rate of transcription from an RNA polymerase II promoter." [GOC:txnOH] synonym: "activation of transcription from an RNA polymerase II promoter, mating-type specific" NARROW [] synonym: "stimulation of transcription from an RNA polymerase II promoter, mating-type specific" NARROW [] synonym: "up regulation of transcription from an RNA polymerase II promoter, mating-type specific" EXACT [] synonym: "up-regulation of transcription from an RNA polymerase II promoter, mating-type specific" EXACT [] synonym: "upregulation of transcription from an RNA polymerase II promoter, mating-type specific" EXACT [] is_a: GO:0001196 ! regulation of mating-type specific transcription from RNA polymerase II promoter is_a: GO:0045895 ! positive regulation of mating-type specific transcription, DNA-templated intersection_of: GO:0045895 ! positive regulation of mating-type specific transcription, DNA-templated intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter relationship: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: kchris creation_date: 2011-11-23T09:31:33Z [Term] id: GO:0001198 name: negative regulation of mating-type specific transcription from RNA polymerase II promoter namespace: biological_process def: "Any mating-type specific process that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter." [GOC:txnOH] synonym: "down regulation of RNA polymerase II transcription, mating-type specific" EXACT [] synonym: "down-regulation of RNA polymerase II transcription, mating-type specific" EXACT [] synonym: "downregulation of RNA polymerase II transcription, mating-type specific" EXACT [] synonym: "inhibition of RNA polymerase II transcription, mating-type specific" NARROW [] is_a: GO:0001196 ! regulation of mating-type specific transcription from RNA polymerase II promoter is_a: GO:0045894 ! negative regulation of mating-type specific transcription, DNA-templated intersection_of: GO:0045894 ! negative regulation of mating-type specific transcription, DNA-templated intersection_of: regulates GO:0006366 ! transcription from RNA polymerase II promoter relationship: regulates GO:0006366 ! transcription from RNA polymerase II promoter created_by: kchris creation_date: 2011-11-23T09:36:06Z [Term] id: GO:0001199 name: transcription factor activity, metal ion regulated sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to modulate transcription by an RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. synonym: "metal ion regulated sequence-specific DNA binding transcription factor activity" EXACT [] is_a: GO:0003700 ! transcription factor activity, sequence-specific DNA binding relationship: has_part GO:0046872 ! metal ion binding relationship: part_of GO:0071248 ! cellular response to metal ion created_by: kchris creation_date: 2011-11-23T10:52:49Z [Term] id: GO:0001200 name: RNA polymerase II transcription factor activity, metal ion regulated sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to modulate transcription by RNA polymerase II. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. synonym: "metal ion regulated sequence-specific DNA binding RNA polymerase II transcription factor activity" EXACT [] is_a: GO:0000981 ! RNA polymerase II transcription factor activity, sequence-specific DNA binding is_a: GO:0001199 ! transcription factor activity, metal ion regulated sequence-specific DNA binding created_by: kchris creation_date: 2011-11-23T11:18:49Z [Term] id: GO:0001201 name: RNA polymerase II transcription factor activity, metal ion regulated core promoter proximal region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor that binds the core promoter proximal region in order to modulate transcription by RNA polymerase II. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. synonym: "metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity" EXACT [] is_a: GO:0000982 ! transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding is_a: GO:0001200 ! RNA polymerase II transcription factor activity, metal ion regulated sequence-specific DNA binding created_by: kchris creation_date: 2011-11-23T11:22:42Z [Term] id: GO:0001202 name: RNA polymerase II transcription factor activity, copper ion regulated core promoter proximal region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with copper(I) (Cu+) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of copper(I) (Cu+), such a way that copper ion binding regulates the activity of the transcription factor, perhaps by regulating the ability to interact selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II), or by regulating some other function of the transcription factor, in order to modulate transcription by RNAP II." [GOC:txnOH, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. synonym: "copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity" EXACT [] is_a: GO:0001201 ! RNA polymerase II transcription factor activity, metal ion regulated core promoter proximal region sequence-specific binding relationship: has_part GO:0005507 ! copper ion binding relationship: part_of GO:0071280 ! cellular response to copper ion created_by: kchris creation_date: 2011-11-23T11:27:57Z [Term] id: GO:0001203 name: RNA polymerase II transcription factor activity, zinc ion regulated core promoter proximal region sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with zinc (Zn) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of zinc (Zn), in such a way that zinc ion binding regulates the activity of the transcription factor, perhaps by regulating the ability to interact selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II), or by regulating some other function of the transcription factor, in order to modulate transcription by RNAP II." [GOC:txnOH, PMID:22084422] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. synonym: "zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity" EXACT [] is_a: GO:0001201 ! RNA polymerase II transcription factor activity, metal ion regulated core promoter proximal region sequence-specific binding relationship: has_part GO:0008270 ! zinc ion binding relationship: part_of GO:0071294 ! cellular response to zinc ion created_by: kchris creation_date: 2011-11-23T11:36:25Z [Term] id: GO:0001204 name: bacterial-type RNA polymerase transcription factor activity, metal ion regulated sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to modulate transcription by a bacterial-type RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. synonym: "metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity" EXACT [] is_a: GO:0001130 ! bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding is_a: GO:0001199 ! transcription factor activity, metal ion regulated sequence-specific DNA binding created_by: kchris creation_date: 2011-11-23T12:07:06Z [Term] id: GO:0001205 name: transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:txnOH] synonym: "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" EXACT [] synonym: "sequence-specific distal enhancer binding RNA polymerase II transcription factor activity involved in positive regulation of transcription" EXACT [] is_a: GO:0001228 ! transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding is_a: GO:0003705 ! transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding created_by: kchris creation_date: 2012-01-26T03:10:20Z [Term] id: GO:0001206 name: transcriptional repressor activity, RNA polymerase II distal enhancer sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:txnOH] synonym: "RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" EXACT [] synonym: "sequence-specific distal enhancer binding RNA polymerase II transcription factor activity involved in negative regulation of transcription" EXACT [] is_a: GO:0001227 ! transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding is_a: GO:0003705 ! transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding created_by: kchris creation_date: 2012-01-26T03:10:40Z [Term] id: GO:0001207 name: histone displacement namespace: biological_process def: "The removal of histones, including histone dimers, from nucleosomes within chromatin." [GOC:krc, PMID:15525516, PMID:17496903, PMID:21807128] is_a: GO:0034728 ! nucleosome organization created_by: karen creation_date: 2012-03-27T10:56:56Z [Term] id: GO:0001208 name: histone H2A-H2B dimer displacement namespace: biological_process def: "The removal of a H2A-H2B histone dimer from a nucleosome within chromatin." [GOC:krc, PMID:15525516, PMID:17496903, PMID:21807128] is_a: GO:0001207 ! histone displacement created_by: karen creation_date: 2012-03-27T11:03:40Z [Term] id: GO:0001209 name: transcriptional activator activity, metal ion regulated sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of cellular DNA-dependent transcription by an RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. synonym: "metal ion regulated sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" EXACT [] is_a: GO:0001199 ! transcription factor activity, metal ion regulated sequence-specific DNA binding relationship: part_of GO:0045893 ! positive regulation of transcription, DNA-templated created_by: kchris creation_date: 2012-04-04T02:26:42Z [Term] id: GO:0001210 name: transcriptional repressor activity, metal ion regulated sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of cellular DNA-dependent transcription by an RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. synonym: "metal ion regulated sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" EXACT [] is_a: GO:0001199 ! transcription factor activity, metal ion regulated sequence-specific DNA binding relationship: part_of GO:0045892 ! negative regulation of transcription, DNA-templated created_by: kchris creation_date: 2012-04-04T02:53:25Z [Term] id: GO:0001211 name: RNA polymerase II transcriptional activator activity, copper ion regulated core promoter proximal region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with copper(I) (Cu+) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of copper(I) (Cu+), such a way that copper ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:txnOH, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. synonym: "copper ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in positive regulation of transcription" EXACT [] is_a: GO:0001202 ! RNA polymerase II transcription factor activity, copper ion regulated core promoter proximal region sequence-specific binding is_a: GO:0001213 ! RNA polymerase II transcriptional activator activity, metal ion regulated core promoter proximal region sequence-specific binding created_by: kchris creation_date: 2012-04-04T03:03:00Z [Term] id: GO:0001212 name: RNA polymerase II transcriptional activator activity, zinc ion regulated core promoter proximal region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with zinc (Zn) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of zinc (Zn), such a way that copper ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:txnOH] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. synonym: "zinc ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in positive regulation of transcription" EXACT [] is_a: GO:0001203 ! RNA polymerase II transcription factor activity, zinc ion regulated core promoter proximal region sequence-specific DNA binding is_a: GO:0001213 ! RNA polymerase II transcriptional activator activity, metal ion regulated core promoter proximal region sequence-specific binding created_by: kchris creation_date: 2012-04-04T03:13:34Z [Term] id: GO:0001213 name: RNA polymerase II transcriptional activator activity, metal ion regulated core promoter proximal region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of metal ion, such a way that metal ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:txnOH, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. synonym: "metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in positive regulation of transcription" EXACT [] is_a: GO:0001077 ! transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding is_a: GO:0001201 ! RNA polymerase II transcription factor activity, metal ion regulated core promoter proximal region sequence-specific binding created_by: kchris creation_date: 2012-04-04T03:18:43Z [Term] id: GO:0001214 name: RNA polymerase II transcriptional repressor activity, metal ion regulated core promoter proximal region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) and interacting selectively and non-covalently with metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of metal ion, such a way that metal ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:txnOH, PMID:22084422, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. synonym: "metal ion regulated core promoter proximal region sequence-specific DNA binding RNA polymerase II transcription factor activity involved in negative regulation of transcription" EXACT [] is_a: GO:0001078 ! transcriptional repressor activity, RNA polymerase II core promoter proximal region sequence-specific binding is_a: GO:0001201 ! RNA polymerase II transcription factor activity, metal ion regulated core promoter proximal region sequence-specific binding created_by: kchris creation_date: 2012-04-04T03:33:08Z [Term] id: GO:0001215 name: bacterial-type RNA polymerase transcriptional activator activity, metal ion regulated sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to activate or increase the frequency, rate or extent of cellular DNA-dependent transcription by a bacterial-type RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. synonym: "metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in positive regulation of transcription" EXACT [] is_a: GO:0001204 ! bacterial-type RNA polymerase transcription factor activity, metal ion regulated sequence-specific DNA binding is_a: GO:0001209 ! transcriptional activator activity, metal ion regulated sequence-specific DNA binding created_by: kchris creation_date: 2012-04-04T03:47:42Z [Term] id: GO:0001216 name: bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:krc] synonym: "sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in positive regulation of transcription" EXACT [] is_a: GO:0001130 ! bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding relationship: part_of GO:0045893 ! positive regulation of transcription, DNA-templated created_by: kchris creation_date: 2012-04-04T03:55:59Z [Term] id: GO:0001217 name: bacterial-type RNA polymerase transcriptional repressor activity, sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by bacterial-type RNA polymerase. The transcription factor may or may not also interact selectively with a protein or macromolecular complex." [GOC:krc] synonym: "sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription" EXACT [] is_a: GO:0001130 ! bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding relationship: part_of GO:0045892 ! negative regulation of transcription, DNA-templated created_by: kchris creation_date: 2012-04-04T03:57:16Z [Term] id: GO:0001218 name: bacterial-type RNA polymerase transcriptional repressor activity, metal ion regulated sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with any metal ion(s) and responding, e.g. by conformational change, to changes in the cellular level of those metal ions, in such a way that metal ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of cellular DNA-dependent transcription by a bacterial-type RNA polymerase. Specific mechanisms include increasing or decreasing the ability of the transcription factor to interact selectively and non-covalently with a specific DNA sequence (for example S. cerevisiae Cup2p or the prokaryotic SmtB/ArsR family, changing the conformation of transcription factor bound DNA between the apo- and metal-bound forms of the transcription factor. Additional mechanisms may exist." [GOC:txnOH, PMID:12829264, PMID:12829265, PMID:2674688] comment: This term is intended for sequence specific DNA binding transcription factors whose transcription factor activity is regulated by binding of a metal ion, e.g. copper, zinc, etc. Do not use this term for transcription factors which bind a metal ion all the time, where binding of that metal ion does not regulate the DNA binding, or some other activity, required for the gene product to act as a transcription factor. synonym: "metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription" EXACT [] is_a: GO:0001204 ! bacterial-type RNA polymerase transcription factor activity, metal ion regulated sequence-specific DNA binding is_a: GO:0001210 ! transcriptional repressor activity, metal ion regulated sequence-specific DNA binding created_by: kchris creation_date: 2012-04-05T10:46:50Z [Term] id: GO:0001219 name: bacterial-type RNA polymerase transcriptional repressor activity, copper ion regulated sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with copper(I) (Cu+) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of copper(I) (Cu+), in such a way that copper ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of cellular DNA-dependent transcription by a bacterial-type RNA polymerase." [GOC:krc, PMID:12829264, PMID:12829265, PMID:19928961] synonym: "copper ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription" EXACT [] synonym: "copper ion sensor" RELATED [] is_a: GO:0001218 ! bacterial-type RNA polymerase transcriptional repressor activity, metal ion regulated sequence-specific DNA binding relationship: has_part GO:0005507 ! copper ion binding relationship: part_of GO:0071280 ! cellular response to copper ion created_by: kchris creation_date: 2012-04-05T11:13:34Z [Term] id: GO:0001220 name: bacterial-type RNA polymerase transcriptional repressor activity, cadmium ion regulated sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with a specific bacterial-type transcription regulatory DNA sequence and interacting selectively and non-covalently with cadmium (Cd) ion(s) and responding, e.g. by conformational change, to changes in the cellular level of cadmium (Cd), in such a way that cadmium (Cd) ion binding regulates the activity of the transcription factor in order to stop, prevent, or reduce the frequency, rate or extent of cellular DNA-dependent transcription by a bacterial-type RNA polymerase." [GOC:krc, PMID:12829264, PMID:12829265, PMID:19456862] synonym: "cadmium ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity involved in negative regulation of transcription" EXACT [] synonym: "cadmium ion sensor" RELATED [] is_a: GO:0001218 ! bacterial-type RNA polymerase transcriptional repressor activity, metal ion regulated sequence-specific DNA binding relationship: has_part GO:0046870 ! cadmium ion binding relationship: part_of GO:0071276 ! cellular response to cadmium ion created_by: kchris creation_date: 2012-04-05T11:46:06Z [Term] id: GO:0001221 name: transcription cofactor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a transcription cofactor, any protein involved in regulation of transcription via protein-protein interactions with transcription factors and other transcription regulatory proteins. Cofactors do not bind DNA directly, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery." [GOC:krc] is_a: GO:0008134 ! transcription factor binding created_by: kchris creation_date: 2012-04-16T03:19:05Z [Term] id: GO:0001222 name: transcription corepressor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a transcription corepressor, any protein involved in negative regulation of transcription via protein-protein interactions with transcription factors and other proteins that negatively regulate transcription. Transcription corepressors do not bind DNA directly, but rather mediate protein-protein interactions between repressing transcription factors and the basal transcription machinery." [GOC:krc] is_a: GO:0001221 ! transcription cofactor binding created_by: kchris creation_date: 2012-04-16T03:27:26Z [Term] id: GO:0001223 name: transcription coactivator binding namespace: molecular_function def: "Interacting selectively and non-covalently with a transcription coactivator, any protein involved in positive regulation of transcription via protein-protein interactions with transcription factors and other proteins that positively regulate transcription. Transcription coactivators do not bind DNA directly, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery." [GOC:krc] is_a: GO:0001221 ! transcription cofactor binding created_by: kchris creation_date: 2012-04-16T03:30:16Z [Term] id: GO:0001224 name: RNA polymerase II transcription cofactor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a transcription cofactor for RNA polymerase II, any protein involved in regulation of transcription via protein-protein interactions with RNA polymerase II transcription factors and other transcription regulatory proteins. Cofactors do not bind DNA directly, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery of RNA polymerase II." [GOC:krc] is_a: GO:0001221 ! transcription cofactor binding created_by: kchris creation_date: 2012-04-16T03:37:06Z [Term] id: GO:0001225 name: RNA polymerase II transcription coactivator binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II transcription coactivator, any protein involved in positive regulation of transcription of RNA polymerase II via protein-protein interactions with transcription factors and other proteins that positively regulate transcription. Transcription coactivators do not bind DNA directly, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery of RNA polymerase II." [GOC:krc] is_a: GO:0001223 ! transcription coactivator binding is_a: GO:0001224 ! RNA polymerase II transcription cofactor binding created_by: kchris creation_date: 2012-04-16T03:39:41Z [Term] id: GO:0001226 name: RNA polymerase II transcription corepressor binding namespace: molecular_function def: "Interacting selectively and non-covalently with an RNA polymerase II transcription corepressor, any protein involved in negative regulation of transcription by RNA polymerase II via protein-protein interactions with transcription factors and other proteins that negatively regulate transcription. Transcription corepressors do not bind DNA directly, but rather mediate protein-protein interactions between repressing transcription factors and the basal transcription machinery of RNA polymerase II." [GOC:krc] is_a: GO:0001222 ! transcription corepressor binding is_a: GO:0001224 ! RNA polymerase II transcription cofactor binding created_by: kchris creation_date: 2012-04-16T03:39:47Z [Term] id: GO:0001227 name: transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in the regulatory region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter." [GOC:krc] synonym: "RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" EXACT [] is_a: GO:0000981 ! RNA polymerase II transcription factor activity, sequence-specific DNA binding relationship: part_of GO:0000122 ! negative regulation of transcription from RNA polymerase II promoter created_by: kchris creation_date: 2012-04-16T04:41:29Z [Term] id: GO:0001228 name: transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding namespace: molecular_function def: "Interacting selectively and non-covalently with a sequence of DNA that is in the transcription regulatory region for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter." [GOC:krc] synonym: "RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" EXACT [] is_a: GO:0000981 ! RNA polymerase II transcription factor activity, sequence-specific DNA binding relationship: part_of GO:0006366 ! transcription from RNA polymerase II promoter relationship: part_of GO:0045944 ! positive regulation of transcription from RNA polymerase II promoter created_by: kchris creation_date: 2012-04-16T04:44:21Z [Term] id: GO:0001300 name: chronological cell aging namespace: biological_process def: "The process associated with progression of the cell from its inception to the end of its lifespan that occurs when the cell is in a non-dividing, or quiescent, state." [GOC:jh, PMID:12044934] synonym: "chronological cell ageing" EXACT [] is_a: GO:0007569 ! cell aging [Term] id: GO:0001301 name: progressive alteration of chromatin involved in cell aging namespace: biological_process def: "Any chromatin organization process that occurs during the lifespan of the cell that results in changes in chromatin structure. Such changes may lead to gene dysregulation and ultimately to a loss in cell homeostasis, bringing about an aging phenotype." [GOC:jh, GOC:vw, PMID:12044938] synonym: "age-dependent accumulation of genetic damage" RELATED [] synonym: "progressive alteration of chromatin during cell ageing" EXACT [] synonym: "progressive alteration of chromatin during cell aging" RELATED [GOC:dph, GOC:tb] is_a: GO:0006325 ! chromatin organization intersection_of: GO:0006325 ! chromatin organization intersection_of: part_of GO:0007569 ! cell aging relationship: part_of GO:0007569 ! cell aging [Term] id: GO:0001302 name: replicative cell aging namespace: biological_process def: "The process associated with progression of the cell from its inception to the end of its lifespan that occurs as the cell continues cycles of growth and division." [GOC:jh, PMID:12044934] synonym: "replicative cell ageing" EXACT [] is_a: GO:0007569 ! cell aging [Term] id: GO:0001303 name: nucleolar fragmentation involved in replicative aging namespace: biological_process def: "A nucleolar fragmentation process that gives rise to multiple rounded structures and that occurs in conjunction with increasing age in dividing cells." [GOC:jh, PMID:9891807] synonym: "nucleolar fragmentation during replicative ageing" RELATED [] synonym: "nucleolar fragmentation during replicative aging" RELATED [GOC:dph, GOC:tb] is_a: GO:0007576 ! nucleolar fragmentation intersection_of: GO:0007576 ! nucleolar fragmentation intersection_of: part_of GO:0001302 ! replicative cell aging relationship: part_of GO:0001302 ! replicative cell aging [Term] id: GO:0001304 name: progressive alteration of chromatin involved in replicative cell aging namespace: biological_process def: "A process that results in changes in chromatin structure contributing to replicative cell aging." [GOC:dph, GOC:jh, GOC:tb] synonym: "progressive alteration of chromatin during replicative cell ageing" EXACT [] synonym: "progressive alteration of chromatin during replicative cell aging" RELATED [GOC:dph, GOC:tb] is_a: GO:0001301 ! progressive alteration of chromatin involved in cell aging intersection_of: GO:0001301 ! progressive alteration of chromatin involved in cell aging intersection_of: part_of GO:0001302 ! replicative cell aging relationship: part_of GO:0001302 ! replicative cell aging [Term] id: GO:0001305 name: progressive alteration of chromatin involved in chronological cell aging namespace: biological_process def: "A process that results in changes in chromatin structure contributing to chronological cell aging, occurring in non-dividing cells." [GOC:dph, GOC:jh, GOC:tb] synonym: "progressive alteration of chromatin during chronological cell ageing" RELATED [] synonym: "progressive alteration of chromatin during chronological cell aging" RELATED [GOC:dph, GOC:tb] is_a: GO:0001301 ! progressive alteration of chromatin involved in cell aging intersection_of: GO:0001301 ! progressive alteration of chromatin involved in cell aging intersection_of: part_of GO:0001300 ! chronological cell aging relationship: part_of GO:0001300 ! chronological cell aging [Term] id: GO:0001306 name: age-dependent response to oxidative stress namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, where the change varies according to the age of the cell or organism." [GOC:jh, PMID:12044938] is_a: GO:0006979 ! response to oxidative stress relationship: part_of GO:0007571 ! age-dependent general metabolic decline [Term] id: GO:0001307 name: extrachromosomal circular DNA accumulation involved in replicative cell aging namespace: biological_process def: "Increase in abundance of circular DNA molecules in dividing cells as they age. These molecules originate in the chromosome but are excised and circularized, often by intramolecular homologous recombination between direct tandem repeats, and then replicated independently of chromosomal replication." [GOC:jh] synonym: "extrachromosomal circular DNA accumulation during replicative cell ageing" RELATED [] synonym: "extrachromosomal circular DNA accumulation during replicative cell aging" RELATED [GOC:dph, GOC:tb] is_a: GO:0001304 ! progressive alteration of chromatin involved in replicative cell aging is_a: GO:0007580 ! extrachromosomal circular DNA accumulation involved in cell aging [Term] id: GO:0001308 name: negative regulation of chromatin silencing involved in replicative cell aging namespace: biological_process def: "The process, which occurs as a dividing cell ages, leading to expression of genes that are typically not expressed due to silencing by regulatory proteins." [GOC:jh, PMID:12044934] synonym: "loss of chromatin silencing during replicative cell ageing" RELATED [] synonym: "loss of chromatin silencing involved in replicative cell aging" EXACT [] is_a: GO:0001304 ! progressive alteration of chromatin involved in replicative cell aging is_a: GO:0031936 ! negative regulation of chromatin silencing intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006342 ! chromatin silencing intersection_of: part_of GO:0001302 ! replicative cell aging relationship: negatively_regulates GO:0006342 ! chromatin silencing relationship: part_of GO:0001302 ! replicative cell aging [Term] id: GO:0001309 name: obsolete age-dependent telomere shortening namespace: biological_process def: "OBSOLETE. Progressive reduction in length of the telomeres, the termini of eukaryotic chromosomes, that occurs as part of the cellular aging process." [GOC:jh, PMID:9891807] comment: This term was made obsolete because it represents a phenotype. synonym: "age-dependent telomere shortening" EXACT [] is_obsolete: true consider: GO:1903824 [Term] id: GO:0001310 name: extrachromosomal rDNA circle accumulation involved in replicative cell aging namespace: biological_process def: "Increase in abundance of circular DNA molecules containing ribosomal DNA repeats in dividing cells as they age. These molecules originate in the chromosome but are excised and circularized, often by intramolecular homologous recombination between direct tandem repeats, and then replicated independently of chromosomal replication." [GOC:jh, PMID:12044934] synonym: "extrachromosomal rDNA circle accumulation during replicative cell ageing" RELATED [] synonym: "extrachromosomal rDNA circle accumulation during replicative cell aging" RELATED [GOC:dph, GOC:tb] synonym: "extrachromosomal ribosomal DNA circle accumulation during replicative cell aging" RELATED [] is_a: GO:0001307 ! extrachromosomal circular DNA accumulation involved in replicative cell aging [Term] id: GO:0001311 name: formation of extrachromosomal circular rDNA by homologous recombination involved in replicative cell aging namespace: biological_process def: "Excision from the chromosome and circularization of DNA molecules encoding ribosomal RNA in dividing cells as they age." [GOC:jh, PMID:12044934] synonym: "assembly of extrachromosomal circular rDNA by homologous recombination involved in replicative cell aging" RELATED [] synonym: "formation of extrachromosomal circular rDNA by homologous recombination during replicative cell ageing" RELATED [] synonym: "formation of extrachromosomal circular rDNA by homologous recombination during replicative cell aging" RELATED [GOC:dph, GOC:tb] synonym: "formation of extrachromosomal circular ribosomal DNA by homologous recombination during replicative cell aging" RELATED [] is_a: GO:0001313 ! formation of extrachromosomal circular DNA involved in replicative cell aging is_a: GO:0045458 ! recombination within rDNA repeats relationship: part_of GO:0001310 ! extrachromosomal rDNA circle accumulation involved in replicative cell aging [Term] id: GO:0001312 name: replication of extrachromosomal rDNA circles involved in replicative cell aging namespace: biological_process def: "Replication of rDNA following its excision from the chromosome of dividing cells as they age. Extrachromosomal rDNA forms a circle that contains at least one autonomously replicating sequence (ARS), which supports replication independent of chromosomal replication." [GOC:jh, PMID:12044934] synonym: "replication of extrachromosomal rDNA circles during replicative cell ageing" RELATED [] synonym: "replication of extrachromosomal rDNA circles during replicative cell aging" RELATED [GOC:dph, GOC:tb] synonym: "replication of extrachromosomal ribosomal DNA circles during replicative cell aging" RELATED [] is_a: GO:0001314 ! replication of extrachromosomal circular DNA involved in replicative cell aging relationship: part_of GO:0001310 ! extrachromosomal rDNA circle accumulation involved in replicative cell aging [Term] id: GO:0001313 name: formation of extrachromosomal circular DNA involved in replicative cell aging namespace: biological_process def: "Excision from the chromosome and circularization of a region of chromosomal DNA, generally, but not always, via homologous recombination between direct tandem repeats, in dividing cells as they age." [GOC:jh] synonym: "assembly of extrachromosomal circular DNA involved in replicative cell aging" EXACT [] synonym: "formation of extrachromosomal circular DNA during replicative cell ageing" RELATED [] synonym: "formation of extrachromosomal circular DNA during replicative cell aging" RELATED [GOC:dph, GOC:tb] is_a: GO:0001325 ! formation of extrachromosomal circular DNA intersection_of: GO:0001325 ! formation of extrachromosomal circular DNA intersection_of: part_of GO:0001302 ! replicative cell aging relationship: part_of GO:0001302 ! replicative cell aging relationship: part_of GO:0001307 ! extrachromosomal circular DNA accumulation involved in replicative cell aging [Term] id: GO:0001314 name: replication of extrachromosomal circular DNA involved in replicative cell aging namespace: biological_process def: "Replication of circular DNA following excision from the chromosome of dividing cells as they age; replication of extrachromosomal circular DNA generally occurs independently of chromosomal replication." [GOC:jh] synonym: "replication of extrachromosomal circular DNA during replicative cell ageing" EXACT [] synonym: "replication of extrachromosomal circular DNA during replicative cell aging" RELATED [GOC:dph, GOC:tb] is_a: GO:0001326 ! replication of extrachromosomal circular DNA intersection_of: GO:0001326 ! replication of extrachromosomal circular DNA intersection_of: part_of GO:0001302 ! replicative cell aging relationship: part_of GO:0001302 ! replicative cell aging relationship: part_of GO:0001307 ! extrachromosomal circular DNA accumulation involved in replicative cell aging [Term] id: GO:0001315 name: age-dependent response to reactive oxygen species namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of reactive oxygen species, where the change varies according to the age of the cell or organism." [GOC:jh, PMID:12044938] subset: gosubset_prok synonym: "age-dependent response to active oxygen species" EXACT [] synonym: "age-dependent response to AOS" EXACT [] synonym: "age-dependent response to reactive oxidative species" EXACT [] synonym: "age-dependent response to reactive oxygen intermediate" EXACT [] synonym: "age-dependent response to ROI" EXACT [] synonym: "age-dependent response to ROS" EXACT [] is_a: GO:0000302 ! response to reactive oxygen species is_a: GO:0001306 ! age-dependent response to oxidative stress [Term] id: GO:0001316 name: age-dependent response to reactive oxygen species involved in replicative cell aging namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) occurring during the process of replicative cell aging as a result of reactive oxygen species, where the change varies according to the age of the cell or organism." [GOC:jh] synonym: "age-dependent response to active oxygen species during replicative cell aging" RELATED [] synonym: "age-dependent response to AOS during replicative cell aging" EXACT [] synonym: "age-dependent response to reactive oxidative species during replicative cell aging" EXACT [] synonym: "age-dependent response to reactive oxygen intermediate during replicative cell aging" RELATED [] synonym: "age-dependent response to reactive oxygen species during replicative cell ageing" EXACT [] synonym: "age-dependent response to reactive oxygen species during replicative cell aging" RELATED [GOC:dph, GOC:tb] synonym: "age-dependent response to ROI during replicative cell aging" RELATED [] synonym: "age-dependent response to ROS during replicative cell aging" RELATED [] is_a: GO:0001322 ! age-dependent response to oxidative stress involved in replicative cell aging is_a: GO:0072353 ! cellular age-dependent response to reactive oxygen species [Term] id: GO:0001317 name: accumulation of oxidatively modified proteins involved in replicative cell aging namespace: biological_process def: "Accumulation of proteins that have undergone reactions with reactive oxygen species in aging dividing cells and exhibit modifications such as increased protein carbonyl content, oxidized methionine, protein hydrophobicity, and cross-linking." [GOC:jh] synonym: "accumulation of oxidatively modified proteins during replicative cell ageing" RELATED [] synonym: "accumulation of oxidatively modified proteins during replicative cell aging" RELATED [GOC:dph, GOC:tb] is_a: GO:0001316 ! age-dependent response to reactive oxygen species involved in replicative cell aging [Term] id: GO:0001318 name: formation of oxidatively modified proteins involved in replicative cell aging namespace: biological_process def: "Chemical reaction, between proteins and reactive oxygen species, that occurs in dividing cells as they age and leads to a variety of changes in the affected proteins, including increases in protein carbonyl content, oxidized methionine, protein hydrophobicity, and cross-linking." [GOC:jh] synonym: "formation of oxidatively modified proteins during replicative cell ageing" RELATED [] synonym: "formation of oxidatively modified proteins during replicative cell aging" RELATED [GOC:dph, GOC:tb] is_a: GO:0006464 ! cellular protein modification process relationship: part_of GO:0001317 ! accumulation of oxidatively modified proteins involved in replicative cell aging [Term] id: GO:0001319 name: inheritance of oxidatively modified proteins involved in replicative cell aging namespace: biological_process def: "A protein localization process in which progeny cells acquire, or are barred from acquiring, proteins that have been altered by reaction with reactive oxygen species in dividing aging cells." [GOC:jh] synonym: "inheritance of oxidatively modified proteins during replicative cell ageing" RELATED [] synonym: "inheritance of oxidatively modified proteins during replicative cell aging" RELATED [GOC:dph, GOC:tb] is_a: GO:0008105 ! asymmetric protein localization relationship: part_of GO:0001317 ! accumulation of oxidatively modified proteins involved in replicative cell aging [Term] id: GO:0001320 name: age-dependent response to reactive oxygen species involved in chronological cell aging namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) occurring in non-dividing cells as they age as a result of reactive oxygen species, where the change varies according to the age of the cell or organism." [GOC:jh] synonym: "age-dependent response to active oxygen species during chronological cell aging" RELATED [] synonym: "age-dependent response to AOS during chronological cell aging" RELATED [] synonym: "age-dependent response to reactive oxidative species during chronological cell aging" RELATED [] synonym: "age-dependent response to reactive oxygen intermediate during chronological cell aging" RELATED [] synonym: "age-dependent response to reactive oxygen species during chronological cell ageing" RELATED [] synonym: "age-dependent response to reactive oxygen species during chronological cell aging" RELATED [GOC:dph, GOC:tb] synonym: "age-dependent response to ROI during chronological cell aging" RELATED [] synonym: "age-dependent response to ROS during chronological cell aging" RELATED [] is_a: GO:0001324 ! age-dependent response to oxidative stress involved in chronological cell aging is_a: GO:0072353 ! cellular age-dependent response to reactive oxygen species intersection_of: GO:0001315 ! age-dependent response to reactive oxygen species intersection_of: part_of GO:0001300 ! chronological cell aging relationship: part_of GO:0001300 ! chronological cell aging [Term] id: GO:0001321 name: age-dependent general metabolic decline involved in replicative cell aging namespace: biological_process def: "A process of general metabolic decline that arises in dividing cells as they age, and alters cellular metabolism to cause a decline in cell function." [GOC:jh, GOC:mah] synonym: "age-dependent general metabolic decline during replicative cell ageing" RELATED [] synonym: "age-dependent general metabolic decline involved in replicative cell aging" RELATED [GOC:dph, GOC:tb] is_a: GO:0007571 ! age-dependent general metabolic decline intersection_of: GO:0007571 ! age-dependent general metabolic decline intersection_of: part_of GO:0001302 ! replicative cell aging relationship: part_of GO:0001302 ! replicative cell aging [Term] id: GO:0001322 name: age-dependent response to oxidative stress involved in replicative cell aging namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) occurring in dividing cells as they age as a result of oxidative stress, where the change varies according to the age of the cell or organism." [GOC:jh] synonym: "age-dependent response to oxidative stress during replicative cell ageing" RELATED [] synonym: "age-dependent response to oxidative stress during replicative cell aging" RELATED [GOC:dph, GOC:tb] is_a: GO:0001306 ! age-dependent response to oxidative stress intersection_of: GO:0001306 ! age-dependent response to oxidative stress intersection_of: part_of GO:0001321 ! age-dependent general metabolic decline involved in replicative cell aging relationship: part_of GO:0001321 ! age-dependent general metabolic decline involved in replicative cell aging relationship: part_of GO:0034599 ! cellular response to oxidative stress [Term] id: GO:0001323 name: age-dependent general metabolic decline involved in chronological cell aging namespace: biological_process def: "A process of general metabolic decline that arises in non-dividing cells as they age, and alters cellular metabolism to cause a decline in cell function." [GOC:jh, GOC:mah] synonym: "age-dependent general metabolic decline during chronological cell ageing" RELATED [] synonym: "age-dependent general metabolic decline during chronological cell aging" RELATED [GOC:dph, GOC:tb] is_a: GO:0007571 ! age-dependent general metabolic decline intersection_of: GO:0007571 ! age-dependent general metabolic decline intersection_of: part_of GO:0001300 ! chronological cell aging relationship: part_of GO:0001300 ! chronological cell aging [Term] id: GO:0001324 name: age-dependent response to oxidative stress involved in chronological cell aging namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) occurring in non-dividing cells as they age as a result of oxidative stress, where the change varies according to the age of the cell or organism." [GOC:jh] synonym: "age-dependent response to oxidative stress during chronological cell ageing" RELATED [] synonym: "age-dependent response to oxidative stress during chronological cell aging" RELATED [GOC:dph, GOC:tb] is_a: GO:0001306 ! age-dependent response to oxidative stress is_a: GO:0034599 ! cellular response to oxidative stress intersection_of: GO:0001306 ! age-dependent response to oxidative stress intersection_of: part_of GO:0001300 ! chronological cell aging relationship: part_of GO:0001300 ! chronological cell aging relationship: part_of GO:0001323 ! age-dependent general metabolic decline involved in chronological cell aging [Term] id: GO:0001325 name: formation of extrachromosomal circular DNA namespace: biological_process def: "Excision from the chromosome and circularization of a region of chromosomal DNA, generally, but not always, via homologous recombination between direct tandem repeats." [GOC:jh, PMID:12044938] subset: gosubset_prok synonym: "assembly of extrachromosomal circular DNA" EXACT [] is_a: GO:0006259 ! DNA metabolic process is_a: GO:0022607 ! cellular component assembly [Term] id: GO:0001326 name: replication of extrachromosomal circular DNA namespace: biological_process def: "Replication of circular DNA following excision from the chromosome; replication of extrachromosomal circular DNA generally occurs independently of chromosomal replication." [GOC:jh] subset: gosubset_prok is_a: GO:0006260 ! DNA replication [Term] id: GO:0001400 name: mating projection base namespace: cellular_component def: "The region where the mating projection meets the bulk of the cell, in unicellular fungi exposed to mating pheromone." [GOC:mcc] synonym: "base of shmoo tip" NARROW [] synonym: "conjugation tube base" NARROW [] is_a: GO:0044463 ! cell projection part relationship: part_of GO:0005937 ! mating projection [Term] id: GO:0001401 name: mitochondrial sorting and assembly machinery complex namespace: cellular_component def: "A large complex of the mitochondrial outer membrane that mediates sorting of some imported proteins to the outer membrane and their assembly in the membrane; functions after import of incoming proteins by the mitochondrial outer membrane translocase complex." [PMID:12891361] comment: See also the cellular component term 'mitochondrial outer membrane translocase complex ; GO:0005742'. synonym: "SAM complex" EXACT [] synonym: "TOB complex" EXACT [] is_a: GO:0098799 ! outer mitochondrial membrane protein complex relationship: part_of GO:0005741 ! mitochondrial outer membrane [Term] id: GO:0001402 name: signal transduction involved in filamentous growth namespace: biological_process def: "Relaying of environmental signals promoting filamentous growth." [GOC:mcc, PMID:9728395] synonym: "MAPKKK cascade (pseudohyphal growth)" RELATED [] synonym: "signal transduction during filamentous growth" RELATED [GOC:dph, GOC:tb] is_a: GO:0007165 ! signal transduction intersection_of: GO:0007165 ! signal transduction intersection_of: part_of GO:0030447 ! filamentous growth relationship: part_of GO:0030447 ! filamentous growth [Term] id: GO:0001403 name: invasive growth in response to glucose limitation namespace: biological_process def: "A growth pattern exhibited by budding haploid cells under certain growth conditions, in which cells retain the typical axial budding pattern of haploids, but become elongated and fail to separate after division; during growth on a solid substrate, this results in penetration of cells into the agar medium. An example of this process is found in Saccharomyces cerevisiae." [GOC:mcc, PMID:9728395] comment: Note that this term should not be used to describe the invasion of host tissues by pathogenic organisms, which is described by the biological process term 'entry into host ; GO:0044409', nor should it be used to describe growth of diseased cells of an organism into the surrounding normal tissue, which is outside of the scope of GO. subset: goslim_yeast synonym: "colony morphology" RELATED [] is_a: GO:0036267 ! invasive filamentous growth [Term] id: GO:0001404 name: obsolete invasive growth namespace: biological_process def: "OBSOLETE. Growth of a pathogenic organism that results in penetration into cells or tissues of the host organism. This often (but not necessarily) includes a filamentous growth form, and also can include secretion of proteases and lipases to break down host tissue." [GOC:mcc, PMID:9728395] comment: This term was made obsolete because more appropriate terms were created. synonym: "invasive growth" EXACT [] synonym: "tissue invasion" EXACT [] is_obsolete: true consider: GO:0044409 [Term] id: GO:0001405 name: presequence translocase-associated import motor namespace: cellular_component def: "Protein complex located on the matrix side of the mitochondrial inner membrane and associated with the presequence translocase complex; hydrolyzes ATP to provide the force to drive import of proteins into the mitochondrial matrix." [GOC:mcc, PMID:14517234, PMID:14638855] synonym: "mitochondrial import motor" EXACT [] synonym: "PAM complex" EXACT [] synonym: "pre-sequence translocase-associated import motor" EXACT [] is_a: GO:0098800 ! inner mitochondrial membrane protein complex relationship: part_of GO:0005744 ! mitochondrial inner membrane presequence translocase complex [Term] id: GO:0001406 name: glycerophosphodiester transmembrane transporter activity namespace: molecular_function def: "Enables the transfer of glycerophosphodiesters from one side of a membrane to the other. Glycerophosphodiesters are small molecules composed of glycerol-3-phosphate and an alcohol, for example, glycerophosphoinositol." [GOC:mcc, PMID:12912892] is_a: GO:0015605 ! organophosphate ester transmembrane transporter activity relationship: part_of GO:0001407 ! glycerophosphodiester transport [Term] id: GO:0001407 name: glycerophosphodiester transport namespace: biological_process def: "The directed movement of glycerophosphodiesters into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Glycerophosphodiesters are small molecules composed of glycerol-3-phosphate and an alcohol, for example, glycerophosphoinositol." [GOC:mcc, PMID:12912892] is_a: GO:0015748 ! organophosphate ester transport [Term] id: GO:0001408 name: guanine nucleotide transport namespace: biological_process def: "The directed movement of guanine nucleotides, GTP, GDP, and/or GMP, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mcc] is_a: GO:0015865 ! purine nucleotide transport [Term] id: GO:0001409 name: guanine nucleotide transmembrane transporter activity namespace: molecular_function def: "Catalysis of the transfer of guanine nucleotides (GMP, GDP, and GTP) from one side of the membrane to the other." [GOC:mcc] is_a: GO:0015216 ! purine nucleotide transmembrane transporter activity relationship: part_of GO:1903790 ! guanine nucleotide transmembrane transport [Term] id: GO:0001410 name: chlamydospore formation namespace: biological_process alt_id: GO:0055027 def: "The process whose specific outcome is the progression of the chlamydospore over time, from its formation to the mature structure. A chlamydospores is a mitotic (asexual) one-celled spore, produced primarily for survival, not dispersal, originating endogenously and singly within part of a pre-existing cell and possessing an inner secondary and often thickened cell wall. An example of this is found in Candida albicans." [GOC:mcc, GOC:mtg_sensu, ISBN:085199377X, PMID:14663094] synonym: "chlamydospore development" EXACT [] is_a: GO:0043936 ! asexual sporulation resulting in formation of a cellular spore is_a: GO:0048468 ! cell development [Term] id: GO:0001411 name: hyphal tip namespace: cellular_component def: "The end, or tip, of a fungal hypha, where polarized growth occurs during hyphal elongation." [GOC:mcc] subset: goslim_candida is_a: GO:0030427 ! site of polarized growth [Term] id: GO:0001501 name: skeletal system development namespace: biological_process def: "The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton)." [GOC:dph, GOC:jid, GOC:tb, http://www.stedmans.com/] synonym: "skeletal development" EXACT [] is_a: GO:0048731 ! system development [Term] id: GO:0001502 name: cartilage condensation namespace: biological_process def: "The condensation of mesenchymal cells that have been committed to differentiate into chondrocytes." [ISBN:0878932437] is_a: GO:0098743 ! cell aggregation relationship: part_of GO:0048705 ! skeletal system morphogenesis relationship: part_of GO:0051216 ! cartilage development [Term] id: GO:0001503 name: ossification namespace: biological_process def: "The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance." [GOC:mtg_mpo, PMID:17572649] comment: Note that this term does not have a 'developmental process' parent because ossification isn't necessarily developmental, can also occur as part of bone remodeling. Instead use 'ossification involved in bone maturation ; GO:0043931'. synonym: "bone biosynthesis" EXACT [] synonym: "bone formation" EXACT [] synonym: "osteogenesis" EXACT [] xref: Wikipedia:Ossification is_a: GO:0044707 ! single-multicellular organism process [Term] id: GO:0001504 name: neurotransmitter uptake namespace: biological_process def: "The directed movement of neurotransmitters into neurons or glial cells. This process leads to inactivation and recycling of neurotransmitters." [ISBN:0123668387] subset: goslim_synapse synonym: "neurotransmitter import" EXACT [GOC:dph, GOC:tb] synonym: "neurotransmitter import into glial cell" NARROW [] synonym: "neurotransmitter import into neuron" NARROW [] synonym: "neurotransmitter recycling" BROAD [] xref: Reactome:REACT_106095 "Neurotransmitter uptake and Metabolism In Glial Cells, Gallus gallus" xref: Reactome:REACT_106673 "Neurotransmitter uptake and Metabolism In Glial Cells, Bos taurus" xref: Reactome:REACT_107830 "Neurotransmitter uptake and Metabolism In Glial Cells, Arabidopsis thaliana" xref: Reactome:REACT_114027 "Neurotransmitter uptake and Metabolism In Glial Cells, Staphylococcus aureus N315" xref: Reactome:REACT_13594 "Neurotransmitter uptake and Metabolism In Glial Cells, Homo sapiens" xref: Reactome:REACT_29399 "Neurotransmitter uptake and Metabolism In Glial Cells, Drosophila melanogaster" xref: Reactome:REACT_30311 "Neurotransmitter uptake and Metabolism In Glial Cells, Rattus norvegicus" xref: Reactome:REACT_82534 "Neurotransmitter uptake and Metabolism In Glial Cells, Caenorhabditis elegans" xref: Reactome:REACT_88126 "Neurotransmitter uptake and Metabolism In Glial Cells, Escherichia coli" xref: Reactome:REACT_89424 "Neurotransmitter uptake and Metabolism In Glial Cells, Sus scrofa" xref: Reactome:REACT_92363 "Neurotransmitter uptake and Metabolism In Glial Cells, Canis familiaris" xref: Reactome:REACT_93291 "Neurotransmitter uptake and Metabolism In Glial Cells, Taeniopygia guttata" xref: Reactome:REACT_94616 "Neurotransmitter uptake and Metabolism In Glial Cells, Schizosaccharomyces pombe" xref: Reactome:REACT_97761 "Neurotransmitter uptake and Metabolism In Glial Cells, Saccharomyces cerevisiae" xref: Reactome:REACT_98224 "Neurotransmitter uptake and Metabolism In Glial Cells, Oryza sativa" xref: Reactome:REACT_98482 "Neurotransmitter uptake and Metabolism In Glial Cells, Xenopus tropicalis" xref: Reactome:REACT_98978 "Neurotransmitter uptake and Metabolism In Glial Cells, Danio rerio" xref: Reactome:REACT_99735 "Neurotransmitter uptake and Metabolism In Glial Cells, Mus musculus" is_a: GO:0001505 ! regulation of neurotransmitter levels is_a: GO:0006836 ! neurotransmitter transport is_a: GO:0098657 ! import into cell [Term] id: GO:0001505 name: regulation of neurotransmitter levels namespace: biological_process def: "Any process that modulates levels of neurotransmitter." [GOC:jl] is_a: GO:0065008 ! regulation of biological quality [Term] id: GO:0001506 name: obsolete neurotransmitter biosynthetic process and storage namespace: biological_process def: "OBSOLETE. The chemical reactions and pathways resulting in the formation of neurotransmitters and the storage of the synthesized molecules." [GOC:go_curators, ISBN:0123668387] comment: This term was made obsolete because it is an amalgamation of its two children. synonym: "neurotransmitter anabolism and storage" EXACT [] synonym: "neurotransmitter biosynthetic process and storage" EXACT [] synonym: "neurotransmitter formation and storage" EXACT [] synonym: "neurotransmitter synthesis and storage" EXACT [] is_obsolete: true consider: GO:0042136 consider: GO:0042137 [Term] id: GO:0001507 name: acetylcholine catabolic process in synaptic cleft namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of acetylcholine that occurs in the synaptic cleft during synaptic transmission." [GOC:ai] synonym: "acetylcholine breakdown in synaptic cleft" EXACT [] synonym: "acetylcholine degradation in synaptic cleft" EXACT [] is_a: GO:0006581 ! acetylcholine catabolic process intersection_of: GO:0006581 ! acetylcholine catabolic process intersection_of: occurs_in GO:0043083 ! synaptic cleft relationship: occurs_in GO:0043083 ! synaptic cleft relationship: part_of GO:0007271 ! synaptic transmission, cholinergic [Term] id: GO:0001508 name: action potential namespace: biological_process def: "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8] comment: Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. is_a: GO:0042391 ! regulation of membrane potential [Term] id: GO:0001509 name: obsolete legumain activity namespace: molecular_function def: "OBSOLETE. Catalysis of the hydrolysis of proteins and small-molecule substrates at Asn-Xaa bonds." [EC:3.4.22.34] comment: This term was made obsolete because it represents a gene product. synonym: "asparaginyl endopeptidase activity" RELATED [EC:3.4.22.34] synonym: "bean endopeptidase activity" RELATED [EC:3.4.22.34] synonym: "citvac" RELATED [EC:3.4.22.34] synonym: "hemoglobinase activity" RELATED [EC:3.4.22.34] synonym: "legumain activity" EXACT [] synonym: "phaseolin activity" RELATED [EC:3.4.22.34] synonym: "proteinase B" RELATED [EC:3.4.22.34] synonym: "PRSC1 gene product (Homo sapiens)" RELATED [EC:3.4.22.34] synonym: "vicilin peptidohydrolase activity" RELATED [EC:3.4.22.34] xref: EC:3.4.22.34 xref: MetaCyc:3.4.22.34-RXN is_obsolete: true replaced_by: GO:0004197 [Term] id: GO:0001510 name: RNA methylation namespace: biological_process def: "Posttranscriptional addition of a methyl group to either a nucleotide or 2'-O ribose in a polyribonucleotide. Usually uses S-adenosylmethionine as a cofactor." [GOC:hjd] subset: gosubset_prok is_a: GO:0009451 ! RNA modification is_a: GO:0043414 ! macromolecule methylation [Term] id: GO:0001511 name: obsolete fibrillin namespace: molecular_function def: "OBSOLETE. Large glycoprotein that is a calcium binding component of connective tissue microfibrils containing 34 six-cysteine (EGF-like) repeats and five eight-cysteine (TGFbeta-1 binding protein-like) repeats. Defects associated with Marfan syndrome." [ISBN:0198506732] comment: This term was made obsolete because it represents a gene product. synonym: "fibrillin" EXACT [] is_obsolete: true consider: GO:0001527 consider: GO:0005509 [Term] id: GO:0001512 name: dihydronicotinamide riboside quinone reductase activity namespace: molecular_function def: "Catalysis of the reaction: 1-(beta-D-ribofuranosyl)-1,4-dihydronicotinamide + a quinone = 1-(beta-D-ribofuranosyl)nicotinamide + a hydroquinone." [EC:1.10.99.2] synonym: "1-(beta-D-ribofuranosyl)-1,4-dihydronicotinamide:quinone oxidoreductase activity" EXACT [EC:1.10.99.2] synonym: "N-ribosyldihydronicotinamide dehydrogenase (quinone) activity" EXACT [EC:1.10.99.2] synonym: "NAD(P)H:quinone oxidoreductase 2 activity" EXACT [EC:1.10.99.2] synonym: "NAD(P)H:quinone oxidoreductase-2" RELATED [EC:1.10.99.2] synonym: "NAD(P)H:quinone oxidoreductase2" RELATED [EC:1.10.99.2] synonym: "NQO(2) activity" EXACT [EC:1.10.99.2] synonym: "NQO2" RELATED [EC:1.10.99.2] synonym: "NRH:quinone oxidoreductase 2 activity" NARROW [EC:1.10.99.2] synonym: "QR2 activity" RELATED [EC:1.10.99.2] synonym: "quinone reductase 2 activity" RELATED [EC:1.10.99.2] synonym: "ribosyldihydronicotinamide dehydrogenase (quinone) activity" EXACT [] xref: EC:1.10.99.2 xref: MetaCyc:1.10.99.2-RXN is_a: GO:0016491 ! oxidoreductase activity [Term] id: GO:0001514 name: selenocysteine incorporation namespace: biological_process def: "The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine." [RESID:AA0022] subset: gosubset_prok xref: RESID:AA0022 is_a: GO:0006451 ! translational readthrough [Term] id: GO:0001515 name: opioid peptide activity namespace: molecular_function def: "Naturally occurring peptide that is an opioid (any non-alkaloid having an opiate-like effect that can be reversed by naloxone or other recognized morphine antagonist). These include Leu- and Met-enkephalin, dynorphin and neoendorphin, alpha, beta, gamma and delta endorphins formed from beta-lipotropin, various pronase-resistant peptides such as beta casamorphin, and other peptides whose opiate-like action seems to be indirect." [ISBN:0198506732] subset: goslim_chembl is_a: GO:0005102 ! receptor binding [Term] id: GO:0001516 name: prostaglandin biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring." [GOC:ai] subset: gosubset_prok synonym: "prostaglandin anabolism" EXACT [] synonym: "prostaglandin biosynthesis" EXACT [] synonym: "prostaglandin formation" EXACT [] synonym: "prostaglandin synthesis" EXACT [] is_a: GO:0006693 ! prostaglandin metabolic process is_a: GO:0046457 ! prostanoid biosynthetic process [Term] id: GO:0001517 name: N-acetylglucosamine 6-O-sulfotransferase activity namespace: molecular_function def: "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + N-acetyl-D-glucosamine = adenosine 3',5'-bisphosphate + N-acetyl-D-glucosamine 6-sulfate." [GOC:ai, GOC:hjd] subset: goslim_chembl synonym: "N-acetylglucosamine 6-O-sulphotransferase activity" EXACT [] xref: EC:2.8.2.- is_a: GO:0008146 ! sulfotransferase activity [Term] id: GO:0001518 name: voltage-gated sodium channel complex namespace: cellular_component def: "A sodium channel in a cell membrane whose opening is governed by the membrane potential." [ISBN:0198506732] synonym: "voltage gated sodium channel complex" EXACT [] synonym: "voltage-dependent sodium channel complex" EXACT [] synonym: "voltage-sensitive sodium channel complex" EXACT [] xref: NIF_Subcellular:sao785001660 is_a: GO:0034706 ! sodium channel complex is_a: GO:0098797 ! plasma membrane protein complex relationship: part_of GO:0005887 ! integral component of plasma membrane [Term] id: GO:0001519 name: peptide amidation namespace: biological_process def: "The posttranslational conversion of C-terminal glycine-extended peptides to C-terminal alpha-amidated peptides. Occurs to over half of all peptide hormones to give bioactive peptides. This is a two step process catalyzed by a peptidyl-glycine alpha-hydroxylating monooxygenase and a peptidyl-alpha-hydroxyglycine alpha-amidating lyase. In some organisms, this process is catalyzed by two separate enzymes, whereas in higher organisms, one polypeptide catalyzes both reactions." [PMID:11028916] subset: gosubset_prok is_a: GO:0031179 ! peptide modification [Term] id: GO:0001520 name: outer dense fiber namespace: cellular_component def: "A supramolecular fiber found in the flagella of mammalian sperm that surrounds the nine microtubule doublets. These dense fibers are stiff and noncontractile. In human, they consist of about 10 major and at least 15 minor proteins, where all major proteins are ODF1, ODF2 or ODF2-related proteins." [GOC:cilia, GOC:krc, ISBN:0824072820, PMID:10381817, PMID:21586547, PMID:25361759] synonym: "outer dense fibre" EXACT [] is_a: GO:0044441 ! ciliary part is_a: GO:0097223 ! sperm part is_a: GO:0099513 ! polymeric cytoskeletal fiber relationship: part_of GO:0036126 ! sperm flagellum [Term] id: GO:0001522 name: pseudouridine synthesis namespace: biological_process def: "The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs." [GOC:hjd, GOC:mah] subset: gosubset_prok synonym: "pseudouridylation" EXACT [] xref: Wikipedia:Pseudouridine xref: Wikipedia:Pseudouridylation is_a: GO:0009451 ! RNA modification [Term] id: GO:0001523 name: retinoid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity." [ISBN:0198506732] subset: gosubset_prok synonym: "retinoid metabolism" EXACT [] xref: Reactome:REACT_24968 "Vitamin A uptake in enterocytes, Homo sapiens" is_a: GO:0016101 ! diterpenoid metabolic process [Term] id: GO:0001524 name: obsolete globin namespace: molecular_function def: "OBSOLETE. The colorless and basic protein moiety of hemoglobin and myoglobins." [GOC:ai, ISBN:0198506732] comment: This term was made obsolete because it represents a gene product. synonym: "globin" EXACT [] is_obsolete: true replaced_by: GO:0005344 [Term] id: GO:0001525 name: angiogenesis namespace: biological_process def: "Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels." [ISBN:0878932453] synonym: "blood vessel formation from pre-existing blood vessels" EXACT systematic_synonym [] xref: Wikipedia:Angiogenesis is_a: GO:0044767 ! single-organism developmental process is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis relationship: part_of GO:0048514 ! blood vessel morphogenesis [Term] id: GO:0001526 name: obsolete proteoglycan sulfate transfer namespace: biological_process def: "OBSOLETE. Transfer of sulfate to a proteoglycan (a glycoprotein whose carbohydrate units are glycosaminoglycans) using 3'-phosphoadenyl sulfate." [GOC:hjd] comment: This term was made obsolete because it represents a group of molecular functions. synonym: "proteoglycan sulfate transfer" EXACT [] synonym: "proteoglycan sulphate transfer" EXACT [] is_obsolete: true consider: GO:0006029 consider: GO:0006790 consider: GO:0050698 [Term] id: GO:0001527 name: microfibril namespace: cellular_component def: "Extracellular matrix components occurring independently or along with elastin. Thought to have force-bearing functions in tendon. In addition to fibrillins, microfibrils may contain other associated proteins." [http://www.xrefer.com/entry/490235] synonym: "extended fibrils" EXACT [] synonym: "fibrillin" RELATED [] is_a: GO:0043205 ! fibril [Term] id: GO:0001528 name: obsolete elastin namespace: molecular_function def: "OBSOLETE. A major structural protein of mammalian connective tissues; composed of one third glycine, and also rich in proline, alanine, and valine. Chains are cross-linked together via lysine residues." [ISBN:0198506732] comment: This term was made obsolete because it represents a gene product. synonym: "elastin" EXACT [] is_obsolete: true replaced_by: GO:0030023 [Term] id: GO:0001529 name: obsolete elastin namespace: cellular_component def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah] comment: This term was made obsolete because it represents a gene product. synonym: "elastin" EXACT [] is_obsolete: true replaced_by: GO:0030023 [Term] id: GO:0001530 name: lipopolysaccharide binding namespace: molecular_function def: "Interacting selectively and non-covalently with lipopolysaccharide." [PMID:11079463] synonym: "endotoxin binding" BROAD [] synonym: "LPS binding" EXACT [] is_a: GO:0008289 ! lipid binding is_a: GO:0097367 ! carbohydrate derivative binding [Term] id: GO:0001531 name: interleukin-21 receptor binding namespace: molecular_function def: "Interacting selectively and non-covalently with the interleukin-21 receptor." [GOC:ai] synonym: "IL-21" NARROW [] synonym: "interleukin-21 receptor ligand" NARROW [] is_a: GO:0005126 ! cytokine receptor binding [Term] id: GO:0001532 name: interleukin-21 receptor activity namespace: molecular_function def: "Combining with interleukin-21 and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:jl, GOC:signaling] synonym: "IL-21 receptor activity" EXACT [GOC:mah] synonym: "IL-21R" EXACT [] is_a: GO:0004896 ! cytokine receptor activity relationship: has_part GO:0019977 ! interleukin-21 binding relationship: part_of GO:0038114 ! interleukin-21-mediated signaling pathway [Term] id: GO:0001533 name: cornified envelope namespace: cellular_component def: "A type of plasma membrane that has been modified through addition of distinct intracellular and extracellular components, including ceramide, found in cornifying epithelial cells (corneocytes)." [GOC:add, PMID:11112355, PMID:11590230, PMID:15803139] is_a: GO:0005886 ! plasma membrane [Term] id: GO:0001534 name: radial spoke namespace: cellular_component def: "Protein complex that links the outer microtubule doublet of the ciliary or flagellum axoneme with the sheath that surrounds the central pair of microtubules. Composed of a stalk that attaches to each doublet microtubule and a globular structure (spoke head) that projects toward the central pair of microtubules." [ISBN:0124325653, PMID:9450971] subset: goslim_pir xref: Wikipedia:Radial_spoke is_a: GO:0043234 ! protein complex is_a: GO:0044447 ! axoneme part [Term] id: GO:0001535 name: radial spoke head namespace: cellular_component def: "Protein complex forming part of eukaryotic flagellar apparatus." [GOC:cilia, GOC:hjd, GOC:krc] synonym: "radial spokehead" EXACT [] is_a: GO:0043234 ! protein complex is_a: GO:0044447 ! axoneme part relationship: part_of GO:0001534 ! radial spoke [Term] id: GO:0001536 name: radial spoke stalk namespace: cellular_component def: "Globular portion of the radial spoke that projects towards the central pair of microtubules." [GOC:hjd] is_a: GO:0043234 ! protein complex is_a: GO:0044447 ! axoneme part relationship: part_of GO:0001534 ! radial spoke [Term] id: GO:0001537 name: N-acetylgalactosamine 4-O-sulfotransferase activity namespace: molecular_function def: "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + N-acetyl-D-galactosamine = adenosine 3',5'-bisphosphate + N-acetyl-D-galactosamine 4-sulfate." [EC:2.8.2.-, GOC:ai] synonym: "N-acetylgalactosamine 4-O-sulphotransferase activity" EXACT [] xref: EC:2.8.2.- is_a: GO:0008146 ! sulfotransferase activity [Term] id: GO:0001539 name: cilium or flagellum-dependent cell motility namespace: biological_process def: "Cell motility due to movement of eukaryotic cilia or bacterial-type flagella or archaeal-type flagella." [GOC:cilia, GOC:hjd, GOC:krc] comment: Note that we deem eukaryotic cilia and microtubule-based flagella to be equivalent, while the bacterial- and archaeal-type flagella have a different structure. The former are microtubule-based structures that lash back and forth and are present only in eukaryotes, while the latter achieve motility by rotation. Bacterial- and archaeal-type flagella are superficially similar but have a different molecular composition and fine structure. These three structures never co-exist in the same organism. Therefore, GO:0001539 'cilium or flagellum-dependent cell motility' is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term. Direct annotations to GO:0001539 'cilium or flagellum-dependent cell motility' may be amended during annotation QC. subset: gocheck_do_not_manually_annotate subset: gosubset_prok synonym: "ciliary or bacterial-type flagellar motility" RELATED [] synonym: "ciliary/flagellar motility" EXACT [] is_a: GO:0048870 ! cell motility [Term] id: GO:0001540 name: beta-amyloid binding namespace: molecular_function def: "Interacting selectively and non-covalently with beta-amyloid peptide/protein and/or its precursor." [GOC:hjd] subset: goslim_chembl is_a: GO:0042277 ! peptide binding [Term] id: GO:0001541 name: ovarian follicle development namespace: biological_process def: "The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure." [GOC:go_curators] synonym: "follicular phase" RELATED [] is_a: GO:0022602 ! ovulation cycle process is_a: GO:0044767 ! single-organism developmental process is_a: GO:0048608 ! reproductive structure development relationship: part_of GO:0008585 ! female gonad development [Term] id: GO:0001542 name: ovulation from ovarian follicle namespace: biological_process def: "The process leading to the rupture of the follicle, releasing the centrally located oocyte into the oviduct. An example of this is found in Mus musculus." [GOC:mtg_sensu, http://ovary.stanford.edu] is_a: GO:0022602 ! ovulation cycle process is_a: GO:0030728 ! ovulation relationship: part_of GO:0008585 ! female gonad development [Term] id: GO:0001543 name: ovarian follicle rupture namespace: biological_process def: "Disruption of theca cell layer releasing follicular fluid and/or the oocyte." [http://ovary.stanford.edu] is_a: GO:0022602 ! ovulation cycle process relationship: part_of GO:0001542 ! ovulation from ovarian follicle [Term] id: GO:0001544 name: initiation of primordial ovarian follicle growth namespace: biological_process def: "Increase in size of primordial follicles including proliferation and shape changes of granulosa and/or theca cells until oocyte is surrounded by one layer of cuboidal shaped granulosa cells (primary follicle)." [http://ovary.stanford.edu] is_a: GO:0022602 ! ovulation cycle process relationship: part_of GO:0001541 ! ovarian follicle development [Term] id: GO:0001545 name: primary ovarian follicle growth namespace: biological_process def: "Increase in size of primary follicles including oocyte growth and granulosa and/or theca cell proliferation until more than one layer of granulosa cells is present (preantral follicle)." [GOC:mtg_mpo, http://ovary.stanford.edu] is_a: GO:0022602 ! ovulation cycle process is_a: GO:0040007 ! growth relationship: part_of GO:0001541 ! ovarian follicle development [Term] id: GO:0001546 name: preantral ovarian follicle growth namespace: biological_process def: "Increase in size of follicles surrounded by two or more layers of granulosa cells up to the onset of antrum formation." [http://ovary.stanford.edu] is_a: GO:0022602 ! ovulation cycle process is_a: GO:0040007 ! growth relationship: part_of GO:0001541 ! ovarian follicle development relationship: part_of GO:0048162 ! multi-layer follicle stage [Term] id: GO:0001547 name: antral ovarian follicle growth namespace: biological_process def: "Increase in size of antral follicles due to cell proliferation and/or growth of the antral cavity." [http://ovary.stanford.edu] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0022602 ! ovulation cycle process is_a: GO:0048589 ! developmental growth relationship: part_of GO:0001541 ! ovarian follicle development [Term] id: GO:0001548 name: follicular fluid formation in ovarian follicle antrum namespace: biological_process def: "The menstrual cycle process that results in the formation of one central cavity separating the oocyte/cumulus complex from mural granulosa and theca cells during the various stages of oogenesis." [GOC:dph, GOC:tb, http://ovary.stanford.edu] synonym: "ovarian follicle antrum/follicular fluid biosynthesis" EXACT [] synonym: "ovarian follicle antrum/follicular fluid formation" EXACT [] is_a: GO:0022602 ! ovulation cycle process relationship: part_of GO:0001547 ! antral ovarian follicle growth [Term] id: GO:0001549 name: cumulus cell differentiation namespace: biological_process def: "The process in which a subpopulation of granulosa cells surrounding the oocyte acquires the specialized features of an ovarian cumulus cell." [http://ovary.stanford.edu] synonym: "ovarian cumulus cell differentiation" EXACT [] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism is_a: GO:0022602 ! ovulation cycle process is_a: GO:0030855 ! epithelial cell differentiation relationship: part_of GO:0001547 ! antral ovarian follicle growth relationship: part_of GO:0048165 ! fused antrum stage [Term] id: GO:0001550 name: ovarian cumulus expansion namespace: biological_process def: "Increase in size of the cumulus surrounding the oocyte including change in morphology due to proliferation and dispersion of cumulus cells." [http://ovary.stanford.edu] synonym: "ovarian cumulus growth" RELATED [] is_a: GO:0022602 ! ovulation cycle process is_a: GO:0040007 ! growth relationship: part_of GO:0001547 ! antral ovarian follicle growth relationship: part_of GO:0048165 ! fused antrum stage [Term] id: GO:0001551 name: ovarian follicle endowment namespace: biological_process def: "Association of oocytes with supporting epithelial granulosa cells to form primordial follicles." [http://ovary.stanford.edu] is_a: GO:0022602 ! ovulation cycle process relationship: part_of GO:0001541 ! ovarian follicle development [Term] id: GO:0001552 name: ovarian follicle atresia namespace: biological_process def: "A periodic process in which immature ovarian follicles degenerate and are subsequently re-absorbed." [GOC:mtg_apoptosis, http://ovary.stanford.edu, PMID:18638134] is_a: GO:0003006 ! developmental process involved in reproduction relationship: has_part GO:0097191 ! extrinsic apoptotic signaling pathway relationship: part_of GO:0008585 ! female gonad development [Term] id: GO:0001553 name: luteinization namespace: biological_process def: "The set of processes resulting in differentiation of theca and granulosa cells into luteal cells and in the formation of a corpus luteum after ovulation." [http://ovary.stanford.edu] synonym: "luteal phase" RELATED [] xref: Wikipedia:Luteal_phase xref: Wikipedia:Luteinization is_a: GO:0022602 ! ovulation cycle process relationship: part_of GO:0008585 ! female gonad development [Term] id: GO:0001554 name: luteolysis namespace: biological_process def: "The lysis or structural demise of the corpus luteum. During normal luteolysis, two closely related events occur. First, there is loss of the capacity to synthesize and secrete progesterone (functional luteolysis) followed by loss of the cells that comprise the corpus luteum (structural luteolysis). Preventing luteolysis is crucial to maintain pregnancy." [http://ovary.stanford.edu, PMID:10617764] xref: Wikipedia:Luteolysis is_a: GO:0022602 ! ovulation cycle process relationship: part_of GO:0008585 ! female gonad development [Term] id: GO:0001555 name: oocyte growth namespace: biological_process def: "The developmental growth process in which an oocyte irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." [http://ovary.stanford.edu] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism is_a: GO:0048588 ! developmental cell growth relationship: part_of GO:0048599 ! oocyte development [Term] id: GO:0001556 name: oocyte maturation namespace: biological_process def: "A developmental process, independent of morphogenetic (shape) change, that is required for an oocyte to attain its fully functional state. Oocyte maturation commences after reinitiation of meiosis commonly starting with germinal vesicle breakdown, and continues up to the second meiotic arrest prior to fertilization." [GOC:devbiol, http://ovary.stanford.edu] xref: Wikipedia:Oocyte_maturation is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism is_a: GO:0048469 ! cell maturation relationship: part_of GO:0048599 ! oocyte development [Term] id: GO:0001557 name: obsolete metabolic process resulting in cell growth namespace: biological_process def: "OBSOLETE. The chemical reactions that occur in living organisms that result in an increase in the mass (size) of a cell." [GOC:dph] comment: This term was made obsolete as part of the metabolism rearrangements, because it is redundant with other terms. synonym: "metabolic process resulting in cell growth" EXACT [] is_obsolete: true consider: GO:0008152 consider: GO:0016049 [Term] id: GO:0001558 name: regulation of cell growth namespace: biological_process def: "Any process that modulates the frequency, rate, extent or direction of cell growth." [GOC:go_curators] subset: gosubset_prok xref: Reactome:REACT_6201 "DTOR is positively regulated by DRheb-GTP, Drosophila melanogaster" is_a: GO:0040008 ! regulation of growth is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0016049 ! cell growth relationship: regulates GO:0016049 ! cell growth [Term] id: GO:0001559 name: regulation of cell growth by detection of nuclear:cytoplasmic ratio namespace: biological_process def: "Any process in which the size of the nucleus with respect to the cytoplasm modulates the frequency, rate or extent of cell growth, the irreversible increase in size of a cell over time." [GOC:dph] synonym: "detection of nuclear:cytoplasmic ratio to regulate cell growth" EXACT [] synonym: "interpretation of nuclear:cytoplasmic ratio to regulate cell growth" EXACT [] synonym: "regulation of cell growth by nuclear:cytoplasmic ratio" EXACT [] synonym: "regulation of cell growth by sensing of nuclear:cytoplasmic ratio" EXACT [] is_a: GO:0016475 ! detection of nuclear:cytoplasmic ratio is_a: GO:0061387 ! regulation of extent of cell growth intersection_of: GO:0016475 ! detection of nuclear:cytoplasmic ratio intersection_of: regulates GO:0016049 ! cell growth relationship: regulates GO:0016049 ! cell growth [Term] id: GO:0001560 name: regulation of cell growth by extracellular stimulus namespace: biological_process def: "Any process in which external signals modulate the frequency, rate or extent of cell growth, the irreversible increase in size of a cell over time." [GOC:dph] synonym: "interpretation of external signals that regulate cell growth" EXACT [] synonym: "regulation of cell growth by detection of exogenous stimulus" EXACT [] synonym: "regulation of cell growth by sensing of exogenous stimulus" EXACT [] synonym: "regulation of growth by exogenous signal" EXACT [] synonym: "regulation of growth by exogenous stimuli" EXACT [] synonym: "regulation of growth by exogenous stimulus" EXACT [] synonym: "regulation of growth by external signal" EXACT [] synonym: "regulation of growth by external stimuli" EXACT [] synonym: "regulation of growth by external stimulus" EXACT [] is_a: GO:0001558 ! regulation of cell growth intersection_of: GO:0001558 ! regulation of cell growth intersection_of: part_of GO:0031668 ! cellular response to extracellular stimulus relationship: part_of GO:0031668 ! cellular response to extracellular stimulus [Term] id: GO:0001561 name: fatty acid alpha-oxidation namespace: biological_process def: "A metabolic pathway by which 3-methyl branched fatty acids are degraded. These compounds are not degraded by the normal peroxisomal beta-oxidation pathway, because the 3-methyl blocks the dehydrogenation of the hydroxyl group by hydroxyacyl-CoA dehydrogenase. The 3-methyl branched fatty acid is converted in several steps to pristenic acid, which can then feed into the beta-oxidative pathway." [http://www.peroxisome.org/Scientist/Biochemistry/alpha-oxidation.html] subset: gosubset_prok xref: MetaCyc:PWY-2501 xref: Reactome:REACT_103076 "Alpha-oxidation of phytanate, Dictyostelium discoideum" xref: Reactome:REACT_106518 "Alpha-oxidation of phytanate, Drosophila melanogaster" xref: Reactome:REACT_106956 "Alpha-oxidation of phytanate, Mus musculus" xref: Reactome:REACT_107335 "Alpha-oxidation of phytanate, Taeniopygia guttata" xref: Reactome:REACT_109097 "Alpha-oxidation of phytanate, Saccharomyces cerevisiae" xref: Reactome:REACT_17003 "Alpha-oxidation of phytanate, Homo sapiens" xref: Reactome:REACT_29885 "Alpha-oxidation of phytanate, Oryza sativa" xref: Reactome:REACT_47735 "Alpha-oxidation of phytanate, Gallus gallus" xref: Reactome:REACT_78088 "Alpha-oxidation of phytanate, Bos taurus" xref: Reactome:REACT_81097 "Alpha-oxidation of phytanate, Xenopus tropicalis" xref: Reactome:REACT_83317 "Alpha-oxidation of phytanate, Caenorhabditis elegans" xref: Reactome:REACT_87622 "Alpha-oxidation of phytanate, Sus scrofa" xref: Reactome:REACT_87835 "Alpha-oxidation of phytanate, Arabidopsis thaliana" xref: Reactome:REACT_90750 "Alpha-oxidation of phytanate, Canis familiaris" xref: Reactome:REACT_92361 "Alpha-oxidation of phytanate, Mycobacterium tuberculosis" xref: Reactome:REACT_94726 "Alpha-oxidation of phytanate, Escherichia coli" xref: Reactome:REACT_94872 "Alpha-oxidation of phytanate, Rattus norvegicus" xref: Reactome:REACT_96409 "Alpha-oxidation of phytanate, Danio rerio" xref: Reactome:REACT_98637 "Alpha-oxidation of phytanate, Schizosaccharomyces pombe" is_a: GO:0009062 ! fatty acid catabolic process is_a: GO:0019395 ! fatty acid oxidation [Term] id: GO:0001562 name: response to protozoan namespace: biological_process alt_id: GO:0042833 def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a protozoan." [GOC:ai] synonym: "resistance to pathogenic protozoa" RELATED [] synonym: "response to protozoa" EXACT [] synonym: "response to protozoon" EXACT [] is_a: GO:0051707 ! response to other organism [Term] id: GO:0001563 name: detection of protozoan namespace: biological_process def: "The series of events in which a stimulus from a protozoan is received and converted into a molecular signal." [GOC:ai] synonym: "detection of protozoa" EXACT [] synonym: "detection of protozoon" EXACT [] synonym: "perception of protozoa" RELATED [] is_a: GO:0001562 ! response to protozoan is_a: GO:0098543 ! detection of other organism [Term] id: GO:0001564 name: obsolete resistance to pathogenic protozoa namespace: biological_process def: "OBSOLETE (was not defined before being made obsolete)." [GOC:go_curators] comment: This term was made obsolete because 'resistance' implies a phenotype rather than a biological process. synonym: "resistance to pathogenic protozoa" EXACT [] is_obsolete: true replaced_by: GO:0001562 [Term] id: GO:0001565 name: phorbol ester receptor activity namespace: molecular_function def: "Combining with a phorbol ester and transmitting the signal to initiate a change in cell activity." [GOC:ai, GOC:signaling, PMID:10506570] is_a: GO:0038023 ! signaling receptor activity [Term] id: GO:0001566 name: non-kinase phorbol ester receptor activity namespace: molecular_function def: "Combining with a phorbol ester and transmitting the signal by a mechanism independent of kinase activity." [PMID:10506570] is_a: GO:0001565 ! phorbol ester receptor activity [Term] id: GO:0001567 name: cholesterol 25-hydroxylase activity namespace: molecular_function def: "Catalysis of the reaction: AH(2) + cholesterol + O(2) = 25-hydroxycholesterol + A + H(2)O." [EC:1.14.99.38, RHEA:21107] synonym: "cholesterol 25-monooxygenase activity" EXACT [EC:1.14.99.38] synonym: "cholesterol,hydrogen-donor:oxygen oxidoreductase (25-hydroxylating) activity" EXACT [EC:1.14.99.38] xref: EC:1.14.99.38 xref: KEGG:R07218 xref: MetaCyc:1.14.99.38-RXN xref: RHEA:21107 is_a: GO:0008395 ! steroid hydroxylase activity is_a: GO:0016705 ! oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Term] id: GO:0001568 name: blood vessel development namespace: biological_process def: "The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood." [GOC:hjd, UBERON:0001981] is_a: GO:0044767 ! single-organism developmental process is_a: GO:0048856 ! anatomical structure development relationship: part_of GO:0001944 ! vasculature development [Term] id: GO:0001569 name: patterning of blood vessels namespace: biological_process def: "The process that regulates the coordinated growth and sprouting of blood vessels giving rise to the organized vascular system." [GOC:dph] synonym: "branching involved in blood vessel morphogenesis" EXACT [GOC:dph] is_a: GO:0007389 ! pattern specification process is_a: GO:0048754 ! branching morphogenesis of an epithelial tube relationship: part_of GO:0001525 ! angiogenesis [Term] id: GO:0001570 name: vasculogenesis namespace: biological_process def: "The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes." [PMID:8999798] synonym: "vascular morphogenesis" EXACT [] xref: Wikipedia:Vasculogenesis is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0048514 ! blood vessel morphogenesis [Term] id: GO:0001571 name: non-tyrosine kinase fibroblast growth factor receptor activity namespace: molecular_function def: "Combining with fibroblast growth factor (FGF) and transmitting the signal from one side of the membrane to the other by a mechanism independent of tyrosine kinase activity." [GOC:signaling, PMID:11418238] synonym: "non-tyrosine kinase FGF receptor activity" EXACT [] synonym: "non-tyrosine kinase FGFR activity" EXACT [] is_a: GO:0004888 ! transmembrane signaling receptor activity [Term] id: GO:0001572 name: lactosylceramide biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of lactosylceramides, Gal-beta-(1->4)-Glc-beta(1->1') ceramides, any compound formed by the replacement of the glycosidic C1 hydroxyl group of lactose by a ceramide group. They are the precursors of both gangliosides and globosides." [ISBN:0198506732, ISBN:0471586501] subset: gosubset_prok synonym: "lactosylceramide anabolism" EXACT [] synonym: "lactosylceramide biosynthesis" EXACT [] synonym: "lactosylceramide formation" EXACT [] synonym: "lactosylceramide synthesis" EXACT [] is_a: GO:0006688 ! glycosphingolipid biosynthetic process is_a: GO:0046478 ! lactosylceramide metabolic process is_a: GO:0046513 ! ceramide biosynthetic process [Term] id: GO:0001573 name: ganglioside metabolic process namespace: biological_process def: "The chemical reactions and pathways involving ceramide oligosaccharides carrying in addition to other sugar residues, one or more sialic acid residues." [ISBN:0198506732] subset: gosubset_prok synonym: "ganglioside metabolism" EXACT [] is_a: GO:0006672 ! ceramide metabolic process is_a: GO:0006687 ! glycosphingolipid metabolic process [Term] id: GO:0001574 name: ganglioside biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of ceramide oligosaccharides carrying in addition to other sugar residues, one or more sialic acid residues." [ISBN:0198506732] subset: gosubset_prok synonym: "ganglioside anabolism" EXACT [] synonym: "ganglioside biosynthesis" EXACT [] synonym: "ganglioside formation" EXACT [] synonym: "ganglioside synthesis" EXACT [] is_a: GO:0001573 ! ganglioside metabolic process is_a: GO:0006688 ! glycosphingolipid biosynthetic process is_a: GO:0046513 ! ceramide biosynthetic process [Term] id: GO:0001575 name: globoside metabolic process namespace: biological_process def: "The chemical reactions and pathways involving globosides, globotetraosylceramides, ceramides containing a core structure of GalNAc-beta-(1->3)-Gal-alpha-(1->4)-Glc(I). Globosides are the major neutral glycosphingolipid in normal kidneys and erythrocytes." [ISBN:0198506732] subset: gosubset_prok synonym: "globoside metabolism" EXACT [] is_a: GO:0006687 ! glycosphingolipid metabolic process [Term] id: GO:0001576 name: globoside biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of a ceramide with a core structure of GalNAc-beta-(1->3)-Gal-alpha-(1->4)-Glc(I)." [ISBN:0198506732] subset: gosubset_prok synonym: "globoside anabolism" EXACT [] synonym: "globoside biosynthesis" EXACT [] synonym: "globoside formation" EXACT [] synonym: "globoside synthesis" EXACT [] is_a: GO:0001575 ! globoside metabolic process is_a: GO:0006688 ! glycosphingolipid biosynthetic process [Term] id: GO:0001577 name: obsolete galectin namespace: molecular_function def: "OBSOLETE. A lectin that exhibits calcium independent binding of beta-galactoside sugars." [PMID:9786891] comment: This term was made obsolete because it refers to a class of gene products. synonym: "galectin" EXACT [] synonym: "S-type lectin" EXACT [] is_obsolete: true consider: GO:0007157 consider: GO:0016936 [Term] id: GO:0001578 name: microtubule bundle formation namespace: biological_process def: "A process that results in a parallel arrangement of microtubules." [GOC:dph] synonym: "microtubule bundling" EXACT [] is_a: GO:0000226 ! microtubule cytoskeleton organization [Term] id: GO:0001579 name: medium-chain fatty acid transport namespace: biological_process def: "The directed movement of medium-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A medium-chain fatty acid is a fatty acid with a chain length of between C6 and C12." [CHEBI:59554, GOC:ai] is_a: GO:0015908 ! fatty acid transport [Term] id: GO:0001580 name: detection of chemical stimulus involved in sensory perception of bitter taste namespace: biological_process def: "The series of events required for a bitter taste stimulus to be received and converted to a molecular signal." [GOC:go_curators] synonym: "bitter taste detection" EXACT [] synonym: "perception of bitter taste, detection of chemical stimulus" EXACT [] synonym: "perception of bitter taste, sensory transduction of chemical stimulus" EXACT [] synonym: "sensory detection of bitter taste" EXACT [] synonym: "sensory detection of chemical stimulus during perception of bitter taste" EXACT [] synonym: "sensory transduction of bitter taste" EXACT [] synonym: "sensory transduction of chemical stimulus during perception of bitter taste" EXACT [] is_a: GO:0050912 ! detection of chemical stimulus involved in sensory perception of taste intersection_of: GO:0009593 ! detection of chemical stimulus intersection_of: part_of GO:0050913 ! sensory perception of bitter taste relationship: part_of GO:0050913 ! sensory perception of bitter taste [Term] id: GO:0001581 name: detection of chemical stimulus involved in sensory perception of sour taste namespace: biological_process def: "The series of events required for a sour taste stimulus to be received and converted to a molecular signal." [GOC:go_curators] synonym: "perception of sour taste, detection of chemical stimulus" EXACT [] synonym: "perception of sour taste, sensory transduction of chemical stimulus" EXACT [] synonym: "sensory detection of chemical stimulus during perception of sour taste" EXACT [] synonym: "sensory detection of sour taste" EXACT [] synonym: "sensory transduction of chemical stimulus during perception of sour taste" EXACT [] synonym: "sensory transduction of sour taste" EXACT [] synonym: "sour taste detection" EXACT [] is_a: GO:0050912 ! detection of chemical stimulus involved in sensory perception of taste intersection_of: GO:0009593 ! detection of chemical stimulus intersection_of: part_of GO:0050915 ! sensory perception of sour taste relationship: part_of GO:0050915 ! sensory perception of sour taste [Term] id: GO:0001582 name: detection of chemical stimulus involved in sensory perception of sweet taste namespace: biological_process def: "The series of events required for a sweet taste stimulus to be received and converted to a molecular signal." [GOC:go_curators] synonym: "perception of sweet taste, detection of chemical stimulus" EXACT [] synonym: "perception of sweet taste, sensory transduction of chemical stimulus" EXACT [] synonym: "sensory detection of chemical stimulus during perception of sweet taste" EXACT [] synonym: "sensory detection of sweet taste" EXACT [] synonym: "sensory transduction of chemical stimulus during perception of sweet taste" EXACT [] synonym: "sensory transduction of sweet taste" EXACT [] synonym: "sweet taste detection" EXACT [] is_a: GO:0050912 ! detection of chemical stimulus involved in sensory perception of taste intersection_of: GO:0009593 ! detection of chemical stimulus intersection_of: part_of GO:0050916 ! sensory perception of sweet taste relationship: part_of GO:0050916 ! sensory perception of sweet taste [Term] id: GO:0001583 name: detection of chemical stimulus involved in sensory perception of salty taste namespace: biological_process def: "The series of events required for a salty taste stimulus to be received and converted to a molecular signal." [GOC:go_curators] synonym: "perception of salty taste, detection of chemical stimulus" EXACT [] synonym: "perception of salty taste, sensory transduction of chemical stimulus" EXACT [] synonym: "salty taste detection" EXACT [] synonym: "sensory detection of chemical stimulus during perception of salty taste" EXACT [] synonym: "sensory detection of salty taste" EXACT [] synonym: "sensory transduction of chemical stimulus during perception of salty taste" EXACT [] synonym: "sensory transduction of salty taste" EXACT [] is_a: GO:0050912 ! detection of chemical stimulus involved in sensory perception of taste intersection_of: GO:0009593 ! detection of chemical stimulus intersection_of: part_of GO:0050914 ! sensory perception of salty taste relationship: part_of GO:0050914 ! sensory perception of salty taste [Term] id: GO:0001584 name: obsolete rhodopsin-like receptor activity namespace: molecular_function alt_id: GO:0001620 def: "OBSOLETE. A G-protein coupled receptor that is structurally/functionally related to the rhodopsin receptor." [GOC:dph, GOC:mah, GOC:tb, IUPHAR_GPCR:1505] comment: This term was made obsolete because it represents a gene product and is named based on protein features. subset: gosubset_prok synonym: "Class A G protein coupled receptor" EXACT [] synonym: "Class A G-protein coupled receptor" EXACT [] synonym: "Class A GPCR" EXACT [] synonym: "class A orphan receptor activity" EXACT [] synonym: "rhodopsin-like receptor activity" EXACT [] is_obsolete: true [Term] id: GO:0001586 name: Gi/o-coupled serotonin receptor activity namespace: molecular_function def: "Combining with serotonin and transmitting the signal across the membrane by activation of the Gi/o subunit of an associated cytoplasmic heterotrimeric G protein complex. The Gi/o subunit subsequently inhibits adenylate cyclase and results in a decrease in cyclic AMP (cAMP) levels." [GOC:mah, PMID:18571247] synonym: "5-HT1 receptor activity" EXACT [GOC:bf] synonym: "serotonin receptor activity, coupled via Gi/o" EXACT [GOC:bf] is_a: GO:0004993 ! G-protein coupled serotonin receptor activity [Term] id: GO:0001587 name: Gq/11-coupled serotonin receptor activity namespace: molecular_function def: "Combining with serotonin and transmitting the signal across the membrane by activation of the Gq/11 subunit of an associated cytoplasmic heterotrimeric G protein complex. The Gq/11 subunit subsequently activates phospholipase C and results in an increase in inositol triphosphate (IP3) levels." [GOC:bf, GOC:mah, PMID:18571247, PMID:18703043] synonym: "5-HT2 receptor activity" BROAD [GOC:bf] synonym: "serotonin receptor activity, coupled via Gq/11" EXACT [GOC:bf] is_a: GO:0004993 ! G-protein coupled serotonin receptor activity [Term] id: GO:0001588 name: dopamine neurotransmitter receptor activity, coupled via Gs namespace: molecular_function alt_id: GO:0001589 alt_id: GO:0001590 def: "Combining with the neurotransmitter dopamine and activating adenylate cyclase via coupling to Gs to initiate a change in cell activity." [GOC:mah, ISBN:0953351033, IUPHAR_RECEPTOR:2252, IUPHAR_RECEPTOR:2260] synonym: "dopamine D1 receptor activity" NARROW [GOC:bf] synonym: "dopamine D5 receptor activity" NARROW [GOC:bf] is_a: GO:0004952 ! dopamine neurotransmitter receptor activity [Term] id: GO:0001591 name: dopamine neurotransmitter receptor activity, coupled via Gi/Go namespace: molecular_function alt_id: GO:0001592 alt_id: GO:0001593 alt_id: GO:0001670 def: "Combining with the neurotransmitter dopamine and activating adenylate cyclase via coupling to Gi/Go to initiate a change in cell activity." [GOC:mah, ISBN:0953351033, IUPHAR_RECEPTOR:2254, IUPHAR_RECEPTOR:2256, IUPHAR_RECEPTOR:2258] synonym: "dopamine D2 receptor activity" NARROW [GOC:bf] synonym: "dopamine D3 receptor activity" NARROW [GOC:bf] synonym: "dopamine D4 receptor activity" NARROW [GOC:bf] is_a: GO:0004952 ! dopamine neurotransmitter receptor activity [Term] id: GO:0001594 name: trace-amine receptor activity namespace: molecular_function def: "Combining with a trace amine to initiate a change in cell activity. Trace amines are biogenic amines that are synthesized from aromatic amino acids and are substrates for monoamine oxidase, and are therefore detectable only at trace levels in mammals." [GOC:mah, PMID:19325074] is_a: GO:0008227 ! G-protein coupled amine receptor activity [Term] id: GO:0001595 name: angiotensin receptor activity namespace: molecular_function def: "Combining with angiotensin to initiate a change in cell activity." [GOC:ai] is_a: GO:0008528 ! G-protein coupled peptide receptor activity relationship: part_of GO:0038166 ! angiotensin-activated signaling pathway [Term] id: GO:0001596 name: angiotensin type I receptor activity namespace: molecular_function def: "An angiotensin receptor activity that acts via Gq-mediated activation of phospholipase C followed by phosphoinositide hydrolysis and Ca2+ signaling, and may act via additional signaling mechanisms." [GOC:mah, PMID:10977869] synonym: "PLC-activating angiotensin receptor activity" EXACT [GOC:bf] is_a: GO:0001595 ! angiotensin receptor activity relationship: part_of GO:0086097 ! phospholipase C-activating angiotensin-activated signaling pathway [Term] id: GO:0001597 name: obsolete apelin-like receptor namespace: molecular_function def: "OBSOLETE (was not defined before being made obsolete)." [GOC:jl] comment: This term was made obsolete because the function it represents does not exist. synonym: "apelin-like receptor" EXACT [] synonym: "APJ-like receptor" EXACT [] is_obsolete: true consider: GO:0031704 [Term] id: GO:0001598 name: obsolete chemokine receptor-like receptor activity namespace: molecular_function def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah] comment: This term was made obsolete because it represents a gene product, was not defined, and is named based on protein features. synonym: "chemokine receptor-like receptor activity" EXACT [] is_obsolete: true [Term] id: GO:0001601 name: peptide YY receptor activity namespace: molecular_function def: "Combining with gut peptide YY to initiate a change in cell activity." [PMID:9315606] is_a: GO:0004983 ! neuropeptide Y receptor activity [Term] id: GO:0001602 name: pancreatic polypeptide receptor activity namespace: molecular_function def: "Combining with pancreatic polypeptide PP to initiate a change in cell activity." [PMID:9315606] is_a: GO:0004983 ! neuropeptide Y receptor activity [Term] id: GO:0001603 name: obsolete vasopressin-like receptor activity namespace: molecular_function def: "OBSOLETE (was not defined before being made obsolete)." [GOC:curators] synonym: "vasopressin-like receptor activity" EXACT [] is_obsolete: true [Term] id: GO:0001604 name: urotensin II receptor activity namespace: molecular_function def: "Combining with urotensin II to initiate a change in cell activity." [GOC:mah, PMID:15102493] is_a: GO:0008528 ! G-protein coupled peptide receptor activity [Term] id: GO:0001605 name: adrenomedullin receptor activity namespace: molecular_function def: "Combining with adrenomedullin to initiate a change in cell activity." [GOC:ai] synonym: "G10D receptor" NARROW [] is_a: GO:0097642 ! calcitonin family receptor activity [Term] id: GO:0001606 name: obsolete GPR37/endothelin B-like receptor activity namespace: molecular_function def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah] comment: This term was made obsolete because it represents a gene product, was not defined, and is named based on protein features. synonym: "GPR37/endothelin B-like receptor activity" EXACT [] is_obsolete: true [Term] id: GO:0001607 name: neuromedin U receptor activity namespace: molecular_function def: "Combining with neuromedin U to initiate a change in cell activity." [GOC:ai] synonym: "NMUR activity" EXACT [] is_a: GO:0008188 ! neuropeptide receptor activity relationship: has_part GO:0042924 ! neuromedin U binding [Term] id: GO:0001608 name: G-protein coupled nucleotide receptor activity namespace: molecular_function def: "Combining with a nucleotide and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, GOC:dph, IUPHAR_GPCR:1294] synonym: "G protein coupled nucleotide receptor activity" EXACT [] synonym: "G-protein-coupled nucleotide receptor activity" EXACT [] synonym: "nucleotide receptor activity, G protein coupled" EXACT [] synonym: "nucleotide receptor activity, G-protein coupled" EXACT [GOC:bf] is_a: GO:0004930 ! G-protein coupled receptor activity [Term] id: GO:0001609 name: G-protein coupled adenosine receptor activity namespace: molecular_function alt_id: GO:0001610 alt_id: GO:0001611 alt_id: GO:0001612 alt_id: GO:0001613 alt_id: GO:0008501 def: "Combining with adenosine and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, GOC:mah, PMID:9755289] synonym: "A1 adenosine receptor activity, G protein coupled" NARROW [] synonym: "A1 adenosine receptor activity, G-protein coupled" NARROW [] synonym: "A2A adenosine receptor activity, G protein coupled" NARROW [] synonym: "A2A adenosine receptor activity, G-protein coupled" NARROW [] synonym: "A2B adenosine receptor activity, G protein coupled" NARROW [] synonym: "A2B adenosine receptor activity, G-protein coupled" NARROW [] synonym: "A3 adenosine receptor activity, G protein coupled" NARROW [] synonym: "A3 adenosine receptor activity, G-protein coupled" NARROW [] synonym: "adenosine nucleotide receptor" BROAD [] synonym: "adenosine receptor activity, G protein coupled" EXACT [] synonym: "adenosine receptor activity, G-protein coupled" EXACT [GOC:bf] synonym: "G protein coupled A1 adenosine receptor activity" NARROW [] synonym: "G protein coupled A2A adenosine receptor activity" NARROW [] synonym: "G protein coupled A2B adenosine receptor activity" NARROW [] synonym: "G protein coupled A3 adenosine receptor activity" NARROW [] synonym: "G protein coupled adenosine receptor activity" EXACT [] synonym: "G-protein-coupled A1 adenosine receptor activity" NARROW [] synonym: "G-protein-coupled A2A adenosine receptor activity" NARROW [] synonym: "G-protein-coupled A2B adenosine receptor activity" NARROW [] synonym: "G-protein-coupled A3 adenosine receptor activity" NARROW [] synonym: "G-protein-coupled adenosine receptor activity" EXACT [] synonym: "P1 receptor" EXACT [PMID:9755289] xref: Reactome:REACT_105855 "TRKA activation by adenosine A2a receptor, Bos taurus" xref: Reactome:REACT_110350 "TRKA activation by adenosine A2a receptor, Canis familiaris" xref: Reactome:REACT_11079 "TrkA activation by adenosine A2a receptor, Rattus norvegicus" xref: Reactome:REACT_29695 "TRKA activation by adenosine A2a receptor, Sus scrofa" xref: Reactome:REACT_36513 "TRKA activation by adenosine A2a receptor, Gallus gallus" xref: Reactome:REACT_79823 "TRKA activation by adenosine A2a receptor, Danio rerio" xref: Reactome:REACT_89799 "TRKA activation by adenosine A2a receptor, Taeniopygia guttata" xref: Reactome:REACT_97530 "TRKA activation by adenosine A2a receptor, Xenopus tropicalis" xref: Reactome:REACT_9980 "TRKA activation by adenosine A2a receptor, Homo sapiens" xref: Reactome:REACT_99869 "TRKA activation by adenosine A2a receptor, Mus musculus" is_a: GO:0004930 ! G-protein coupled receptor activity is_a: GO:0035586 ! purinergic receptor activity relationship: part_of GO:0001973 ! adenosine receptor signaling pathway [Term] id: GO:0001614 name: purinergic nucleotide receptor activity namespace: molecular_function def: "Combining with a purine nucleotide and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:mah, GOC:signaling] synonym: "P2 receptor" RELATED [PMID:9755289] is_a: GO:0016502 ! nucleotide receptor activity is_a: GO:0035586 ! purinergic receptor activity relationship: has_part GO:0017076 ! purine nucleotide binding relationship: part_of GO:0035590 ! purinergic nucleotide receptor signaling pathway [Term] id: GO:0001615 name: obsolete thyrotropin releasing hormone and secretagogue-like receptors activity namespace: molecular_function def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah] comment: This term was made obsolete because it represents a gene product, was not defined, and is named based on protein features. synonym: "thyrotropin releasing hormone and secretagogue-like receptors activity" EXACT [] is_obsolete: true [Term] id: GO:0001616 name: growth hormone secretagogue receptor activity namespace: molecular_function def: "Combining with ghrelin to initiate a change in cell activity." [GOC:mah, PMID:17983853] synonym: "ghrelin receptor activity" EXACT [GOC:mah, PMID:17983853] is_a: GO:0004930 ! G-protein coupled receptor activity [Term] id: GO:0001617 name: obsolete growth hormone secretagogue-like receptor activity namespace: molecular_function def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah] comment: This term was made obsolete because it represents a gene product, was not defined, and is named based on protein features. synonym: "growth hormone secretagogue-like receptor activity" EXACT [] is_obsolete: true [Term] id: GO:0001618 name: virus receptor activity namespace: molecular_function def: "Combining with a virus component and mediating entry of the virus into the cell." [GOC:bf, GOC:dph, PMID:7621403, UniProtKB-KW:KW-1183] subset: goslim_chembl synonym: "viral receptor activity" EXACT [] is_a: GO:0004872 ! receptor activity relationship: part_of GO:0046718 ! viral entry into host cell [Term] id: GO:0001619 name: obsolete lysosphingolipid and lysophosphatidic acid receptor activity namespace: molecular_function def: "Combining with lysosphingolipid or lysophosphatidic acid to initiate a change in cell activity." [GOC:dph] synonym: "lysosphingolipid and lysophosphatidic acid receptor activity" EXACT [] is_obsolete: true consider: GO:0038036 consider: GO:0070915 [Term] id: GO:0001621 name: ADP receptor activity namespace: molecular_function def: "Combining with ADP and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:mah, GOC:signaling, PMID:11196645] synonym: "K101 receptor" NARROW [] synonym: "platelet ADP receptor activity" NARROW [GOC:mah] is_a: GO:0045028 ! G-protein coupled purinergic nucleotide receptor activity relationship: has_part GO:0043531 ! ADP binding [Term] id: GO:0001626 name: nociceptin receptor activity namespace: molecular_function def: "Combining with the peptide nociceptin, and transmitting the signal across the membrane by activating an associated G-protein." [GOC:bf, GOC:mah, PMID:18670432] synonym: "nociceptin/orphanin-FQ receptor activity" EXACT [GOC:bf] synonym: "OFQ receptor activity" EXACT [PR:000012940] synonym: "ORPH receptor" EXACT [] synonym: "orphanin-FQ receptor activity" EXACT [GOC:bf] synonym: "X-opioid receptor activity" RELATED [GOC:bf] is_a: GO:0004985 ! opioid receptor activity [Term] id: GO:0001627 name: obsolete leucine-rich G-protein receptor-like receptor activity namespace: molecular_function def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah] comment: This term was made obsolete because it represents a gene product, was not defined, and is named based on protein features. synonym: "leucine-rich G protein receptor-like receptor activity" EXACT [] synonym: "leucine-rich G-protein receptor-like receptor activity" EXACT [] synonym: "LGR-like receptor" EXACT [] is_obsolete: true [Term] id: GO:0001628 name: obsolete gastropyloric receptor activity namespace: molecular_function def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah] comment: This term was made obsolete because the gastropyloric receptor is a type of neuron. synonym: "gastropyloric receptor activity" EXACT [] synonym: "GPR receptor" EXACT [] is_obsolete: true [Term] id: GO:0001629 name: obsolete G-protein receptor 45-like receptor activity namespace: molecular_function def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah] comment: This term was made obsolete because it represents a gene product, was not defined, and is named based on protein features. synonym: "G protein receptor 45-like receptor activity" EXACT [] synonym: "G-protein receptor 45-like receptor activity" EXACT [] synonym: "GPR45-like receptor" EXACT [] is_obsolete: true [Term] id: GO:0001630 name: obsolete GP40-like receptor activity namespace: molecular_function def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah] comment: This term was made obsolete because it represents a gene product, was not defined, and is named based on protein features. synonym: "GP40-like receptor activity" EXACT [] is_obsolete: true [Term] id: GO:0001631 name: cysteinyl leukotriene receptor activity namespace: molecular_function def: "Combining with a cysteinyl leukotriene to initiate a change in cell activity. Cysteinyl leukotrienes are leukotrienes that contain a peptide group based on cysteine." [GOC:ai, ISBN:0198506732] synonym: "CysLT receptor" EXACT [] is_a: GO:0004974 ! leukotriene receptor activity [Term] id: GO:0001632 name: leukotriene B4 receptor activity namespace: molecular_function def: "Combining with leukotriene B4, LTB4, to initiate a change in cell activity. Leukotriene B4 is also known as (6Z, 8E, 10E, 14Z)-(5S, 12R)-5,12-dihydroxyicosa-6,8,10,14-tetraen-1-oate." [GOC:ai, ISBN:0198506732] synonym: "BLT receptor" NARROW [] is_a: GO:0004974 ! leukotriene receptor activity [Term] id: GO:0001633 name: obsolete secretin-like receptor activity namespace: molecular_function alt_id: GO:0001638 def: "OBSOLETE. A G-protein coupled receptor that is structurally/functionally related to the secretin receptor." [GOC:mah, IUPHAR_GPCR:1506] comment: This term was made obsolete because it represents a gene product and is named based on protein features. synonym: "class B G protein coupled receptor" EXACT [] synonym: "class B G-protein coupled receptor" EXACT [] synonym: "class B GPCR" EXACT [] synonym: "class B orphan receptor activity" EXACT [] synonym: "secretin-like receptor activity" EXACT [] is_obsolete: true [Term] id: GO:0001634 name: pituitary adenylate cyclase-activating polypeptide receptor activity namespace: molecular_function alt_id: GO:0016522 def: "A G-protein coupled receptor that interacts with pituitary adenylate cyclase-activating polypeptide." [GOC:dph, GOC:tb] synonym: "PACAP receptor" EXACT [] synonym: "pituitary adenylate cyclase activating polypeptide receptor" EXACT [] synonym: "pituitary adenylate cyclase activating protein receptor activity" EXACT [GOC:dph, GOC:tb] synonym: "pituitary adenylate cyclase-activating peptide receptor activity" RELATED [] synonym: "pituitary adenylate cyclase-activating polypeptide receptor activity" RELATED [] synonym: "pituitary adenylyl cyclase activating protein receptor activity" EXACT [] xref: Reactome:REACT_10128 "TRKA activation by PACAP type 1 receptor, Homo sapiens" xref: Reactome:REACT_101685 "TRKA activation by PACAP type 1 receptor, Canis familiaris" xref: Reactome:REACT_109490 "TRKA activation by PACAP type 1 receptor, Taeniopygia guttata" xref: Reactome:REACT_11114 "TrkA activation by PACAP type 1 receptor, Rattus norvegicus" xref: Reactome:REACT_34105 "TRKA activation by PACAP type 1 receptor, Mus musculus" xref: Reactome:REACT_86120 "TRKA activation by PACAP type 1 receptor, Xenopus tropicalis" xref: Reactome:REACT_87714 "TRKA activation by PACAP type 1 receptor, Bos taurus" xref: Reactome:REACT_91558 "TRKA activation by PACAP type 1 receptor, Danio rerio" xref: Reactome:REACT_92997 "TRKA activation by PACAP type 1 receptor, Gallus gallus" xref: Reactome:REACT_96326 "TRKA activation by PACAP type 1 receptor, Sus scrofa" is_a: GO:0004930 ! G-protein coupled receptor activity [Term] id: GO:0001635 name: calcitonin gene-related peptide receptor activity namespace: molecular_function def: "Combining with a calcitonin gene-related polypeptide (CGRP) to initiate a change in cell activity." [GOC:mah, PMID:12037140] synonym: "calcitonin gene-related polypeptide receptor activity" EXACT [] synonym: "CGRP receptor" EXACT [] xref: Wikipedia:CALCRL is_a: GO:0097642 ! calcitonin family receptor activity [Term] id: GO:0001636 name: obsolete corticotrophin-releasing factor gastric inhibitory peptide-like receptor activity namespace: molecular_function def: "OBSOLETE (was not defined before being made obsolete)." [GOC:mah] comment: This term was made obsolete because it represents a gene product, was not defined, and is named based on protein features. synonym: "corticotrophin-releasing factor gastric inhibitory peptide-like receptor activity" EXACT [] is_obsolete: true [Term] id: GO:0001637 name: G-protein coupled chemoattractant receptor activity namespace: molecular_function def: "Combining with a chemoattractant and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, GOC:mah] synonym: "G protein chemoattractant receptor activity" EXACT [] synonym: "G-protein chemoattractant receptor activity" EXACT [GOC:bf] is_a: GO:0008528 ! G-protein coupled peptide receptor activity [Term] id: GO:0001639 name: PLC activating G-protein coupled glutamate receptor activity namespace: molecular_function def: "A G-protein coupled receptor that binds glutamate and is linked to the inositol 1,4,5-trisphosphate/calcium signaling system." [PMID:9016303] synonym: "Group I metabotropic glutamate receptor" RELATED [] synonym: "group I metabotropic glutamate receptor activity" RELATED [] synonym: "phospholipase C activating metabotropic glutamate receptor activity" EXACT [] synonym: "PLC activating metabotropic glutamate receptor activity" EXACT [GOC:bf] is_a: GO:0098988 ! G-protein coupled glutamate receptor activity relationship: part_of GO:0007206 ! phospholipase C-activating G-protein coupled glutamate receptor signaling pathway [Term] id: GO:0001640 name: adenylate cyclase inhibiting G-protein coupled glutamate receptor activity namespace: molecular_function def: "Combining with glutamate and transmitting the signal across the membrane by activating the alpha-subunit of an associated heterotrimeric G-protein complex to inhibit downstream adenylate cyclase activity." [GOC:bf, GOC:dph] synonym: "adenylate cyclase inhibiting metabotropic glutamate receptor activity" RELATED [GOC:bf] synonym: "adenylyl cyclase inhibiting metabotropic glutamate receptor activity" EXACT [] is_a: GO:0098988 ! G-protein coupled glutamate receptor activity relationship: part_of GO:0007196 ! adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway [Term] id: GO:0001641 name: group II metabotropic glutamate receptor activity namespace: molecular_function def: "A G-protein coupled receptor that is activated by trans-1-aminocyclopentane-1,3-dicarboxylic acid (t-ACPD) and inhibits adenylate cyclase activity." [GOC:dph] is_a: GO:0001640 ! adenylate cyclase inhibiting G-protein coupled glutamate receptor activity [Term] id: GO:0001642 name: group III metabotropic glutamate receptor activity namespace: molecular_function def: "A G-protein coupled receptor that is activated by L-AP-4 and inhibits adenylate cyclase activity." [PMID:9016303] is_a: GO:0001640 ! adenylate cyclase inhibiting G-protein coupled glutamate receptor activity [Term] id: GO:0001646 name: cAMP receptor activity namespace: molecular_function alt_id: GO:0001644 def: "Combining with cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:pg] synonym: "3',5' cAMP receptor activity" EXACT [] synonym: "3',5'-cAMP receptor activity" EXACT [] synonym: "adenosine 3',5'-cyclophosphate receptor activity" EXACT [] synonym: "class E G protein coupled receptor" BROAD [] synonym: "class E G-protein coupled receptor" BROAD [] synonym: "class E GPCR" BROAD [] synonym: "cyclic AMP receptor activity" EXACT [] is_a: GO:0001614 ! purinergic nucleotide receptor activity relationship: has_part GO:0030552 ! cAMP binding [Term] id: GO:0001647 name: G-protein coupled cytokinin receptor activity namespace: molecular_function def: "Combining with cytokinin and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." [GOC:bf, GOC:dph] synonym: "cytokinin receptor activity, G-protein coupled" EXACT [GOC:bf] synonym: "G protein coupled cytokinin receptor activity" EXACT [] synonym: "G-protein-coupled cytokinin receptor activity" EXACT [] is_a: GO:0004930 ! G-protein coupled receptor activity is_a: GO:0009884 ! cytokinin receptor activity [Term] id: GO:0001648 name: proteinase activated receptor activity namespace: molecular_function def: "A G-protein coupled peptide receptor activity that is initiated by cleavage of the N terminus of the receptor by a serine protease, resulting in the generation of a new tethered ligand that interacts with the receptor." [GOC:mah, PMID:11356985] is_a: GO:0008528 ! G-protein coupled peptide receptor activity [Term] id: GO:0001649 name: osteoblast differentiation namespace: biological_process def: "The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone." [CL:0000062, GO_REF:0000034, GOC:jid] synonym: "osteoblast cell differentiation" EXACT [] is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0001503 ! ossification [Term] id: GO:0001650 name: fibrillar center namespace: cellular_component def: "A structure found most metazoan nucleoli, but not usually found in lower eukaryotes; surrounded by the dense fibrillar component; the zone of transcription from multiple copies of the pre-rRNA genes is in the border region between these two structures." [PMID:10754561] synonym: "fibrillar centre" EXACT [] is_a: GO:0044452 ! nucleolar part [Term] id: GO:0001651 name: dense fibrillar component namespace: cellular_component def: "A structure found in the nucleolus, which contains newly synthesized preribosomal RNA (pre-rRNA) and a collection of proteins." [PMID:10754561] synonym: "pars fibrosa" BROAD [NIF_Subcellular:sao1841764412] xref: NIF_Subcellular:sao1841764412 is_a: GO:0044452 ! nucleolar part [Term] id: GO:0001652 name: granular component namespace: cellular_component def: "A structure found in the nucleolus, which contains nearly completed preribosomal particles destined for the cytoplasm." [PMID:10754561] synonym: "pars granulosa" BROAD [NIF_Subcellular:sao1217793903] xref: NIF_Subcellular:sao1217793903 is_a: GO:0044452 ! nucleolar part [Term] id: GO:0001653 name: peptide receptor activity namespace: molecular_function def: "Combining with an extracellular or intracellular peptide to initiate a change in cell activity." [GOC:jl] synonym: "endogenous peptide receptor activity" NARROW [] synonym: "exogenous peptide receptor activity" NARROW [] is_a: GO:0038023 ! signaling receptor activity relationship: has_part GO:0042277 ! peptide binding [Term] id: GO:0001654 name: eye development namespace: biological_process alt_id: GO:0042460 def: "The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight." [GOC:jid, GOC:jl] xref: Wikipedia:Eye_development is_a: GO:0007423 ! sensory organ development [Term] id: GO:0001655 name: urogenital system development namespace: biological_process def: "The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure." [GOC:go_curators] is_a: GO:0048731 ! system development [Term] id: GO:0001656 name: metanephros development namespace: biological_process def: "The process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine." [GOC:bf, ISBN:0192800752] is_a: GO:0001822 ! kidney development [Term] id: GO:0001657 name: ureteric bud development namespace: biological_process def: "The process whose specific outcome is the progression of the ureteric bud over time, from its formation to the mature structure." [GOC:go_curators] is_a: GO:0072164 ! mesonephric tubule development relationship: part_of GO:0072001 ! renal system development [Term] id: GO:0001658 name: branching involved in ureteric bud morphogenesis namespace: biological_process def: "The process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules." [GOC:dph, PMID:16916378] synonym: "ureteric bud branching" EXACT [GOC:dph] is_a: GO:0048754 ! branching morphogenesis of an epithelial tube intersection_of: GO:0001763 ! morphogenesis of a branching structure intersection_of: part_of GO:0060675 ! ureteric bud morphogenesis relationship: part_of GO:0060675 ! ureteric bud morphogenesis [Term] id: GO:0001659 name: temperature homeostasis namespace: biological_process def: "A homeostatic process in which an organism modulates its internal body temperature." [GOC:jl] synonym: "thermoregulation" EXACT [GOC:dph, GOC:tb] xref: Wikipedia:Thermoregulation is_a: GO:0048871 ! multicellular organismal homeostasis [Term] id: GO:0001660 name: fever generation namespace: biological_process def: "The heat generation process that results in a rise in body temperature above the normal, often as a response to infection." [GOC:dph, GOC:jl] synonym: "pyrexia" BROAD [] xref: Wikipedia:Fever is_a: GO:0006953 ! acute-phase response is_a: GO:0031649 ! heat generation [Term] id: GO:0001661 name: conditioned taste aversion namespace: biological_process def: "A conditioned aversion to a specific chemical compound as a result of that compound being coupled with a noxious stimulus." [GOC:dph, PMID:9920659] xref: Wikipedia:Conditioned_taste_aversion xref: Wikipedia:Taste_aversion is_a: GO:0007631 ! feeding behavior is_a: GO:0008306 ! associative learning [Term] id: GO:0001662 name: behavioral fear response namespace: biological_process def: "An acute behavioral change resulting from a perceived external threat." [GOC:dph, PMID:9920659] synonym: "behavioural fear response" EXACT [] is_a: GO:0002209 ! behavioral defense response is_a: GO:0042596 ! fear response is_a: GO:0044708 ! single-organism behavior [Term] id: GO:0001664 name: G-protein coupled receptor binding namespace: molecular_function def: "Interacting selectively and non-covalently with a G-protein coupled receptor." [GOC:ceb, GOC:dph] synonym: "G protein coupled receptor binding" EXACT [] synonym: "G protein coupled receptor ligand" NARROW [] synonym: "G-protein-coupled receptor binding" EXACT [GOC:bf] synonym: "G-protein-coupled receptor ligand" NARROW [] xref: Reactome:REACT_21309 "Activation of GRIK3 homomer, Homo sapiens" is_a: GO:0005102 ! receptor binding [Term] id: GO:0001665 name: alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: CMP-N-acetylneuraminate + glycano-(1->3)-(N-acetyl-alpha-D-galactosaminyl)-glycoprotein = CMP + glycano-[(2->6)-alpha-N-acetylneuraminyl]-(N-acetyl-D-galactosaminyl)-glycoprotein." [EC:2.4.99.3] synonym: "CMP-N-acetylneuraminate:glycano-1,3-(N-acetyl-alpha-D-galactosaminyl)-glycoprotein alpha-2,6-N-acetylneuraminyltransferase activity" EXACT [EC:2.4.99.3] synonym: "GalNAc alpha-2,6-sialyltransferase I activity" EXACT [EC:2.4.99.3] xref: EC:2.4.99.3 xref: MetaCyc:2.4.99.3-RXN is_a: GO:0008373 ! sialyltransferase activity [Term] id: GO:0001666 name: response to hypoxia namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level." [GOC:hjd] comment: Note that this term should not be confused with 'response to anoxia ; GO:0034059'. Note that in laboratory studies, hypoxia is typically studied at O2 concentrations ranging from 0.1 - 5%. synonym: "response to hypoxic stress" EXACT [] synonym: "response to intermittent hypoxia" NARROW [] synonym: "response to lowered oxygen tension" EXACT [] synonym: "response to sustained hypoxia" NARROW [] is_a: GO:0006950 ! response to stress is_a: GO:0036293 ! response to decreased oxygen levels [Term] id: GO:0001667 name: ameboidal-type cell migration namespace: biological_process def: "Cell migration that is accomplished by extension and retraction of a pseudopodium." [GOC:dph] comment: Note that this term refer to a mode of migration rather than to any particular cell type. synonym: "ameboid cell migration" EXACT [] synonym: "amoeboid cell migration" EXACT [] synonym: "amoeboidal cell migration" EXACT [] is_a: GO:0016477 ! cell migration [Term] id: GO:0001669 name: acrosomal vesicle namespace: cellular_component def: "A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome." [ISBN:0124325653, ISBN:0198506732] synonym: "acrosomal granule" EXACT [GOC:sart] synonym: "acrosome" EXACT [GOC:dph] xref: Wikipedia:Acrosome is_a: GO:0030141 ! secretory granule is_a: GO:0097223 ! sperm part [Term] id: GO:0001671 name: ATPase activator activity namespace: molecular_function def: "Binds to and increases the ATP hydrolysis activity of an ATPase." [GOC:ajp] synonym: "ATPase stimulator activity" EXACT [] is_a: GO:0008047 ! enzyme activator activity is_a: GO:0060590 ! ATPase regulator activity relationship: part_of GO:0032781 ! positive regulation of ATPase activity relationship: positively_regulates GO:0016887 ! ATPase activity [Term] id: GO:0001672 name: regulation of chromatin assembly or disassembly namespace: biological_process def: "Any process that modulates the frequency, rate or extent of chromatin assembly or disassembly." [GOC:go_curators] synonym: "regulation of chromatin assembly/disassembly" EXACT [] is_a: GO:1902275 ! regulation of chromatin organization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006333 ! chromatin assembly or disassembly relationship: regulates GO:0006333 ! chromatin assembly or disassembly [Term] id: GO:0001673 name: male germ cell nucleus namespace: cellular_component alt_id: GO:0043081 def: "The nucleus of a male germ cell, a reproductive cell in males." [CL:0000015, GOC:hjd, GOC:mtg_sensu] synonym: "male germ-cell nucleus" EXACT [] is_a: GO:0043073 ! germ cell nucleus [Term] id: GO:0001674 name: female germ cell nucleus namespace: cellular_component alt_id: GO:0043080 def: "The nucleus of the female germ cell, a reproductive cell in females." [CL:0000021, GOC:hjd] synonym: "female germ-cell nucleus" EXACT [] is_a: GO:0043073 ! germ cell nucleus [Term] id: GO:0001675 name: acrosome assembly namespace: biological_process def: "The formation of the acrosome from the spermatid Golgi." [GOC:dph, GOC:hjd, GOC:tb] synonym: "acrosome formation" EXACT [GOC:dph, GOC:tb] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0010927 ! cellular component assembly involved in morphogenesis is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism is_a: GO:0033363 ! secretory granule organization is_a: GO:0070925 ! organelle assembly is_a: GO:1902589 ! single-organism organelle organization relationship: part_of GO:0007286 ! spermatid development [Term] id: GO:0001676 name: long-chain fatty acid metabolic process namespace: biological_process def: "The chemical reactions and pathways involving long-chain fatty acids, A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [CHEBI:15904, GOC:ajp] subset: gosubset_prok synonym: "long-chain fatty acid metabolism" EXACT [] is_a: GO:0006631 ! fatty acid metabolic process [Term] id: GO:0001677 name: formation of translation initiation ternary complex namespace: biological_process def: "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator)." [GOC:hjd] subset: gosubset_prok synonym: "translation initiation ternary complex assembly" EXACT [] is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0006413 ! translational initiation [Term] id: GO:0001678 name: cellular glucose homeostasis namespace: biological_process def: "A cellular homeostatic process involved in the maintenance of an internal steady state of glucose within a cell or between a cell and its external environment." [GOC:dph, GOC:go_curators, GOC:tb] subset: gosubset_prok synonym: "cell glucose homeostasis" EXACT [GOC:dph, GOC:tb] is_a: GO:0042593 ! glucose homeostasis is_a: GO:0055082 ! cellular chemical homeostasis [Term] id: GO:0001680 name: tRNA 3'-terminal CCA addition namespace: biological_process def: "Post-transcriptional addition of the terminal 3' CCA sequence to a tRNA which does not encode this sequence within the primary transcript. CCA addition proceeds by the sequential addition of CTP, CTP, and then ATP to the 3' end of the tRNA, yielding a diphosphate with each nucleotide addition." [EC:2.7.7.72, GOC:go_curators] subset: gosubset_prok synonym: "-C-C-A pyrophosphorylase activity" RELATED [EC:2.7.7.72] synonym: "ATP(CTP)-tRNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72] synonym: "ATP(CTP):tRNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72] synonym: "CCA tRNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72] synonym: "CCA-adding enzyme activity" EXACT [EC:2.7.7.72] synonym: "CCA-adding enzyme, tRNA adenylyltransferase, tRNA cytidylyltransferase, tRNA CCA-pyrophosphorylase activity" EXACT [EC:2.7.7.72] synonym: "CTP(ATP):tRNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72] synonym: "CTP:tRNA cytidylyltransferase activity" NARROW [EC:2.7.7.72] synonym: "ribonucleic cytidylic cytidylic adenylic pyrophosphorylase activity" EXACT [EC:2.7.7.72] synonym: "ribonucleic cytidylyltransferase activity" NARROW [EC:2.7.7.72] synonym: "transfer ribonucleate adenyltransferase activity" NARROW [EC:2.7.7.72] synonym: "transfer ribonucleate adenylyltransferase activity" NARROW [EC:2.7.7.72] synonym: "transfer ribonucleate cytidylyltransferase activity" NARROW [EC:2.7.7.72] synonym: "transfer ribonucleate nucleotidyltransferase activity" BROAD [EC:2.7.7.72] synonym: "transfer ribonucleic acid nucleotidyl transferase activity" BROAD [EC:2.7.7.72] synonym: "transfer ribonucleic adenylyl (cytidylyl) transferase activity" RELATED [EC:2.7.7.72] synonym: "transfer ribonucleic-terminal trinucleotide nucleotidyltransferase activity" BROAD [EC:2.7.7.72] synonym: "transfer RNA adenylyltransferase activity" NARROW [EC:2.7.7.72] synonym: "transfer-RNA nucleotidyltransferase activity" BROAD [EC:2.7.7.72] synonym: "tRNA adenylyl(cytidylyl)transferase activity" BROAD [EC:2.7.7.72] synonym: "tRNA CCA-diphosphorylase activity" RELATED [EC:2.7.7.72] synonym: "tRNA cytidylyltransferase activity" NARROW [EC:2.7.7.72] synonym: "tRNA-nucleotidyltransferase activity" BROAD [EC:2.7.7.72] xref: EC:2.7.7.72 xref: KEGG:R09382 xref: MetaCyc:TRNA-CYTIDYLYLTRANSFERASE-RXN is_a: GO:0042780 ! tRNA 3'-end processing relationship: has_part GO:0052927 ! CTP:tRNA cytidylyltransferase activity relationship: has_part GO:0052928 ! CTP:3'-cytidine-tRNA cytidylyltransferase activity relationship: has_part GO:0052929 ! ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity [Term] id: GO:0001681 name: sialate O-acetylesterase activity namespace: molecular_function def: "Catalysis of the reaction: N-acetyl-O-acetylneuraminate (free or glycosidically bound) + H2O = N-acetylneuraminate + acetate." [EC:3.1.1.53, PMID:1991039] subset: gosubset_prok synonym: "N-acetylneuraminate acetyltransferase activity" EXACT [EC:3.1.1.53] synonym: "N-acyl-O-acetylneuraminate O-acetylhydrolase activity" EXACT [EC:3.1.1.53] synonym: "sialate 9(4)-O-acetylesterase activity" EXACT [] xref: EC:3.1.1.53 xref: MetaCyc:SIALATE-O-ACETYLESTERASE-RXN is_a: GO:0008126 ! acetylesterase activity [Term] id: GO:0001682 name: tRNA 5'-leader removal namespace: biological_process def: "Generation of the mature 5'-end of the tRNA, usually via an endonucleolytic cleavage by RNase P." [PMID:11592395] subset: gosubset_prok synonym: "tRNA 5' leader removal" EXACT [] is_a: GO:0008033 ! tRNA processing [Term] id: GO:0001683 name: obsolete axonemal dynein heavy chain namespace: cellular_component def: "OBSOLETE (was not defined before being made obsolete)." [GOC:jl] comment: This term was made obsolete because it represents a single gene product and not a complex. synonym: "axonemal dynein heavy chain" EXACT [] is_obsolete: true replaced_by: GO:0005858 [Term] id: GO:0001684 name: obsolete axonemal dynein intermediate chain namespace: cellular_component def: "OBSOLETE (was not defined before being made obsolete)." [GOC:jl] comment: This term was made obsolete because it represents a single gene product and not a complex. synonym: "axonemal dynein intermediate chain" EXACT [] is_obsolete: true replaced_by: GO:0005858 [Term] id: GO:0001685 name: obsolete axonemal dynein intermediate light chain namespace: cellular_component def: "OBSOLETE (was not defined before being made obsolete)." [GOC:jl] comment: This term was made obsolete because it represents a single gene product and not a complex. synonym: "axonemal dynein intermediate light chain" EXACT [] is_obsolete: true replaced_by: GO:0005858 [Term] id: GO:0001686 name: obsolete axonemal dynein light chain namespace: cellular_component def: "OBSOLETE (was not defined before being made obsolete)." [GOC:jl] comment: This term was made obsolete because it represents a single gene product and not a complex. synonym: "axonemal dynein light chain" EXACT [] is_obsolete: true replaced_by: GO:0005858 [Term] id: GO:0001687 name: obsolete cytoplasmic dynein heavy chain namespace: cellular_component def: "OBSOLETE (was not defined before being made obsolete)." [GOC:jl] comment: This term was made obsolete because it represents a single gene product and not a complex. synonym: "cytoplasmic dynein heavy chain" EXACT [] is_obsolete: true replaced_by: GO:0005868 [Term] id: GO:0001688 name: obsolete cytoplasmic dynein intermediate chain namespace: cellular_component def: "OBSOLETE (was not defined before being made obsolete)." [GOC:jl] comment: This term was made obsolete because it represents a single gene product and not a complex. synonym: "cytoplasmic dynein intermediate chain" EXACT [] is_obsolete: true replaced_by: GO:0005868 [Term] id: GO:0001689 name: obsolete cytoplasmic dynein intermediate light chain namespace: cellular_component def: "OBSOLETE (was not defined before being made obsolete)." [GOC:jl] comment: This term was made obsolete because it represents a single gene product and not a complex. synonym: "cytoplasmic dynein intermediate light chain" EXACT [] is_obsolete: true replaced_by: GO:0005868 [Term] id: GO:0001690 name: obsolete cytoplasmic dynein light chain namespace: cellular_component def: "OBSOLETE (was not defined before being made obsolete)." [GOC:jl] comment: This term was made obsolete because it represents a single gene product and not a complex. synonym: "cytoplasmic dynein light chain" EXACT [] is_obsolete: true replaced_by: GO:0005868 [Term] id: GO:0001691 name: pseudophosphatase activity namespace: molecular_function def: "Maintains the phosphorylation state of certain molecules by associating with them and preventing them from associating with active phosphatases, and thus inhibiting the enzyme activity without interacting with the enzyme. Often pertains to proteins belonging to dual-specificity phosphatase family but lacking critical active site residues." [GOC:ajp] is_a: GO:0019212 ! phosphatase inhibitor activity [Term] id: GO:0001692 name: histamine metabolic process namespace: biological_process def: "The chemical reactions and pathways involving histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." [GOC:jl, ISBN:0395825172] synonym: "histamine metabolism" EXACT [] is_a: GO:0006576 ! cellular biogenic amine metabolic process is_a: GO:0052803 ! imidazole-containing compound metabolic process [Term] id: GO:0001694 name: histamine biosynthetic process namespace: biological_process alt_id: GO:0001693 def: "The chemical reactions and pathways resulting in the formation of histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." [GOC:jl, ISBN:0395825172] synonym: "histamine anabolism" EXACT [] synonym: "histamine biosynthesis" EXACT [] synonym: "histamine formation" EXACT [] synonym: "histamine synthesis" EXACT [] xref: Reactome:REACT_115661 "Histidine is decarboxylated to histamine, Homo sapiens" is_a: GO:0001692 ! histamine metabolic process is_a: GO:0018130 ! heterocycle biosynthetic process is_a: GO:0019438 ! aromatic compound biosynthetic process is_a: GO:0042401 ! cellular biogenic amine biosynthetic process is_a: GO:1901362 ! organic cyclic compound biosynthetic process [Term] id: GO:0001695 name: histamine catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." [GOC:jl, ISBN:0395825172] synonym: "histamine breakdown" EXACT [] synonym: "histamine catabolism" EXACT [] synonym: "histamine degradation" EXACT [] is_a: GO:0001692 ! histamine metabolic process is_a: GO:0042135 ! neurotransmitter catabolic process is_a: GO:0042402 ! cellular biogenic amine catabolic process is_a: GO:0052805 ! imidazole-containing compound catabolic process [Term] id: GO:0001696 name: gastric acid secretion namespace: biological_process def: "The regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion." [GOC:hjd] synonym: "hydrochloric acid secretion" NARROW [] is_a: GO:0022600 ! digestive system process is_a: GO:0044707 ! single-multicellular organism process is_a: GO:0046717 ! acid secretion [Term] id: GO:0001697 name: histamine-induced gastric acid secretion namespace: biological_process def: "The regulated release of gastric acid induced by the interaction of histamine with H2 type receptor receptors with subsequent activation of adenylate cyclase and elevation of intracellular cyclic AMP." [GOC:hjd] is_a: GO:0001696 ! gastric acid secretion [Term] id: GO:0001698 name: gastrin-induced gastric acid secretion namespace: biological_process def: "The regulated release of gastric acid induced by the interaction of gastrin with its receptor." [GOC:hjd] is_a: GO:0001696 ! gastric acid secretion relationship: has_part GO:0015054 ! gastrin receptor activity [Term] id: GO:0001699 name: acetylcholine-induced gastric acid secretion namespace: biological_process def: "The regulated release of gastric acid by parietal cells in response to acetylcholine." [GOC:hjd] is_a: GO:0001696 ! gastric acid secretion relationship: has_part GO:0015464 ! acetylcholine receptor activity relationship: part_of GO:1905145 ! cellular response to acetylcholine [Term] id: GO:0001700 name: embryonic development via the syncytial blastoderm namespace: biological_process def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster." [GOC:go_curators, GOC:mtg_sensu] is_a: GO:0009792 ! embryo development ending in birth or egg hatching [Term] id: GO:0001701 name: in utero embryonic development namespace: biological_process def: "The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus." [GOC:go_curators, GOC:mtg_sensu] is_a: GO:0043009 ! chordate embryonic development [Term] id: GO:0001702 name: gastrulation with mouth forming second namespace: biological_process alt_id: GO:0010003 alt_id: GO:0048276 def: "A gastrulation process in which the initial invagination becomes the anus and the mouth forms second." [GOC:go_curators, GOC:mtg_sensu] synonym: "deuterostomic gastrulation" EXACT [GOC:dph] is_a: GO:0007369 ! gastrulation [Term] id: GO:0001703 name: gastrulation with mouth forming first namespace: biological_process def: "A gastrulation process in which the initial invagination becomes the mouth and the anus forms second." [GOC:go_curators, GOC:mtg_sensu] synonym: "protostomic gastrulation" NARROW [GOC:dph] is_a: GO:0007369 ! gastrulation [Term] id: GO:0001704 name: formation of primary germ layer namespace: biological_process def: "The formation of the ectoderm, mesoderm and endoderm during gastrulation." [GOC:go_curators] is_a: GO:0044767 ! single-organism developmental process is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis relationship: part_of GO:0007369 ! gastrulation [Term] id: GO:0001705 name: ectoderm formation namespace: biological_process def: "The formation of ectoderm during gastrulation." [GOC:go_curators] is_a: GO:0001704 ! formation of primary germ layer relationship: part_of GO:0007398 ! ectoderm development [Term] id: GO:0001706 name: endoderm formation namespace: biological_process def: "The formation of the endoderm during gastrulation." [GOC:go_curators] synonym: "endoblast formation" NARROW [GOC:dph, GOC:sdb_2009, GOC:tb] is_a: GO:0001704 ! formation of primary germ layer relationship: part_of GO:0007492 ! endoderm development [Term] id: GO:0001707 name: mesoderm formation namespace: biological_process def: "The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts." [GOC:go_curators] is_a: GO:0001704 ! formation of primary germ layer relationship: part_of GO:0048332 ! mesoderm morphogenesis [Term] id: GO:0001708 name: cell fate specification namespace: biological_process def: "The process involved in the specification of cell identity. Once specification has taken place, a cell will be committed to differentiate down a specific pathway if left in its normal environment." [GOC:go_curators] is_a: GO:0048869 ! cellular developmental process relationship: part_of GO:0045165 ! cell fate commitment [Term] id: GO:0001709 name: cell fate determination namespace: biological_process def: "A process involved in cell fate commitment. Once determination has taken place, a cell becomes committed to differentiate down a particular pathway regardless of its environment." [ISBN:0878932437] xref: Wikipedia:Cell_fate_determination is_a: GO:0048869 ! cellular developmental process relationship: part_of GO:0045165 ! cell fate commitment [Term] id: GO:0001710 name: mesodermal cell fate commitment namespace: biological_process def: "The cell differentiation process that results in commitment of a cell to become part of the mesoderm." [GOC:go_curators, ISBN:0878932437] synonym: "mesoderm cell fate commitment" EXACT [] is_a: GO:0060795 ! cell fate commitment involved in formation of primary germ layer relationship: part_of GO:0048333 ! mesodermal cell differentiation [Term] id: GO:0001711 name: endodermal cell fate commitment namespace: biological_process def: "The cell differentiation process that results in commitment of a cell to become part of the endoderm." [GOC:go_curators, ISBN:0878932437] synonym: "endoderm cell fate commitment" EXACT [] is_a: GO:0060795 ! cell fate commitment involved in formation of primary germ layer relationship: part_of GO:0035987 ! endodermal cell differentiation [Term] id: GO:0001712 name: ectodermal cell fate commitment namespace: biological_process def: "The cell differentiation process that results in commitment of a cell to become part of the ectoderm." [GOC:go_curators, ISBN:0878932437] synonym: "ectoderm cell fate commitment" EXACT [] is_a: GO:0060795 ! cell fate commitment involved in formation of primary germ layer relationship: part_of GO:0001705 ! ectoderm formation relationship: part_of GO:0010668 ! ectodermal cell differentiation [Term] id: GO:0001713 name: ectodermal cell fate determination namespace: biological_process def: "The cell fate determination process that results in a cell becoming capable of differentiating autonomously into an ectoderm cell regardless of its environment; upon determination, the cell fate cannot be reversed." [GOC:go_curators, ISBN:0878932437] synonym: "ectoderm cell fate determination" EXACT [] is_a: GO:0001709 ! cell fate determination relationship: part_of GO:0001712 ! ectodermal cell fate commitment [Term] id: GO:0001714 name: endodermal cell fate specification namespace: biological_process def: "The cell fate determination process that results in a cell becoming capable of differentiating autonomously into an endoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:go_curators] synonym: "endoderm cell fate specification" EXACT [] is_a: GO:0001708 ! cell fate specification relationship: part_of GO:0001711 ! endodermal cell fate commitment [Term] id: GO:0001715 name: ectodermal cell fate specification namespace: biological_process def: "The cell fate determination process that results in a cell becoming becomes capable of differentiating autonomously into an ectoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed." [GOC:go_curators] synonym: "ectoderm cell fate specification" EXACT [] is_a: GO:0001708 ! cell fate specification relationship: part_of GO:0001712 ! ectodermal cell fate commitment [Term] id: GO:0001716 name: L-amino-acid oxidase activity namespace: molecular_function def: "Catalysis of the reaction: a L-amino acid + H2O + O2 = a 2-oxo acid + NH3 + hydrogen peroxide." [EC:1.4.3.2] subset: gosubset_prok synonym: "L-amino-acid:oxygen oxidoreductase (deaminating)" EXACT [EC:1.4.3.2] synonym: "ophio-amino-acid oxidase activity" EXACT [EC:1.4.3.2] xref: EC:1.4.3.2 xref: MetaCyc:L-AMINO-ACID-OXIDASE-RXN xref: RHEA:13784 is_a: GO:0016641 ! oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor [Term] id: GO:0001717 name: conversion of seryl-tRNAsec to selenocys-tRNAsec namespace: biological_process def: "The modification process that results in the conversion of serine, carried by a specialized tRNA(ser) (which can read a UGA anticodon), to selenocysteine." [ISBN:155581073X] subset: gosubset_prok is_a: GO:0019988 ! charged-tRNA amino acid modification [Term] id: GO:0001720 name: conversion of lysyl-tRNA to pyrrolysyl-tRNA namespace: biological_process def: "The modification process that results in the conversion of lysine, carried by a specialized lysine-accepting tRNA (possessing a CUA anticodon), to pyrrolysine (a lysine with an amide linkage to a (4R,5R)-4-substituted pyrroline-5-carboxylate)." [PMID:12029131, PMID:12029132, PMID:12121639] subset: gosubset_prok is_a: GO:0019988 ! charged-tRNA amino acid modification [Term] id: GO:0001721 name: obsolete intermediate filament associated protein namespace: cellular_component def: "OBSOLETE. Proteins that associate with intermediate filaments and function in the supramolecular organization of cellular intermediate filament networks." [GOC:ajp, PMID:9484600] comment: This term was made obsolete because it represents a single gene product and not a complex. synonym: "IFAP" EXACT [] synonym: "intermediate filament associated protein" EXACT [] is_obsolete: true replaced_by: GO:0005882 [Term] id: GO:0001722 name: obsolete type I intermediate filament associated protein namespace: cellular_component def: "OBSOLETE. Low molecular weight (10-45 kDa) proteins that associate with intermediate filaments by lateral binding of the filaments and have the effect of creating tight macrofilament aggregates." [GOC:ajp, PMID:9484600] comment: This term was made obsolete because it represents a single gene product and not a complex. synonym: "type I intermediate filament associated protein" EXACT [] is_obsolete: true replaced_by: GO:0005882 [Term] id: GO:0001723 name: obsolete type II intermediate filament associated protein namespace: cellular_component def: "OBSOLETE. High molecular weight (100-300 kDa) proteins that associate with intermediate filaments to cross-link them into loose networks." [GOC:ajp, PMID:9484600] comment: This term was made obsolete because it represents a single gene product and not a complex. synonym: "type II intermediate filament associated protein" EXACT [] is_obsolete: true replaced_by: GO:0005882 [Term] id: GO:0001724 name: obsolete type III intermediate filament associated protein namespace: cellular_component def: "OBSOLETE. Proteins that associate with the ends of intermediate filaments and couple the intermediate filaments to the plasma membrane." [GOC:ajp, PMID:9484600] comment: This term was made obsolete because it represents a single gene product and not a complex. synonym: "type III intermediate filament associated protein" EXACT [] is_obsolete: true replaced_by: GO:0045098 [Term] id: GO:0001725 name: stress fiber namespace: cellular_component def: "A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber." [PMID:16651381] synonym: "actin cable" RELATED [GOC:mah] synonym: "stress fibre" EXACT [] is_a: GO:0042641 ! actomyosin is_a: GO:0097517 ! contractile actin filament bundle [Term] id: GO:0001726 name: ruffle namespace: cellular_component def: "Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork." [ISBN:0124325653] synonym: "membrane ruffle" RELATED [] is_a: GO:0042995 ! cell projection relationship: part_of GO:0031252 ! cell leading edge [Term] id: GO:0001727 name: lipid kinase activity namespace: molecular_function def: "Catalysis of the phosphorylation of a simple or complex lipid." [GOC:hjd] subset: gosubset_prok is_a: GO:0016301 ! kinase activity relationship: part_of GO:0046834 ! lipid phosphorylation [Term] id: GO:0001729 name: ceramide kinase activity namespace: molecular_function def: "Catalysis of the reaction: ATP + ceramide = ADP + ceramide-1-phosphate." [EC:2.7.1.138] synonym: "acylsphingosine kinase activity" EXACT [EC:2.7.1.138] synonym: "ATP:ceramide 1-phosphotransferase activity" EXACT [EC:2.7.1.138] xref: EC:2.7.1.138 xref: MetaCyc:CERAMIDE-KINASE-RXN xref: Reactome:REACT_116045 "Ceramide kinase (CERK) mediates the phosphorylation of ceramide, Homo sapiens" xref: RHEA:17932 is_a: GO:0001727 ! lipid kinase activity [Term] id: GO:0001730 name: 2'-5'-oligoadenylate synthetase activity namespace: molecular_function def: "Catalysis of the reaction: ATP = pppA(2'p5'A)n oligomers. This reaction requires the binding of double-stranded RNA." [ISBN:0198506732] synonym: "(2-5')oligo(A) synthetase activity" EXACT [] synonym: "2'-5' oligoadenylate synthetase activity" EXACT [] synonym: "2-5A synthetase activity" EXACT [] synonym: "oligo-2',5'-adenylate synthetase activity" EXACT [] xref: MetaCyc:RXN-10798 is_a: GO:0070566 ! adenylyltransferase activity [Term] id: GO:0001731 name: formation of translation preinitiation complex namespace: biological_process def: "The joining of the small ribosomal subunit, ternary complex, and mRNA." [GOC:hjd] comment: See also the cellular component terms 'eukaryotic 43S preinitiation complex ; GO:0016282', 'eukaryotic 48S initiation complex ; GO:0033290', and their children. subset: gosubset_prok synonym: "formation of translation pre-initiation complex" EXACT [] synonym: "translation preinitiation complex assembly" EXACT [] is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0006413 ! translational initiation [Term] id: GO:0001732 name: formation of cytoplasmic translation initiation complex namespace: biological_process def: "Joining of the large subunit, with release of IF2/eIF2 and IF3/eIF3. This leaves the functional ribosome at the AUG, with the methionyl/formyl-methionyl-tRNA positioned at the P site." [GOC:hjd] subset: gosubset_prok synonym: "cytoplasmic translation initiation complex assembly" EXACT [] synonym: "formation of translation initiation complex" BROAD [] synonym: "translation initiation complex assembly" BROAD [] is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0002183 ! cytoplasmic translational initiation [Term] id: GO:0001733 name: galactosylceramide sulfotransferase activity namespace: molecular_function def: "Catalysis of the reaction: 3'-phosphoadenosine 5'-phosphosulfate + a galactosylceramide = adenosine 3',5'-bisphosphate + a galactosylceramidesulfate." [EC:2.8.2.11, PMID:10727929] synonym: "3'-phosphoadenosine-5'-phosphosulfate-cerebroside sulfotransferase activity" EXACT [EC:2.8.2.11] synonym: "3'-phosphoadenylyl-sulfate:galactosylceramide 3'-sulfotransferase activity" EXACT [EC:2.8.2.11] synonym: "cerebroside sulfotransferase activity" EXACT [] synonym: "galactocerebroside sulfotransferase activity" EXACT [EC:2.8.2.11] synonym: "galactolipid sulfotransferase activity" EXACT [EC:2.8.2.11] synonym: "galactosylceramide sulphotransferase activity" EXACT [] synonym: "glycolipid sulfotransferase activity" EXACT [EC:2.8.2.11] synonym: "glycosphingolipid sulfotransferase activity" EXACT [EC:2.8.2.11] synonym: "GSase" EXACT [EC:2.8.2.11] xref: EC:2.8.2.11 xref: MetaCyc:GALACTOSYLCERAMIDE-SULFOTRANSFERASE-RXN xref: Reactome:REACT_115577 "Galactosylceramide sulfotransferase (GAL3ST1) mediates the sulfation of membrane glycolipids, Homo sapiens" xref: RHEA:20616 is_a: GO:0050694 ! galactose 3-O-sulfotransferase activity [Term] id: GO:0001734 name: mRNA (N6-adenosine)-methyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: S-adenosyl-L-methionine + RRACH = S-adenosyl-L-homocysteine + RRm6ACH; R is a purine, and H is C, A, or U." [GOC:hjd] xref: Reactome:REACT_101890 "Internal Methylation of mRNA, Oryza sativa" xref: Reactome:REACT_1720 "Internal Methylation of mRNA, Homo sapiens" xref: Reactome:REACT_28538 "Internal Methylation of mRNA, Canis familiaris" xref: Reactome:REACT_28726 "Internal Methylation of mRNA, Arabidopsis thaliana" xref: Reactome:REACT_30916 "Internal Methylation of mRNA, Drosophila melanogaster" xref: Reactome:REACT_32129 "Internal Methylation of mRNA, Rattus norvegicus" xref: Reactome:REACT_85371 "Internal Methylation of mRNA, Saccharomyces cerevisiae" xref: Reactome:REACT_88666 "Internal Methylation of mRNA, Mus musculus" xref: Reactome:REACT_90117 "Internal Methylation of mRNA, Bos taurus" xref: Reactome:REACT_91818 "Internal Methylation of mRNA, Plasmodium falciparum" xref: Reactome:REACT_92618 "Internal Methylation of mRNA, Danio rerio" xref: Reactome:REACT_96892 "Internal Methylation of mRNA, Xenopus tropicalis" is_a: GO:0008174 ! mRNA methyltransferase activity [Term] id: GO:0001735 name: prenylcysteine oxidase activity namespace: molecular_function def: "Catalysis of the reaction: S-prenyl-L-cysteine + O2 + H2O = a prenal + L-cysteine + H2O2." [GOC:hjd] synonym: "prenylcysteine lyase activity" EXACT [EC:1.8.3.5] synonym: "S-prenyl-L-cysteine:oxygen oxidoreductase activity" EXACT [EC:1.8.3.5] xref: EC:1.8.3.5 xref: MetaCyc:1.8.3.5-RXN is_a: GO:0016670 ! oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor [Term] id: GO:0001736 name: establishment of planar polarity namespace: biological_process def: "Coordinated organization of groups of cells in the plane of an epithelium, such that they all orient to similar coordinates." [GOC:dph] synonym: "establishment of planar cell polarity" NARROW [] is_a: GO:0007164 ! establishment of tissue polarity relationship: part_of GO:0001738 ! morphogenesis of a polarized epithelium [Term] id: GO:0001737 name: establishment of imaginal disc-derived wing hair orientation namespace: biological_process def: "Orientation of hairs in the imaginal disc-derived wing along a proximal-distal axis, such that each cell of the wing produces one wing hair which points in a distal direction." [GOC:ascb_2009, GOC:dph, GOC:mtg_sensu, GOC:tb, PMID:11239465] synonym: "establishment of wing hair orientation" EXACT [] is_a: GO:0001736 ! establishment of planar polarity is_a: GO:0009886 ! post-embryonic animal morphogenesis relationship: part_of GO:0035317 ! imaginal disc-derived wing hair organization [Term] id: GO:0001738 name: morphogenesis of a polarized epithelium namespace: biological_process def: "The morphogenetic process in which the anatomical structures of a polarized epithelium are generated and organized. A polarized epithelium is an epithelium where the epithelial sheet is oriented with respect to the planar axis." [GOC:dph] synonym: "epithelial polarization" EXACT [GOC:dph] is_a: GO:0002009 ! morphogenesis of an epithelium [Term] id: GO:0001739 name: sex chromatin namespace: cellular_component def: "Chromatin that is part of a sex chromosome." [GOC:dos, ISBN:0198506732] is_a: GO:0005720 ! nuclear heterochromatin intersection_of: GO:0005720 ! nuclear heterochromatin intersection_of: part_of GO:0000803 ! sex chromosome relationship: part_of GO:0000803 ! sex chromosome [Term] id: GO:0001740 name: Barr body namespace: cellular_component def: "A structure found in a female mammalian cell containing an unpaired X chromosome that has become densely heterochromatic, silenced and localized at the nuclear periphery." [GOC:hjd, GOC:mr, NIF_Subcellular:sao1571698684] xref: NIF_Subcellular:sao1571698684 xref: Wikipedia:Barr_body is_a: GO:0000228 ! nuclear chromosome is_a: GO:0000805 ! X chromosome relationship: has_part GO:0098578 ! condensed chromatin of inactivated sex chromosome [Term] id: GO:0001741 name: XY body namespace: cellular_component def: "A structure found in a male mammalian spermatocyte containing an unpaired X chromosome that has become densely heterochromatic, silenced and localized at the nuclear periphery." [GOC:hjd] is_a: GO:0000803 ! sex chromosome relationship: has_part GO:0098578 ! condensed chromatin of inactivated sex chromosome [Term] id: GO:0001742 name: oenocyte differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires the specialized features of an oenocyte. Oenocytes are large secretory cells found in clusters underlying the epidermis of larval abdominal segments." [GOC:go_curators] synonym: "oenocyte cell differentiation" EXACT [] is_a: GO:0030154 ! cell differentiation [Term] id: GO:0001743 name: optic placode formation namespace: biological_process def: "The initial developmental process that will lead to the formation of an eye." [GOC:dph] is_a: GO:0060788 ! ectodermal placode formation relationship: part_of GO:0048598 ! embryonic morphogenesis [Term] id: GO:0001744 name: optic lobe placode formation namespace: biological_process alt_id: GO:0007457 def: "Establishment of the optic placode, a thickened area of densely packed ectoderm cells directly overlying the optic vesicle in the early embryo. In Drosophila, for example, the placode appears in the dorsolateral region of the head in late stage 11 embryos and is the precursor to the larval visual system." [GOC:mtg_sensu, PMID:8402833] synonym: "optic lobe and Bolwig's organ precursor formation" EXACT [] is_a: GO:0060788 ! ectodermal placode formation [Term] id: GO:0001745 name: compound eye morphogenesis namespace: biological_process def: "The morphogenetic process in which the anatomical structures of the compound eye are generated and organized. The adult compound eye is a precise assembly of 700-800 ommatidia. Each ommatidium is composed of 20 cells, identified by cell type and position. An example of compound eye morphogenesis is found in Drosophila melanogaster." [GOC:dph, GOC:mtg_sensu] synonym: "insect-type retina morphogenesis" EXACT [PMID:11735386] is_a: GO:0048592 ! eye morphogenesis relationship: part_of GO:0048749 ! compound eye development [Term] id: GO:0001746 name: Bolwig's organ morphogenesis namespace: biological_process def: "The morphogenetic process in which the anatomical structures of the larval eye in Drosophila are generated and organized. The larval eye in Drosophila is a relatively simple sensory system composed of Bolwig's organs: two clusters, each composed of 12 photoreceptor cells from which axons extend in a single fascicle to the brain." [http://sdb.bio.purdue.edu/fly/torstoll/tailess.htm#bolwigs, PMID:6185380] is_a: GO:0048592 ! eye morphogenesis relationship: part_of GO:0055034 ! Bolwig's organ development [Term] id: GO:0001748 name: optic lobe placode development namespace: biological_process alt_id: GO:0048049 def: "The process whose specific outcome is the progression of the optic placode over time, from its formation to the mature structure. During embryonic stage 12 the placode starts to invaginate, forming a pouch. Cells that will form Bolwig's organ segregate from the ventral lip of this pouch, remaining in the head epidermis. The remainder of the invagination loses contact with the outer surface and becomes the optic lobe. An example of this process is found in Drosophila melanogaster." [GOC:mtg_sensu, PMID:8402833] synonym: "optic lobe and Bolwig's organ precursor development" EXACT [] synonym: "optic placode development" BROAD [] is_a: GO:0044767 ! single-organism developmental process is_a: GO:0048856 ! anatomical structure development [Term] id: GO:0001750 name: photoreceptor outer segment namespace: cellular_component def: "The outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes." [ISBN:0824072820] is_a: GO:0031513 ! nonmotile primary cilium is_a: GO:0097458 ! neuron part [Term] id: GO:0001751 name: compound eye photoreceptor cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires the specialized features of an eye photoreceptor cell." [GOC:go_curators] is_a: GO:0001754 ! eye photoreceptor cell differentiation relationship: part_of GO:0001745 ! compound eye morphogenesis [Term] id: GO:0001752 name: compound eye photoreceptor fate commitment namespace: biological_process alt_id: GO:0007459 def: "The process in which the developmental fate of a cell becomes restricted such that it will develop into a compound eye photoreceptor cell. A photoreceptor cell is a cell that responds to incident electromagnetic radiation. Different classes of photoreceptor have different spectral sensitivities and express different photosensitive pigments." [GOC:mtg_sensu] is_a: GO:0042706 ! eye photoreceptor cell fate commitment relationship: part_of GO:0001751 ! compound eye photoreceptor cell differentiation [Term] id: GO:0001753 name: obsolete adult eye photoreceptor development (sensu Drosophila) namespace: biological_process def: "OBSOLETE. Development of a photoreceptor, a receptor that responds to light, in the adult Drosophila eye." [GOC:go_curators] comment: This term was made obsolete because eye photoreceptors have completed their development by the time the adult phase begins. synonym: "adult eye photoreceptor development (sensu Drosophila)" EXACT [] is_obsolete: true consider: GO:0042051 [Term] id: GO:0001754 name: eye photoreceptor cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell, as found in the eye, the primary visual organ of most organisms." [GOC:go_curators] is_a: GO:0046530 ! photoreceptor cell differentiation relationship: part_of GO:0048592 ! eye morphogenesis [Term] id: GO:0001755 name: neural crest cell migration namespace: biological_process def: "The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo." [GOC:ascb_2009, GOC:dph, GOC:tb, ISBN:0878932437] is_a: GO:0001667 ! ameboidal-type cell migration relationship: part_of GO:0014032 ! neural crest cell development [Term] id: GO:0001756 name: somitogenesis namespace: biological_process def: "The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo." [ISBN:0721662544] synonym: "formation of mesodermal clusters" EXACT systematic_synonym [] xref: Wikipedia:Somitogenesis is_a: GO:0009952 ! anterior/posterior pattern specification is_a: GO:0035282 ! segmentation is_a: GO:0044767 ! single-organism developmental process is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis relationship: part_of GO:0043009 ! chordate embryonic development relationship: part_of GO:0061053 ! somite development [Term] id: GO:0001757 name: somite specification namespace: biological_process def: "The process in which individual somites establish identity during embryogenesis." [GOC:dph] is_a: GO:0007379 ! segment specification is_a: GO:0009880 ! embryonic pattern specification relationship: part_of GO:0001756 ! somitogenesis [Term] id: GO:0001758 name: retinal dehydrogenase activity namespace: molecular_function def: "Catalysis of the reaction: retinal + NAD+ + H2O = retinoate + NADH. Acts on both 11-trans and 13-cis forms of retinal." [EC:1.2.1.36] synonym: "cytosolic retinal dehydrogenase activity" EXACT [EC:1.2.1.36] synonym: "retinal:NAD+ oxidoreductase activity" EXACT [EC:1.2.1.36] xref: EC:1.2.1.36 xref: MetaCyc:RETINAL-DEHYDROGENASE-RXN xref: RHEA:16180 is_a: GO:0016620 ! oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor [Term] id: GO:0001759 name: organ induction namespace: biological_process def: "The interaction of two or more cells or tissues that causes them to change their fates and specify the development of an organ." [ISBN:0878932437] synonym: "induction of an organ" EXACT [GOC:curators] is_a: GO:0003156 ! regulation of animal organ formation is_a: GO:0031128 ! developmental induction is_a: GO:0051094 ! positive regulation of developmental process is_a: GO:0051240 ! positive regulation of multicellular organismal process relationship: positively_regulates GO:0010092 ! specification of animal organ identity [Term] id: GO:0001760 name: aminocarboxymuconate-semialdehyde decarboxylase activity namespace: molecular_function def: "Catalysis of the reaction: 2-amino-3-carboxymuconate 6-semialdehyde + H(+) = 2-aminomuconate 6-semialdehyde + CO(2)." [EC:4.1.1.45, RHEA:16560] subset: gosubset_prok synonym: "2-amino-3-(3-oxoprop-1-en-1-yl)but-2-enedioate carboxy-lyase (2-aminomuconate-semialdehyde-forming)" EXACT [EC:4.1.1.45] synonym: "2-amino-3-(3-oxoprop-1-en-1-yl)but-2-enedioate carboxy-lyase activity" EXACT [EC:4.1.1.45] synonym: "2-amino-3-(3-oxoprop-2-enyl)but-2-enedioate carboxy-lyase activity" EXACT [EC:4.1.1.45] synonym: "ACMSD activity" EXACT [PMID:17288562] synonym: "alpha-amino-beta-carboxymuconate-epsilon-semialdehade decarboxylase activity" EXACT [EC:4.1.1.45] synonym: "alpha-amino-beta-carboxymuconate-epsilon-semialdehyde beta-decarboxylase activity" EXACT [EC:4.1.1.45] synonym: "picolinic acid carboxylase activity" EXACT [EC:4.1.1.45] synonym: "picolinic acid decarboxylase activity" EXACT [EC:4.1.1.45] xref: EC:4.1.1.45 xref: KEGG:R04323 xref: MetaCyc:AMINO-CARBOXYMUCONATE-SEMIALDEHYDE-RXN xref: RHEA:16560 is_a: GO:0016831 ! carboxy-lyase activity [Term] id: GO:0001761 name: beta-alanine transmembrane transporter activity namespace: molecular_function def: "Enables the transfer of beta-alanine from one side of a membrane to the other. Beta-alanine is 3-aminopropanoic acid." [GOC:hjd] synonym: "beta-alanine transporter activity" BROAD [] is_a: GO:0015175 ! neutral amino acid transmembrane transporter activity relationship: part_of GO:0001762 ! beta-alanine transport [Term] id: GO:0001762 name: beta-alanine transport namespace: biological_process def: "The directed movement of beta-alanine, 3-aminopropanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:hjd] is_a: GO:0015804 ! neutral amino acid transport [Term] id: GO:0001763 name: morphogenesis of a branching structure namespace: biological_process def: "The process in which the anatomical structures of branches are generated and organized. A branch is a division or offshoot from a main stem. Examples in animals would include blood vessels, nerves, lymphatics and other endothelial or epithelial tubes." [ISBN:0721662544] synonym: "branching morphogenesis" EXACT [GOC:dph] is_a: GO:0009653 ! anatomical structure morphogenesis is_a: GO:0044707 ! single-multicellular organism process is_a: GO:0044767 ! single-organism developmental process [Term] id: GO:0001764 name: neuron migration namespace: biological_process def: "The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature." [CL:0000540, GOC:go_curators] synonym: "neuron chemotaxis" EXACT [GOC:curators] synonym: "neuron guidance" RELATED [GOC:curators] synonym: "neuronal migration" EXACT [] xref: Wikipedia:Neural_development#Neuron_migration xref: Wikipedia:Neuron_migration is_a: GO:0016477 ! cell migration relationship: part_of GO:0048699 ! generation of neurons [Term] id: GO:0001765 name: membrane raft assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of a set of components to form a membrane raft, a small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalizes cellular processes." [PMID:12648772, PMID:12803918, PMID:16645198] synonym: "lipid raft assembly" EXACT [GOC:mah] synonym: "lipid raft formation" RELATED [] synonym: "membrane raft formation" RELATED [GOC:mah] is_a: GO:0031579 ! membrane raft organization is_a: GO:0071709 ! membrane assembly [Term] id: GO:0001766 name: membrane raft polarization namespace: biological_process def: "The clustering and aggregation of membrane rafts at a single cellular pole during activation of particular cell types, such as lymphocytes." [PMID:12615889] synonym: "lipid raft polarization" EXACT [] is_a: GO:0031580 ! membrane raft distribution [Term] id: GO:0001767 name: establishment of lymphocyte polarity namespace: biological_process def: "The directed orientation of lymphocyte signaling molecules and associated membrane rafts towards a chemokine gradient or a contact point with an appropriate activating cell." [GOC:mgi_curators, PMID:11244041, PMID:12615889] synonym: "lymphocyte polarization" EXACT [] is_a: GO:0030010 ! establishment of cell polarity relationship: part_of GO:0046649 ! lymphocyte activation [Term] id: GO:0001768 name: establishment of T cell polarity namespace: biological_process def: "The directed orientation of T cell signaling molecules and associated membrane rafts towards a chemokine gradient or a contact point with antigen presenting cell." [GOC:mgi_curators, PMID:11244041, PMID:12615889] synonym: "establishment of T lymphocyte polarity" EXACT [] synonym: "establishment of T-cell polarity" EXACT [] synonym: "establishment of T-lymphocyte polarity" EXACT [] synonym: "T cell polarization" EXACT [] synonym: "T lymphocyte polarization" EXACT [] synonym: "T-cell polarization" EXACT [] is_a: GO:0001767 ! establishment of lymphocyte polarity relationship: part_of GO:0042110 ! T cell activation [Term] id: GO:0001769 name: establishment of B cell polarity namespace: biological_process def: "The directed orientation of B cell signaling molecules and associated membrane rafts towards a chemokine gradient of a contact point with an antigen displaying cell." [GOC:mgi_curators, PMID:12615889, PMID:9692889] comment: Note that 'antigen displaying cell' in this term encompasses cell types such as follicular dendritic cells which display the unprocessed antigens of a B cell, leading to activation of the B cells and antigen uptake and processing by the B cells. synonym: "B cell polarization" EXACT [] synonym: "B lymphocyte polarization" EXACT [] synonym: "B-cell polarization" EXACT [] synonym: "establishment of B lymphocyte polarity" EXACT [] synonym: "establishment of B-cell polarity" EXACT [] synonym: "establishment of B-lymphocyte polarity" EXACT [] is_a: GO:0001767 ! establishment of lymphocyte polarity relationship: part_of GO:0042113 ! B cell activation [Term] id: GO:0001770 name: establishment of natural killer cell polarity namespace: biological_process def: "The directed orientation of natural killer cell signaling molecules and associated membrane rafts towards a chemokine gradient or a contact point with a cell displaying natural killer cell activating ligands." [GOC:mgi_curators, PMID:12615886, PMID:9759849] synonym: "establishment of NK cell polarity" EXACT [] synonym: "natural killer cell polarization" EXACT [] synonym: "NK cell polarization" EXACT [] is_a: GO:0001767 ! establishment of lymphocyte polarity relationship: part_of GO:0030101 ! natural killer cell activation [Term] id: GO:0001771 name: immunological synapse formation namespace: biological_process def: "The formation of an area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and target cell, which facilitates activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction." [GOC:mgi_curators, PMID:11244041, PMID:11376330] synonym: "formation of immunological synapse" EXACT [GOC:curators] is_a: GO:0009988 ! cell-cell recognition relationship: part_of GO:0046649 ! lymphocyte activation [Term] id: GO:0001772 name: immunological synapse namespace: cellular_component def: "An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction." [GOC:mgi_curators, PMID:11244041, PMID:11376300] synonym: "c-SMAC" NARROW [PMID:14724296] synonym: "supramolecular activation cluster" EXACT [PMID:14724296] xref: Wikipedia:Immunological_synapse is_a: GO:0044459 ! plasma membrane part [Term] id: GO:0001773 name: myeloid dendritic cell activation namespace: biological_process def: "The change in morphology and behavior of a dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." [GOC:mgi_curators, ISBN:0781735149] is_a: GO:0002274 ! myeloid leukocyte activation [Term] id: GO:0001774 name: microglial cell activation namespace: biological_process def: "The change in morphology and behavior of a microglial cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." [GOC:mgi_curators, PMID:10626665, PMID:10695728, PMID:12580336, PMID:9893949] is_a: GO:0042116 ! macrophage activation [Term] id: GO:0001775 name: cell activation namespace: biological_process def: "A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand." [GOC:mgi_curators] subset: goslim_pir is_a: GO:0044763 ! single-organism cellular process [Term] id: GO:0001776 name: leukocyte homeostasis namespace: biological_process def: "The process of regulating the proliferation and elimination of cells of the immune system such that the total number of cells of a particular cell type within a whole or part of an organism is stable over time in the absence of an outside stimulus." [GOC:add, ISBN:0781735149] comment: Note that this term represents the return of immune system cell levels to stable numbers following an immune response as well as the proliferation and elimination of cells of the immune system required to maintain stable numbers in the absence of an outside stimulus. synonym: "immune cell homeostasis" EXACT [] synonym: "leucocyte homeostasis" EXACT [] is_a: GO:0002376 ! immune system process is_a: GO:0048872 ! homeostasis of number of cells [Term] id: GO:0001777 name: T cell homeostatic proliferation namespace: biological_process def: "The non-specific expansion of T cell populations within a whole or part of an organism to reach to a total number of T cells which will then remain stable over time in the absence of an external stimulus." [GOC:mgi_curators, ISBN:0781735149] synonym: "resting T cell proliferation" EXACT [] synonym: "resting T-cell proliferation" EXACT [] synonym: "T lymphocyte homeostatic proliferation" EXACT [] synonym: "T-cell homeostatic proliferation" EXACT [] synonym: "T-lymphocyte homeostatic proliferation" EXACT [] is_a: GO:0042098 ! T cell proliferation relationship: part_of GO:0042592 ! homeostatic process relationship: part_of GO:0043029 ! T cell homeostasis [Term] id: GO:0001778 name: plasma membrane repair namespace: biological_process def: "The resealing of a cell plasma membrane after cellular wounding due to, for instance, mechanical stress." [GOC:add, PMID:12925704] is_a: GO:0007009 ! plasma membrane organization relationship: part_of GO:0042060 ! wound healing [Term] id: GO:0001779 name: natural killer cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires the specialized features of a natural killer cell." [GOC:add, ISBN:0781735149] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "natural killer cell development" RELATED [GOC:add] synonym: "NK cell differentiation" EXACT [] is_a: GO:0030098 ! lymphocyte differentiation is_a: GO:0030101 ! natural killer cell activation [Term] id: GO:0001780 name: neutrophil homeostasis namespace: biological_process def: "The process of regulating the proliferation and elimination of neutrophils such that the total number of neutrophils within a whole or part of an organism is stable over time in the absence of an outside stimulus." [GOC:add, GOC:pr, PMID:12752675, PMID:12960266] comment: Note that this term represents the return of neutrophil levels to stable numbers following an immune response as well as the proliferation and elimination of neutrophils required to maintain stable numbers in the absence of an outside stimulus. is_a: GO:0001776 ! leukocyte homeostasis is_a: GO:0002262 ! myeloid cell homeostasis [Term] id: GO:0001781 name: neutrophil apoptotic process namespace: biological_process def: "Any apoptotic process in a neutrophil, any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes." [CL:0000775, GOC:add, GOC:mtg_apoptosis, PMID:12752675, PMID:12960266] synonym: "apoptosis of neutrophils" EXACT [] synonym: "neutrophil apoptosis" NARROW [] synonym: "neutrophil programmed cell death by apoptosis" EXACT [] synonym: "programmed cell death of neutrophils by apoptosis" EXACT [] synonym: "programmed cell death, neutrophils" EXACT [] is_a: GO:0006925 ! inflammatory cell apoptotic process is_a: GO:0033028 ! myeloid cell apoptotic process is_a: GO:0071887 ! leukocyte apoptotic process relationship: part_of GO:0001780 ! neutrophil homeostasis [Term] id: GO:0001782 name: B cell homeostasis namespace: biological_process def: "The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus." [GOC:add, ISBN:0781735149, PMID:12956429] comment: Note that this term represents the return of B cell levels to stable numbers following an immune response as well as the proliferation and elimination of B cells required to maintain stable numbers in the absence of an outside stimulus. synonym: "B lymphocyte homeostasis" EXACT [] synonym: "B-cell homeostasis" EXACT [] synonym: "B-lymphocyte homeostasis" EXACT [] is_a: GO:0002260 ! lymphocyte homeostasis [Term] id: GO:0001783 name: B cell apoptotic process namespace: biological_process def: "Any apoptotic process in a B cell, a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity." [CL:0000236, GOC:add, GOC:mtg_apoptosis, ISBN:0781735149] synonym: "apoptosis of B cells" EXACT [] synonym: "apoptosis of B lymphocytes" EXACT [] synonym: "apoptosis of B-cells" EXACT [] synonym: "apoptosis of B-lymphocytes" EXACT [] synonym: "B cell apoptosis" NARROW [] synonym: "B cell programmed cell death by apoptosis" EXACT [] synonym: "B lymphocyte apoptosis" EXACT [] synonym: "B lymphocyte programmed cell death by apoptosis" EXACT [] synonym: "B-cell apoptosis" EXACT [] synonym: "B-cell programmed cell death by apoptosis" EXACT [] synonym: "B-lymphocyte apoptosis" EXACT [] synonym: "B-lymphocyte programmed cell death by apoptosis" EXACT [] synonym: "programmed cell death of B cells by apoptosis" EXACT [] synonym: "programmed cell death of B lymphocytes by apoptosis" EXACT [] synonym: "programmed cell death of B-cells by apoptosis" EXACT [] synonym: "programmed cell death of B-lymphocytes by apoptosis" EXACT [] synonym: "programmed cell death, B cells" EXACT [] synonym: "programmed cell death, B lymphocytes" EXACT [] synonym: "programmed cell death, B-cells" EXACT [] synonym: "programmed cell death, B-lymphocytes" EXACT [] is_a: GO:0070227 ! lymphocyte apoptotic process [Term] id: GO:0001784 name: phosphotyrosine binding namespace: molecular_function def: "Interacting selectively and non-covalently with a phosphorylated tyrosine residue within a protein." [PMID:14636584] is_a: GO:0045309 ! protein phosphorylated amino acid binding [Term] id: GO:0001785 name: prostaglandin J receptor activity namespace: molecular_function def: "Combining with prostaglandin J (PGJ(2)), a metabolite of prostaglandin D (PGD(2)) to initiate a change in cell activity." [PMID:12878180] synonym: "PGJ receptor activity" RELATED [] synonym: "PGJ(2) receptor activity" EXACT [] is_a: GO:0004955 ! prostaglandin receptor activity [Term] id: GO:0001786 name: phosphatidylserine binding namespace: molecular_function def: "Interacting selectively and non-covalently with phosphatidylserine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of L-serine." [ISBN:0198506732, PMID:12000961] is_a: GO:0005543 ! phospholipid binding is_a: GO:0072341 ! modified amino acid binding [Term] id: GO:0001787 name: natural killer cell proliferation namespace: biological_process def: "The expansion of a natural killer cell population by cell division." [GOC:add, ISBN:0781735149] synonym: "NK cell proliferation" EXACT [] is_a: GO:0030101 ! natural killer cell activation is_a: GO:0046651 ! lymphocyte proliferation [Term] id: GO:0001788 name: antibody-dependent cellular cytotoxicity namespace: biological_process def: "Cytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells." [GOC:pr, ISBN:0781735149, PMID:11677095, PMID:9581795] synonym: "ADCC" EXACT [] synonym: "antibody dependent cell death" EXACT [] synonym: "antibody dependent cell killing" EXACT [] synonym: "antibody-dependent cell death" EXACT [] synonym: "antibody-dependent cell killing" EXACT [] synonym: "type VI hypersensitivity" EXACT [] xref: Wikipedia:Antibody-dependent_cell-mediated_cytotoxicity xref: Wikipedia:Antibody-dependent_cellular_cytotoxicity is_a: GO:0001794 ! type IIa hypersensitivity is_a: GO:0001909 ! leukocyte mediated cytotoxicity is_a: GO:0044699 ! single-organism process [Term] id: GO:0001789 name: G-protein coupled receptor signaling pathway, coupled to S1P second messenger namespace: biological_process def: "The series of molecular signals generated as a consequence of an adrenergic receptor binding to its physiological ligand, where the pathway proceeds with activation of sphingosine kinase and a subsequent increase in cellular levels of sphingosine-1-phosphate (S1P)." [GOC:dph, GOC:signaling, PMID:14592418] synonym: "G protein signaling, coupled to S1P second messenger (sphingosine kinase activating)" EXACT [] synonym: "G protein signalling, coupled to S1P second messenger (sphingosine kinase activating)" EXACT [] synonym: "G-protein signalling, coupled to S1P second messenger (sphingosine kinase activating)" EXACT [] synonym: "GPCR signaling pathway via activation of sphingosine kinase activity" EXACT [GOC:signaling] synonym: "sphingosine kinase-activating G-protein coupled receptor signaling pathway" EXACT [GOC:signaling] synonym: "sphingosine kinase-activating GPCR signaling pathway" EXACT [GOC:signaling] is_a: GO:0007186 ! G-protein coupled receptor signaling pathway relationship: has_part GO:1900023 ! positive regulation of D-erythro-sphingosine kinase activity [Term] id: GO:0001790 name: polymeric immunoglobulin binding namespace: molecular_function def: "Interacting selectively and non-covalently with a J-chain-containing polymeric immunoglobulin of the IgA or IgM isotypes." [GOC:add, ISBN:0781735149] is_a: GO:0019865 ! immunoglobulin binding [Term] id: GO:0001791 name: IgM binding namespace: molecular_function def: "Interacting selectively and non-covalently with an immunoglobulin of the IgM isotype." [GOC:add, ISBN:0781735149] is_a: GO:0019865 ! immunoglobulin binding [Term] id: GO:0001792 name: polymeric immunoglobulin receptor activity namespace: molecular_function def: "Combining with a J-chain-containing polymeric immunoglobulin of the IgA or IgM isotypes via the Fc region, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:add, GOC:signaling, ISBN:0781735149] is_a: GO:0019763 ! immunoglobulin receptor activity relationship: has_part GO:0001790 ! polymeric immunoglobulin binding [Term] id: GO:0001793 name: IgM receptor activity namespace: molecular_function def: "Combining with an immunoglobulin of the IgM isotype via the Fc region, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:add, GOC:signaling, ISBN:0781735149] is_a: GO:0019763 ! immunoglobulin receptor activity relationship: has_part GO:0001791 ! IgM binding [Term] id: GO:0001794 name: type IIa hypersensitivity namespace: biological_process def: "An inflammatory response resulting in cell death mediated by activation of the classical complement pathway or induction of effector cell phagocytosis or cytolysis mechanisms via complement or Fc receptors following the binding of antibodies to cell surface antigens on a target cell." [GOC:add, ISBN:0781735149] comment: Note that some type IIb hypersensitivity responses (GO:0001795) are referred to simply as type II hypersensitivity in the earlier literature, but are mechanistically distinct from type IIa hypersensitivity. is_a: GO:0002445 ! type II hypersensitivity [Term] id: GO:0001795 name: type IIb hypersensitivity namespace: biological_process def: "An inflammatory response resulting in cell death or dysfunction mediated by the direct binding of antibody to cellular receptors." [GOC:add, ISBN:0781735149] comment: Note that some type IIa hypersensitivity response (GO:0001794) are referred to simply as type II hypersensitivity in the earlier literature, but are mechanistically distinct from type IIb hypersensitivity. synonym: "type V hypersensitivity" EXACT [] is_a: GO:0002445 ! type II hypersensitivity [Term] id: GO:0001796 name: regulation of type IIa hypersensitivity namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of type IIa hypersensitivity, a type of inflammatory response." [GOC:add, ISBN:0781735149] is_a: GO:0002892 ! regulation of type II hypersensitivity intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001794 ! type IIa hypersensitivity relationship: regulates GO:0001794 ! type IIa hypersensitivity [Term] id: GO:0001797 name: negative regulation of type IIa hypersensitivity namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of type IIa hypersensitivity, a type of inflammatory response." [GOC:add, ISBN:0781735149] synonym: "down regulation of type IIa hypersensitivity" EXACT [] synonym: "down-regulation of type IIa hypersensitivity" EXACT [] synonym: "downregulation of type IIa hypersensitivity" EXACT [] synonym: "inhibition of type IIa hypersensitivity" NARROW [] is_a: GO:0001796 ! regulation of type IIa hypersensitivity is_a: GO:0002893 ! negative regulation of type II hypersensitivity intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001794 ! type IIa hypersensitivity relationship: negatively_regulates GO:0001794 ! type IIa hypersensitivity [Term] id: GO:0001798 name: positive regulation of type IIa hypersensitivity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of type IIa hypersensitivity, a type of inflammatory response." [GOC:add, ISBN:0781735149] synonym: "activation of type IIa hypersensitivity" NARROW [] synonym: "stimulation of type IIa hypersensitivity" NARROW [] synonym: "up regulation of type IIa hypersensitivity" EXACT [] synonym: "up-regulation of type IIa hypersensitivity" EXACT [] synonym: "upregulation of type IIa hypersensitivity" EXACT [] is_a: GO:0001796 ! regulation of type IIa hypersensitivity is_a: GO:0002894 ! positive regulation of type II hypersensitivity intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001794 ! type IIa hypersensitivity relationship: positively_regulates GO:0001794 ! type IIa hypersensitivity [Term] id: GO:0001799 name: regulation of type IIb hypersensitivity namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of type IIb hypersensitivity, a type of inflammatory response." [GOC:add, ISBN:0781735149] is_a: GO:0002892 ! regulation of type II hypersensitivity intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001795 ! type IIb hypersensitivity relationship: regulates GO:0001795 ! type IIb hypersensitivity [Term] id: GO:0001800 name: negative regulation of type IIb hypersensitivity namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of type IIb hypersensitivity, a type of inflammatory response." [GOC:add, ISBN:0781735149] synonym: "down regulation of type IIb hypersensitivity" EXACT [] synonym: "down-regulation of type IIb hypersensitivity" EXACT [] synonym: "downregulation of type IIb hypersensitivity" EXACT [] synonym: "inhibition of type IIb hypersensitivity" NARROW [] is_a: GO:0001799 ! regulation of type IIb hypersensitivity is_a: GO:0002893 ! negative regulation of type II hypersensitivity intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001795 ! type IIb hypersensitivity relationship: negatively_regulates GO:0001795 ! type IIb hypersensitivity [Term] id: GO:0001801 name: positive regulation of type IIb hypersensitivity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of type IIb hypersensitivity, a type of inflammatory response." [GOC:add, ISBN:0781735149] synonym: "activation of type IIb hypersensitivity" NARROW [] synonym: "stimulation of type IIb hypersensitivity" NARROW [] synonym: "up regulation of type IIb hypersensitivity" EXACT [] synonym: "up-regulation of type IIb hypersensitivity" EXACT [] synonym: "upregulation of type IIb hypersensitivity" EXACT [] is_a: GO:0001799 ! regulation of type IIb hypersensitivity is_a: GO:0002894 ! positive regulation of type II hypersensitivity intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001795 ! type IIb hypersensitivity relationship: positively_regulates GO:0001795 ! type IIb hypersensitivity [Term] id: GO:0001802 name: type III hypersensitivity namespace: biological_process def: "An inflammatory response resulting from recognition of immune complexes via complement or Fc receptors on effector cells leading to activation of neutrophils and other leukocytes and damage to bystander tissue." [GOC:add, ISBN:0781735149] comment: Note that the Arthus reaction is an example of type III hypersensitivity. xref: Wikipedia:Type_III_hypersensitivity is_a: GO:0002444 ! myeloid leukocyte mediated immunity is_a: GO:0002524 ! hypersensitivity is_a: GO:0016064 ! immunoglobulin mediated immune response [Term] id: GO:0001803 name: regulation of type III hypersensitivity namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of type III hypersensitivity, a type of inflammatory response." [GOC:add, ISBN:0781735149] is_a: GO:0002883 ! regulation of hypersensitivity is_a: GO:0002886 ! regulation of myeloid leukocyte mediated immunity is_a: GO:0002889 ! regulation of immunoglobulin mediated immune response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001802 ! type III hypersensitivity relationship: regulates GO:0001802 ! type III hypersensitivity [Term] id: GO:0001804 name: negative regulation of type III hypersensitivity namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of type III hypersensitivity, a type of inflammatory response." [GOC:add, ISBN:0781735149] synonym: "down regulation of type III hypersensitivity" EXACT [] synonym: "down-regulation of type III hypersensitivity" EXACT [] synonym: "downregulation of type III hypersensitivity" EXACT [] synonym: "inhibition of type III hypersensitivity" NARROW [] is_a: GO:0001803 ! regulation of type III hypersensitivity is_a: GO:0002884 ! negative regulation of hypersensitivity is_a: GO:0002887 ! negative regulation of myeloid leukocyte mediated immunity is_a: GO:0002890 ! negative regulation of immunoglobulin mediated immune response intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001802 ! type III hypersensitivity relationship: negatively_regulates GO:0001802 ! type III hypersensitivity [Term] id: GO:0001805 name: positive regulation of type III hypersensitivity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of type III hypersensitivity, a type of inflammatory response." [GOC:add, ISBN:0781735149] synonym: "activation of type III hypersensitivity" NARROW [] synonym: "stimulation of type III hypersensitivity" NARROW [] synonym: "up regulation of type III hypersensitivity" EXACT [] synonym: "up-regulation of type III hypersensitivity" EXACT [] synonym: "upregulation of type III hypersensitivity" EXACT [] is_a: GO:0001803 ! regulation of type III hypersensitivity is_a: GO:0002885 ! positive regulation of hypersensitivity is_a: GO:0002888 ! positive regulation of myeloid leukocyte mediated immunity is_a: GO:0002891 ! positive regulation of immunoglobulin mediated immune response intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001802 ! type III hypersensitivity relationship: positively_regulates GO:0001802 ! type III hypersensitivity [Term] id: GO:0001806 name: type IV hypersensitivity namespace: biological_process alt_id: GO:0016069 def: "An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation." [GOC:add, ISBN:0781735149] synonym: "delayed hypersensitivity response" EXACT [] synonym: "delayed-type hypersensitivity" EXACT [] xref: Wikipedia:Type_IV_hypersensitivity is_a: GO:0002456 ! T cell mediated immunity is_a: GO:0002524 ! hypersensitivity [Term] id: GO:0001807 name: regulation of type IV hypersensitivity namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of type IV hypersensitivity, a type of inflammatory response." [GOC:add, ISBN:0781735149] is_a: GO:0002709 ! regulation of T cell mediated immunity is_a: GO:0002883 ! regulation of hypersensitivity intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001806 ! type IV hypersensitivity relationship: regulates GO:0001806 ! type IV hypersensitivity [Term] id: GO:0001808 name: negative regulation of type IV hypersensitivity namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of type IV hypersensitivity, a type of inflammatory response." [GOC:add, ISBN:0781735149] synonym: "down regulation of type IV hypersensitivity" EXACT [] synonym: "down-regulation of type IV hypersensitivity" EXACT [] synonym: "downregulation of type IV hypersensitivity" EXACT [] synonym: "inhibition of type IV hypersensitivity" NARROW [] is_a: GO:0001807 ! regulation of type IV hypersensitivity is_a: GO:0002710 ! negative regulation of T cell mediated immunity is_a: GO:0002884 ! negative regulation of hypersensitivity intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001806 ! type IV hypersensitivity relationship: negatively_regulates GO:0001806 ! type IV hypersensitivity [Term] id: GO:0001809 name: positive regulation of type IV hypersensitivity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of type IV hypersensitivity, a type of inflammatory response." [GOC:add, ISBN:0781735149] synonym: "activation of type IV hypersensitivity" NARROW [] synonym: "stimulation of type IV hypersensitivity" NARROW [] synonym: "up regulation of type IV hypersensitivity" EXACT [] synonym: "up-regulation of type IV hypersensitivity" EXACT [] synonym: "upregulation of type IV hypersensitivity" EXACT [] is_a: GO:0001807 ! regulation of type IV hypersensitivity is_a: GO:0002711 ! positive regulation of T cell mediated immunity is_a: GO:0002885 ! positive regulation of hypersensitivity intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001806 ! type IV hypersensitivity relationship: positively_regulates GO:0001806 ! type IV hypersensitivity [Term] id: GO:0001810 name: regulation of type I hypersensitivity namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of type I hypersensitivity, a type of inflammatory response." [ISBN:0781735149] is_a: GO:0002883 ! regulation of hypersensitivity is_a: GO:0002889 ! regulation of immunoglobulin mediated immune response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0016068 ! type I hypersensitivity relationship: regulates GO:0016068 ! type I hypersensitivity [Term] id: GO:0001811 name: negative regulation of type I hypersensitivity namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of type I hypersensitivity, a type of inflammatory response." [GOC:add, ISBN:0781735149] synonym: "down regulation of type I hypersensitivity" EXACT [] synonym: "down-regulation of type I hypersensitivity" EXACT [] synonym: "downregulation of type I hypersensitivity" EXACT [] synonym: "inhibition of type I hypersensitivity" NARROW [] is_a: GO:0001810 ! regulation of type I hypersensitivity is_a: GO:0002884 ! negative regulation of hypersensitivity is_a: GO:0002890 ! negative regulation of immunoglobulin mediated immune response intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0016068 ! type I hypersensitivity relationship: negatively_regulates GO:0016068 ! type I hypersensitivity [Term] id: GO:0001812 name: positive regulation of type I hypersensitivity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of type I hypersensitivity, a type of inflammatory response." [GOC:add, ISBN:0781735149] synonym: "activation of type I hypersensitivity" NARROW [] synonym: "stimulation of type I hypersensitivity" NARROW [] synonym: "up regulation of type I hypersensitivity" EXACT [] synonym: "up-regulation of type I hypersensitivity" EXACT [] synonym: "upregulation of type I hypersensitivity" EXACT [] is_a: GO:0001810 ! regulation of type I hypersensitivity is_a: GO:0002885 ! positive regulation of hypersensitivity is_a: GO:0002891 ! positive regulation of immunoglobulin mediated immune response intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0016068 ! type I hypersensitivity relationship: positively_regulates GO:0016068 ! type I hypersensitivity [Term] id: GO:0001813 name: regulation of antibody-dependent cellular cytotoxicity namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of antibody-dependent cellular cytotoxicity." [GOC:add, ISBN:0781735149] synonym: "regulation of antibody dependent cell death" EXACT [] synonym: "regulation of antibody dependent cell killing" EXACT [] synonym: "regulation of antibody-dependent cell death" EXACT [] synonym: "regulation of antibody-dependent cell killing" EXACT [] is_a: GO:0001796 ! regulation of type IIa hypersensitivity is_a: GO:0001910 ! regulation of leukocyte mediated cytotoxicity intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001788 ! antibody-dependent cellular cytotoxicity relationship: regulates GO:0001788 ! antibody-dependent cellular cytotoxicity [Term] id: GO:0001814 name: negative regulation of antibody-dependent cellular cytotoxicity namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of antibody-dependent cellular cytotoxicity." [GOC:add, ISBN:0781735149] synonym: "down regulation of antibody-dependent cellular cytotoxicity" EXACT [] synonym: "down-regulation of antibody-dependent cellular cytotoxicity" EXACT [] synonym: "downregulation of antibody-dependent cellular cytotoxicity" EXACT [] synonym: "inhibition of antibody-dependent cellular cytotoxicity" NARROW [] synonym: "negative regulation of antibody dependent cell death" EXACT [] synonym: "negative regulation of antibody dependent cell killing" EXACT [] synonym: "negative regulation of antibody-dependent cell death" EXACT [] synonym: "negative regulation of antibody-dependent cell killing" EXACT [] is_a: GO:0001797 ! negative regulation of type IIa hypersensitivity is_a: GO:0001813 ! regulation of antibody-dependent cellular cytotoxicity is_a: GO:0001911 ! negative regulation of leukocyte mediated cytotoxicity intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001788 ! antibody-dependent cellular cytotoxicity relationship: negatively_regulates GO:0001788 ! antibody-dependent cellular cytotoxicity [Term] id: GO:0001815 name: positive regulation of antibody-dependent cellular cytotoxicity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of antibody-dependent cellular cytotoxicity." [GOC:add, ISBN:0781735149] synonym: "activation of antibody-dependent cellular cytotoxicity" NARROW [] synonym: "positive regulation of antibody dependent cell death" EXACT [] synonym: "positive regulation of antibody dependent cell killing" EXACT [] synonym: "positive regulation of antibody-dependent cell death" EXACT [] synonym: "positive regulation of antibody-dependent cell killing" EXACT [] synonym: "stimulation of antibody-dependent cellular cytotoxicity" NARROW [] synonym: "up regulation of antibody-dependent cellular cytotoxicity" EXACT [] synonym: "up-regulation of antibody-dependent cellular cytotoxicity" EXACT [] synonym: "upregulation of antibody-dependent cellular cytotoxicity" EXACT [] is_a: GO:0001798 ! positive regulation of type IIa hypersensitivity is_a: GO:0001813 ! regulation of antibody-dependent cellular cytotoxicity is_a: GO:0001912 ! positive regulation of leukocyte mediated cytotoxicity intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001788 ! antibody-dependent cellular cytotoxicity relationship: positively_regulates GO:0001788 ! antibody-dependent cellular cytotoxicity [Term] id: GO:0001816 name: cytokine production namespace: biological_process def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] comment: Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules. subset: goslim_pir synonym: "interferon production" NARROW [GOC:add, GOC:mah] synonym: "interleukin production" NARROW [GOC:add, GOC:mah] is_a: GO:0044707 ! single-multicellular organism process [Term] id: GO:0001817 name: regulation of cytokine production namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of production of a cytokine." [GOC:add, ISBN:0781735149] is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001816 ! cytokine production relationship: regulates GO:0001816 ! cytokine production [Term] id: GO:0001818 name: negative regulation of cytokine production namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of production of a cytokine." [GOC:add, ISBN:0781735149] synonym: "down regulation of cytokine production" EXACT [] synonym: "down-regulation of cytokine production" EXACT [] synonym: "downregulation of cytokine production" EXACT [] synonym: "inhibition of cytokine production" NARROW [] is_a: GO:0001817 ! regulation of cytokine production is_a: GO:0051241 ! negative regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001816 ! cytokine production relationship: negatively_regulates GO:0001816 ! cytokine production [Term] id: GO:0001819 name: positive regulation of cytokine production namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of production of a cytokine." [GOC:add, ISBN:0781735149] synonym: "activation of cytokine production" NARROW [] synonym: "stimulation of cytokine production" NARROW [] synonym: "up regulation of cytokine production" EXACT [] synonym: "up-regulation of cytokine production" EXACT [] synonym: "upregulation of cytokine production" EXACT [] is_a: GO:0001817 ! regulation of cytokine production is_a: GO:0051240 ! positive regulation of multicellular organismal process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001816 ! cytokine production relationship: positively_regulates GO:0001816 ! cytokine production [Term] id: GO:0001820 name: serotonin secretion namespace: biological_process def: "The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells." [GOC:ef, ISBN:0198506732, ISBN:0781735149] synonym: "5-HT secretion" EXACT [] synonym: "5-hydroxytryptamine secretion" EXACT [] synonym: "serotonin release" RELATED [GOC:tb] is_a: GO:0006837 ! serotonin transport is_a: GO:0032940 ! secretion by cell [Term] id: GO:0001821 name: histamine secretion namespace: biological_process def: "The regulated release of histamine by a cell or tissue. It is formed by decarboxylation of histidine and it acts through receptors in smooth muscle and in secretory systems." [GOC:mah, ISBN:0198506732, ISBN:0781735149] is_a: GO:0046903 ! secretion is_a: GO:0051608 ! histamine transport [Term] id: GO:0001822 name: kidney development namespace: biological_process def: "The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine." [GOC:dph, GOC:mtg_kidney_jan10, ISBN:0124020607, ISBN:0721662544] synonym: "nephrogenesis" RELATED [GOC:rph] xref: Wikipedia:Kidney_development is_a: GO:0044767 ! single-organism developmental process is_a: GO:0048513 ! animal organ development relationship: part_of GO:0072001 ! renal system development [Term] id: GO:0001823 name: mesonephros development namespace: biological_process def: "The process whose specific outcome is the progression of the mesonephros over time, from its formation to the mature structure. In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the mesonephros will form the mature kidney." [GOC:dph, ISBN:0124020607, ISBN:0721662544, PMID:10535314] synonym: "Wolffian body development" EXACT [GOC:dph] is_a: GO:0001822 ! kidney development [Term] id: GO:0001824 name: blastocyst development namespace: biological_process def: "The process whose specific outcome is the progression of the blastocyst over time, from its formation to the mature structure. The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm." [GOC:dph, ISBN:0124020607, ISBN:0198542771] comment: See also the Anatomical Dictionary for Mouse Development ontology terms 'TS5, embryo ; EMAP:23', 'TS5, inner cell mass ; EMAP:24' and 'TS5, trophectoderm; EMAP:28'. is_a: GO:0044767 ! single-organism developmental process is_a: GO:0048856 ! anatomical structure development relationship: part_of GO:0001701 ! in utero embryonic development [Term] id: GO:0001825 name: blastocyst formation namespace: biological_process def: "The initial formation of a blastocyst from a solid ball of cells known as a morula." [GOC:dph, ISBN:0124020607, ISBN:0198542771] comment: See also the Anatomical Dictionary for Mouse Development ontology term 'TS3, compacted morula ; EMAP:9'. is_a: GO:0044767 ! single-organism developmental process is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis relationship: part_of GO:0001824 ! blastocyst development [Term] id: GO:0001826 name: inner cell mass cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires specialized features of an inner cell mass cell." [GOC:dph, ISBN:0124020607, ISBN:0198542771] comment: See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, inner cell mass ; EMAP:14'. is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0001825 ! blastocyst formation [Term] id: GO:0001827 name: inner cell mass cell fate commitment namespace: biological_process def: "The cell fate commitment of precursor cells that will become inner cell mass cells." [GOC:dph, ISBN:0124020607, ISBN:0198542771] comment: See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, compacted morula ; EMAP:13' and 'TS4, inner cell mass ; EMAP:14'. is_a: GO:0045165 ! cell fate commitment relationship: part_of GO:0001826 ! inner cell mass cell differentiation [Term] id: GO:0001828 name: inner cell mass cellular morphogenesis namespace: biological_process def: "The morphogenesis of cells in the inner cell mass." [GOC:dph, ISBN:0124020607, ISBN:0198542771] comment: See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, inner cell mass ; EMAP:14' and 'TS5, inner cell mass ; EMAP:24'. is_a: GO:0000904 ! cell morphogenesis involved in differentiation is_a: GO:0048598 ! embryonic morphogenesis relationship: part_of GO:0001826 ! inner cell mass cell differentiation [Term] id: GO:0001829 name: trophectodermal cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires the specialized features of a trophectoderm cell." [GOC:dph, ISBN:0124020607, ISBN:0198542771] comment: See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, trophectoderm ; EMAP:19'. synonym: "trophectoderm cell differentiation" EXACT [] is_a: GO:0030154 ! cell differentiation relationship: part_of GO:0001825 ! blastocyst formation [Term] id: GO:0001830 name: trophectodermal cell fate commitment namespace: biological_process def: "The cell fate commitment of precursor cells that will become trophectoderm cells." [GOC:dph, ISBN:0124020607, ISBN:0198542771] comment: See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, trophectoderm ; EMAP:19'. synonym: "trophectoderm cell fate commitment" EXACT [] is_a: GO:0045165 ! cell fate commitment relationship: part_of GO:0001829 ! trophectodermal cell differentiation [Term] id: GO:0001831 name: trophectodermal cellular morphogenesis namespace: biological_process def: "The morphogenesis of trophectoderm cells." [GOC:dph, ISBN:0124020607, ISBN:0198542771] comment: See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, trophectoderm ; EMAP:19', 'TS5, trophectoderm ; EMAP:28' and 'TS6, trophectoderm ; EMAP:39'. synonym: "trophectoderm cellular morphogenesis" EXACT [] is_a: GO:0000904 ! cell morphogenesis involved in differentiation is_a: GO:0048598 ! embryonic morphogenesis relationship: part_of GO:0001829 ! trophectodermal cell differentiation [Term] id: GO:0001832 name: blastocyst growth namespace: biological_process def: "An increase in size of a blastocyst due to expansion of the blastocoelic cavity cell shape changes and cell proliferation." [GOC:dph, ISBN:0124020607, ISBN:0198542771] comment: See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, blastocoelic cavity ; EMAP:17', 'TS5, blastocoelic cavity ; EMAP:27' and 'TS6, blastocoelic cavity ; EMAP:36'. is_a: GO:0048589 ! developmental growth relationship: part_of GO:0001824 ! blastocyst development [Term] id: GO:0001833 name: inner cell mass cell proliferation namespace: biological_process def: "The proliferation of cells in the inner cell mass." [GOC:dph, GOC:isa_complete, ISBN:0124020607, ISBN:0198542771] comment: See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, inner cell mass ; EMAP:14' and 'TS5, inner cell mass ; EMAP:24'. is_a: GO:0008283 ! cell proliferation relationship: part_of GO:0001832 ! blastocyst growth [Term] id: GO:0001834 name: trophectodermal cell proliferation namespace: biological_process def: "The proliferation of cells in the trophectoderm." [GOC:dph, ISBN:0124020607, ISBN:0198542771] comment: See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, trophectoderm ; EMAP:19', 'TS5, trophectoderm ; EMAP:28' and 'TS6, trophectoderm ; EMAP:39'. synonym: "trophectoderm cell proliferation" EXACT [] is_a: GO:0008283 ! cell proliferation relationship: part_of GO:0001832 ! blastocyst growth [Term] id: GO:0001835 name: blastocyst hatching namespace: biological_process def: "The hatching of the cellular blastocyst from the zona pellucida." [GOC:dph, ISBN:0124020607, ISBN:0198542771] comment: See also the Anatomical Dictionary for Mouse Development ontology terms 'TS4, zona pellucida ; EMAP:22' and 'TS5, embryo ; EMAP:23'. is_a: GO:0035188 ! hatching relationship: part_of GO:0001824 ! blastocyst development [Term] id: GO:0001836 name: release of cytochrome c from mitochondria namespace: biological_process def: "The process that results in the movement of cytochrome c from the mitochondrial intermembrane space into the cytosol, which is part of the apoptotic signaling pathway and leads to caspase activation." [GOC:add, GOC:mah, GOC:mtg_apoptosis, ISBN:0721639976, PMID:12925707, PMID:9560217] comment: The release of cytochrome c from mitochondria is a central event in the signaling phase of the apoptotic process, and it is often used by researchers to monitor this type of cell death. Any event that induces apoptosis will at some point induce the release of cytochrome c from mitochondria. Therefore, this term should only be used to annotate gene products that are directly involved in this process. An example is Drp1 (DNM1L, UniProt symbol O00429) in PMID:20850011. is_a: GO:0008637 ! apoptotic mitochondrial changes relationship: part_of GO:0097190 ! apoptotic signaling pathway [Term] id: GO:0001837 name: epithelial to mesenchymal transition namespace: biological_process def: "A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell." [GOC:dph, PMID:14701881] synonym: "EMT" EXACT [] synonym: "epithelial-mesenchymal transition" EXACT [] synonym: "mesenchymal cell differentiation from epithelial cell" EXACT [GOC:BHF, GOC:dph, GOC:rl] is_a: GO:0048762 ! mesenchymal cell differentiation [Term] id: GO:0001838 name: embryonic epithelial tube formation namespace: biological_process def: "The morphogenesis of an embryonic epithelium into a tube-shaped structure." [GOC:dph, ISBN:0824072820] is_a: GO:0072175 ! epithelial tube formation relationship: part_of GO:0016331 ! morphogenesis of embryonic epithelium [Term] id: GO:0001839 name: neural plate morphogenesis namespace: biological_process def: "The process in which the anatomical structures of the neural plate are generated and organized. The neural plate is a specialized region of columnar epithelial cells in the dorsal ectoderm that will give rise to nervous system tissue." [GOC:dph, ISBN:0878932437] is_a: GO:0016331 ! morphogenesis of embryonic epithelium relationship: part_of GO:0001840 ! neural plate development [Term] id: GO:0001840 name: neural plate development namespace: biological_process def: "The process whose specific outcome is the progression of the neural plate over time, from its formation to the mature structure. The neural plate is a flat, thickened layer of ectodermal cells. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system." [GOC:dph, GOC:ef, ISBN:0878932437, ISBN:0878932585] is_a: GO:0060429 ! epithelium development relationship: part_of GO:0043009 ! chordate embryonic development [Term] id: GO:0001841 name: neural tube formation namespace: biological_process alt_id: GO:0001679 def: "The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." [GOC:dph, ISBN:0878932437] synonym: "neural tube morphogenesis" EXACT [GOC:dph] synonym: "neurulation" EXACT [] xref: Wikipedia:Neurulation is_a: GO:0001838 ! embryonic epithelial tube formation relationship: part_of GO:0021915 ! neural tube development [Term] id: GO:0001842 name: neural fold formation namespace: biological_process def: "The process in which the neural fold is formed. The edges of the neural plate thicken and move up to form a U-shaped structure called the neural groove." [GOC:dph, ISBN:0878932437] synonym: "neural groove formation" RELATED [GOC:dph] is_a: GO:0016331 ! morphogenesis of embryonic epithelium is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis is_a: GO:0060571 ! morphogenesis of an epithelial fold relationship: part_of GO:0014020 ! primary neural tube formation [Term] id: GO:0001843 name: neural tube closure namespace: biological_process def: "The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline." [GOC:dph, ISBN:0878932437] is_a: GO:0060606 ! tube closure relationship: part_of GO:0014020 ! primary neural tube formation [Term] id: GO:0001844 name: protein insertion into mitochondrial membrane involved in apoptotic signaling pathway namespace: biological_process def: "The process in which a protein is incorporated into a mitochondrial membrane as the initial phase of the mitochondrial membrane permeabilization that takes place in the apoptotic signaling pathway." [GOC:add, GOC:mtg_apoptosis, PMID:12952892] comment: Note that this term is intended to cover the insertion of pro-apoptotic proteins such as Bax or its homologs into mitochondrial membranes which occurs as an early step in the apoptotic program. synonym: "insertion of proteins into mitochondrial membranes during the induction of apoptosis" NARROW [] synonym: "protein insertion into mitochondrial membrane during induction of apoptosis" NARROW [GOC:dph, GOC:tb] synonym: "protein insertion into mitochondrial membrane involved in induction of apoptosis" NARROW [] synonym: "protein insertion into mitochondrion membrane during induction of apoptosis" NARROW [] xref: Reactome:REACT_101395 "Translocation of BMF to mitochondria, Gallus gallus" xref: Reactome:REACT_101818 "Translocation of BIM to mitochondria, Sus scrofa" xref: Reactome:REACT_102379 "Translocation of BIM to mitochondria, Bos taurus" xref: Reactome:REACT_104 "Translocation of PUMA protein to mitochondria, Homo sapiens" xref: Reactome:REACT_105818 "Translocation of BIM to mitochondria, Rattus norvegicus" xref: Reactome:REACT_105883 "Translocation of activated BAD protein to mitochondria, Bos taurus" xref: Reactome:REACT_109143 "Translocation of activated BAX to the mitochondria, Danio rerio" xref: Reactome:REACT_110253 "Translocation of BMF to mitochondria, Taeniopygia guttata" xref: Reactome:REACT_110902 "Translocation of activated BAD protein to mitochondria, Sus scrofa" xref: Reactome:REACT_112264 "Translocation of activated BAD protein to mitochondria, Xenopus tropicalis" xref: Reactome:REACT_112484 "Translocation of NOXA to mitochondria, Mus musculus" xref: Reactome:REACT_112773 "Translocation of NOXA to mitochondria, Rattus norvegicus" xref: Reactome:REACT_113120 "Translocation of BIM to mitochondria, Xenopus tropicalis" xref: Reactome:REACT_113968 "Translocation of NOXA to mitochondria, Sus scrofa" xref: Reactome:REACT_115488 "Translocation of NOXA to mitochondria, Canis familiaris" xref: Reactome:REACT_1286 "Translocation of activated BAX to the mitochondria, Homo sapiens" xref: Reactome:REACT_1585 "Translocation of NOXA to mitochondria, Homo sapiens" xref: Reactome:REACT_2046 "Translocation of activated BAD protein to mitochondria, Homo sapiens" xref: Reactome:REACT_32202 "Translocation of activated BAX to the mitochondria, Xenopus tropicalis" xref: Reactome:REACT_32704 "Translocation of activated BAD protein to mitochondria, Canis familiaris" xref: Reactome:REACT_600 "Translocation of BMF to mitochondria, Homo sapiens" xref: Reactome:REACT_750 "Translocation of BIM to mitochondria, Homo sapiens" xref: Reactome:REACT_78961 "Translocation of activated BAD protein to mitochondria, Danio rerio" xref: Reactome:REACT_81932 "Translocation of activated BAX to the mitochondria, Bos taurus" xref: Reactome:REACT_83771 "Translocation of BMF to mitochondria, Bos taurus" xref: Reactome:REACT_85921 "Translocation of BIM to mitochondria, Canis familiaris" xref: Reactome:REACT_87251 "Translocation of activated BAD protein to mitochondria, Rattus norvegicus" xref: Reactome:REACT_87865 "Translocation of activated BAX to the mitochondria, Rattus norvegicus" xref: Reactome:REACT_89314 "Translocation of BMF to mitochondria, Rattus norvegicus" xref: Reactome:REACT_91622 "Translocation of activated BAD protein to mitochondria, Mus musculus" xref: Reactome:REACT_92580 "Translocation of activated BAX to the mitochondria, Mus musculus" xref: Reactome:REACT_94530 "Translocation of BMF to mitochondria, Mus musculus" xref: Reactome:REACT_95929 "Translocation of BIM to mitochondria, Mus musculus" xref: Reactome:REACT_97369 "Translocation of activated BAX to the mitochondria, Taeniopygia guttata" xref: Reactome:REACT_97409 "Translocation of activated BAX to the mitochondria, Sus scrofa" xref: Reactome:REACT_97453 "Translocation of BMF to mitochondria, Canis familiaris" xref: Reactome:REACT_99030 "Translocation of activated BAX to the mitochondria, Canis familiaris" xref: Reactome:REACT_99700 "Translocation of BMF to mitochondria, Xenopus tropicalis" is_a: GO:0051204 ! protein insertion into mitochondrial membrane intersection_of: GO:0051204 ! protein insertion into mitochondrial membrane intersection_of: part_of GO:0097190 ! apoptotic signaling pathway relationship: part_of GO:0097190 ! apoptotic signaling pathway relationship: part_of GO:0097345 ! mitochondrial outer membrane permeabilization [Term] id: GO:0001845 name: phagolysosome assembly namespace: biological_process def: "The process that results in the fusion of a phagosome, a vesicle formed by phagocytosis, with a lysosome." [GOC:add, ISBN:0781735149] synonym: "late phagosome biosynthesis" RELATED [] synonym: "late phagosome formation" RELATED [] synonym: "phagolysosome formation" RELATED [GOC:mah] is_a: GO:0007040 ! lysosome organization is_a: GO:0016050 ! vesicle organization is_a: GO:0070925 ! organelle assembly relationship: part_of GO:0006909 ! phagocytosis relationship: part_of GO:0090382 ! phagosome maturation [Term] id: GO:0001846 name: opsonin binding namespace: molecular_function def: "Interacting selectively and non-covalently with an opsonin, such as a complement component or antibody, deposited on the surface of a bacteria, virus, immune complex, or other particulate material." [GOC:add, ISBN:0781735149] comment: Note that an opsonin is a blood serum protein or fragment which when deposited on the surface of a bacteria, virus, immune complex, or other particulate material acts a signal for phagocytosis to cells bearing the appropriate receptors. Not all complement components or fragments and not all antibodies have opsonic properties. is_a: GO:0005515 ! protein binding [Term] id: GO:0001847 name: opsonin receptor activity namespace: molecular_function def: "Combining with an opsonin and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:add, GOC:signaling, ISBN:0781735149] is_a: GO:0004888 ! transmembrane signaling receptor activity relationship: has_part GO:0001846 ! opsonin binding [Term] id: GO:0001848 name: complement binding namespace: molecular_function def: "Interacting selectively and non-covalently with any component or product of the complement cascade." [GOC:add, ISBN:0781735149] comment: Note that the complement cascade includes all of the components involved in the classical complement pathway, the alternative complement pathway, and the lectin complement pathway, as well as the common components of all three pathways. is_a: GO:0005515 ! protein binding [Term] id: GO:0001849 name: complement component C1q binding namespace: molecular_function def: "Interacting selectively and non-covalently with the C1q component of the classical complement cascade." [GOC:add, ISBN:0781735149] is_a: GO:0001846 ! opsonin binding is_a: GO:0001848 ! complement binding [Term] id: GO:0001850 name: complement component C3a binding namespace: molecular_function def: "Interacting selectively and non-covalently with the C3a product of the complement cascade." [GOC:add, ISBN:0781735149] is_a: GO:0001848 ! complement binding [Term] id: GO:0001851 name: complement component C3b binding namespace: molecular_function def: "Interacting selectively and non-covalently with the C3b product of the complement cascade." [GOC:add, ISBN:0781735149] is_a: GO:0001846 ! opsonin binding is_a: GO:0001848 ! complement binding [Term] id: GO:0001852 name: complement component iC3b binding namespace: molecular_function def: "Interacting selectively and non-covalently with the iC3b product of the complement cascade." [GOC:add, ISBN:0781735149] is_a: GO:0001846 ! opsonin binding is_a: GO:0001848 ! complement binding [Term] id: GO:0001853 name: complement component C3dg binding namespace: molecular_function def: "Interacting selectively and non-covalently with the C3dg product of the complement cascade." [GOC:add, ISBN:0781735149] is_a: GO:0001848 ! complement binding [Term] id: GO:0001854 name: complement component C3d binding namespace: molecular_function def: "Interacting selectively and non-covalently with the C3d product of the complement cascade." [GOC:add, ISBN:0781735149] is_a: GO:0001848 ! complement binding [Term] id: GO:0001855 name: complement component C4b binding namespace: molecular_function def: "Interacting selectively and non-covalently with the C4b product of the classical complement cascade." [GOC:add, ISBN:0781735149] is_a: GO:0001846 ! opsonin binding is_a: GO:0001848 ! complement binding [Term] id: GO:0001856 name: complement component C5a binding namespace: molecular_function def: "Interacting selectively and non-covalently with the C5a product of the complement cascade." [GOC:add, ISBN:0781735149] is_a: GO:0001848 ! complement binding [Term] id: GO:0001857 name: complement component C1q receptor activity namespace: molecular_function def: "Combining with the C1q component of the classical complement cascade and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:add, GOC:signaling, ISBN:0781735149] is_a: GO:0001847 ! opsonin receptor activity is_a: GO:0004875 ! complement receptor activity relationship: has_part GO:0001849 ! complement component C1q binding [Term] id: GO:0001858 name: complement component iC3b receptor activity namespace: molecular_function def: "Combining with the iC3b product of the complement cascade and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:add, GOC:signaling, ISBN:0781735149] is_a: GO:0001847 ! opsonin receptor activity is_a: GO:0004875 ! complement receptor activity relationship: has_part GO:0001852 ! complement component iC3b binding [Term] id: GO:0001859 name: complement component C3dg receptor activity namespace: molecular_function def: "Combining with the C3dg product of the complement cascade and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:add, GOC:signaling, ISBN:0781735149] is_a: GO:0004875 ! complement receptor activity relationship: has_part GO:0001853 ! complement component C3dg binding [Term] id: GO:0001860 name: complement component C3d receptor activity namespace: molecular_function def: "Combining with the C3d product of the complement cascade and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:add, GOC:signaling, ISBN:0781735149] is_a: GO:0004875 ! complement receptor activity relationship: has_part GO:0001854 ! complement component C3d binding [Term] id: GO:0001861 name: complement component C4b receptor activity namespace: molecular_function def: "Combining with the C4b product of the classical complement cascade and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:add, GOC:signaling, ISBN:0781735149] is_a: GO:0001847 ! opsonin receptor activity is_a: GO:0004875 ! complement receptor activity relationship: has_part GO:0001855 ! complement component C4b binding [Term] id: GO:0001862 name: collectin binding namespace: molecular_function def: "Interacting selectively and non-covalently with a collectin, a member of a group of structurally related pattern recognition molecules characterized by having a carbohydrate recognition domain of the C-type lectin family at the C-terminus and a collagenous domain at the N-terminus." [GOC:add, ISBN:0781735149] comment: Note that collectins include such proteins as mannose-binding lectins (MBL) and surfactant proteins A and D (SP-A and SP-D). is_a: GO:0001846 ! opsonin binding [Term] id: GO:0001863 name: collectin receptor activity namespace: molecular_function def: "Combining with a collectin and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." [GOC:add, GOC:signaling, ISBN:0781735149] comment: Note that collectins include such proteins as mannose-binding lectin (MBL) and surfactant proteins A and D (SP-A and SP-D). is_a: GO:0001847 ! opsonin receptor activity relationship: has_part GO:0001862 ! collectin binding [Term] id: GO:0001864 name: pentraxin binding namespace: molecular_function def: "Interacting selectively and non-covalently with a pentraxin, a member of a family of inflammatory proteins with a radially symmetric arrangement of five identical, noncovalently linked chains in a pentagonal array." [GOC:add, ISBN:0781735149] comment: Note that pentraxins include such proteins as serum amyloid P component (SAP) and C-reactive protein (CRP). is_a: GO:0001846 ! opsonin binding [Term] id: GO:0001865 name: NK T cell differentiation namespace: biological_process def: "The process in which a precursor cell type acquires the specialized features of a NK T cell." [GOC:add, ISBN:0781735149, PMID:10704459] comment: Note that NK T cells are a distinct lineage of T cells expressing natural killer cell markers and having T cell receptors characterized by the usage of a restricted repertoire of variable region gene segments. Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "natural killer T cell differentiation" EXACT [] synonym: "natural T cell differentiation" EXACT [] synonym: "NK T cell development" RELATED [GOC:add] synonym: "NK T lymphocyte differentiation" EXACT [] synonym: "NK T-cell differentiation" EXACT [] synonym: "NK T-lymphocyte differentiation" EXACT [] synonym: "NKT cell differentiation" EXACT [] synonym: "NT cell differentiation" EXACT [] is_a: GO:0046632 ! alpha-beta T cell differentiation [Term] id: GO:0001866 name: NK T cell proliferation namespace: biological_process def: "The expansion of a NK T cell population by cell division." [GOC:add, ISBN:0781735149, PMID:10704459] comment: Note that NK T cells are a distinct lineage of T cells expressing natural killer cell markers and having T cell receptors characterized by the usage of a restricted repertoire of variable region gene segments. synonym: "natural killer T cell proliferation" EXACT [] synonym: "natural T cell proliferation" EXACT [] synonym: "NK T lymphocyte proliferation" EXACT [] synonym: "NK T-cell proliferation" EXACT [] synonym: "NK T-lymphocyte proliferation" EXACT [] synonym: "NKT cell proliferation" EXACT [] synonym: "NT cell proliferation" EXACT [] is_a: GO:0046633 ! alpha-beta T cell proliferation is_a: GO:0051132 ! NK T cell activation [Term] id: GO:0001867 name: complement activation, lectin pathway namespace: biological_process def: "Any process involved in the activation of any of the steps of the lectin pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes." [GOC:add, ISBN:0781735149] comment: Note that proteins such as mannose-binding lectin (MBL) and certain serum ficolins can activate the lectin complement pathway. synonym: "complement cascade, lectin pathway" EXACT [GOC:add] xref: Reactome:REACT_114752 "Lectin pathway of complement activation, Canis familiaris" xref: Reactome:REACT_30334 "Lectin pathway of complement activation, Rattus norvegicus" xref: Reactome:REACT_31122 "Lectin pathway of complement activation, Bos taurus" xref: Reactome:REACT_33084 "Lectin pathway of complement activation, Mus musculus" xref: Reactome:REACT_7964 "Lectin pathway of complement activation, Homo sapiens" xref: Reactome:REACT_89631 "Lectin pathway of complement activation, Sus scrofa" xref: Reactome:REACT_96749 "Lectin pathway of complement activation, Gallus gallus" is_a: GO:0006956 ! complement activation is_a: GO:0045087 ! innate immune response [Term] id: GO:0001868 name: regulation of complement activation, lectin pathway namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the lectin pathway of complement activation." [GOC:add, ISBN:0781735149] synonym: "regulation of complement cascade, lectin pathway" EXACT [GOC:add] is_a: GO:0030449 ! regulation of complement activation is_a: GO:0045088 ! regulation of innate immune response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001867 ! complement activation, lectin pathway relationship: regulates GO:0001867 ! complement activation, lectin pathway [Term] id: GO:0001869 name: negative regulation of complement activation, lectin pathway namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of complement activation by the lectin pathway." [GOC:add, ISBN:0781735149] synonym: "down regulation of complement activation, lectin pathway" EXACT [] synonym: "down-regulation of complement activation, lectin pathway" EXACT [] synonym: "downregulation of complement activation, lectin pathway" EXACT [] synonym: "inhibition of complement activation, lectin pathway" NARROW [] synonym: "negative regulation of complement cascade, lectin pathway" EXACT [GOC:add] is_a: GO:0001868 ! regulation of complement activation, lectin pathway is_a: GO:0045824 ! negative regulation of innate immune response is_a: GO:0045916 ! negative regulation of complement activation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001867 ! complement activation, lectin pathway relationship: negatively_regulates GO:0001867 ! complement activation, lectin pathway [Term] id: GO:0001870 name: positive regulation of complement activation, lectin pathway namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of complement activation by the lectin pathway." [GOC:add, ISBN:0781735149] synonym: "activation of complement activation, lectin pathway" NARROW [] synonym: "positive regulation of complement cascade, lectin pathway" EXACT [GOC:add] synonym: "stimulation of complement activation, lectin pathway" NARROW [] synonym: "up regulation of complement activation, lectin pathway" EXACT [] synonym: "up-regulation of complement activation, lectin pathway" EXACT [] synonym: "upregulation of complement activation, lectin pathway" EXACT [] is_a: GO:0001868 ! regulation of complement activation, lectin pathway is_a: GO:0045089 ! positive regulation of innate immune response is_a: GO:0045917 ! positive regulation of complement activation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001867 ! complement activation, lectin pathway relationship: positively_regulates GO:0001867 ! complement activation, lectin pathway [Term] id: GO:0001871 name: pattern binding namespace: molecular_function def: "Interacting selectively and non-covalently with a repeating or polymeric structure, such as a polysaccharide or peptidoglycan." [PMID:12072369, PMID:12225919, PMID:12507420, PMID:12925128, PMID:14523544] comment: Note that this term and its child terms are intended for annotation of gene products which function to recognize (bind) the repeating structural units such as polysaccharides or peptidoglycans commonly found in microbial cell walls and virions. If such binding is coupled to signal transduction, use 'pattern recognition receptor activity ; GO:0008329' instead. subset: goslim_pir subset: gosubset_prok synonym: "pattern recognition activity" BROAD [] is_a: GO:0005488 ! binding [Term] id: GO:0001872 name: (1->3)-beta-D-glucan binding namespace: molecular_function alt_id: GO:0080087 def: "Interacting selectively and non-covalently with (1->3)-beta-D-glucans." [PMID:14707091] synonym: "1,3-beta-D-glucan binding" EXACT [] synonym: "callose binding" NARROW [] synonym: "zymosan binding" NARROW [GOC:tb] is_a: GO:0030247 ! polysaccharide binding [Term] id: GO:0001873 name: polysaccharide receptor activity namespace: molecular_function def: "Combining with a polysaccharide and transmitting the signal to initiate a change in cell activity. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." [CHEBI:18154, PMID:14707091] is_a: GO:0008329 ! signaling pattern recognition receptor activity relationship: has_part GO:0030247 ! polysaccharide binding [Term] id: GO:0001874 name: (1->3)-beta-D-glucan receptor activity namespace: molecular_function def: "Combining with (1->3)-beta-D-glucans to initiate a change in cell activity." [PMID:14707091] synonym: "(1,3)-beta-D-glucan receptor activity" EXACT [] synonym: "1,3-beta-D-glucan receptor activity" EXACT [] synonym: "beta-1,3-D-glucan receptor activity" EXACT [] synonym: "zymosan receptor activity" NARROW [GOC:tb] is_a: GO:0001873 ! polysaccharide receptor activity relationship: has_part GO:0001872 ! (1->3)-beta-D-glucan binding [Term] id: GO:0001875 name: lipopolysaccharide receptor activity namespace: molecular_function def: "Combining with a lipopolysaccharide and transmitting the signal across the cell membrane to initiate a change in cell activity. Lipopolysaccharides (LPS) are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system." [PMID:14609719, PMID:15379975] synonym: "endotoxin receptor activity" BROAD [] synonym: "LPS receptor activity" EXACT [] is_a: GO:0008329 ! signaling pattern recognition receptor activity relationship: has_part GO:0001530 ! lipopolysaccharide binding relationship: part_of GO:0031663 ! lipopolysaccharide-mediated signaling pathway [Term] id: GO:0001876 name: lipoarabinomannan binding namespace: molecular_function def: "Interacting selectively and non-covalently with lipoarabinomannan." [PMID:10586073] synonym: "LAM binding" EXACT [] is_a: GO:0001871 ! pattern binding is_a: GO:0034235 ! GPI anchor binding [Term] id: GO:0001877 name: lipoarabinomannan receptor activity namespace: molecular_function def: "Combining with lipoarabinomannan and transmitting the signal to initiate a change in cell activity." [PMID:10586073] synonym: "LAM receptor activity" EXACT [] is_a: GO:0008329 ! signaling pattern recognition receptor activity relationship: has_part GO:0001876 ! lipoarabinomannan binding [Term] id: GO:0001878 name: response to yeast namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a yeast species." [PMID:14707091] comment: defined as response to Saccharomycotina (true yeasts). This excludes fission yeast. is_a: GO:0009620 ! response to fungus [Term] id: GO:0001879 name: detection of yeast namespace: biological_process def: "The series of events in which a stimulus from a yeast is received and converted into a molecular signal." [PMID:14707091] is_a: GO:0001878 ! response to yeast is_a: GO:0016046 ! detection of fungus [Term] id: GO:0001880 name: Mullerian duct regression namespace: biological_process def: "The process in which the Mullerian ducts, primordia of the oviducts, uterus and upper vagina, undergo regression in male embryos." [GOC:dph, PMID:12368913] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0044702 ! single organism reproductive process is_a: GO:0060033 ! anatomical structure regression relationship: part_of GO:0046661 ! male sex differentiation [Term] id: GO:0001881 name: receptor recycling namespace: biological_process def: "The process that results in the return of receptor molecules to an active state and an active cellular location after they have been stimulated by a ligand. An active state is when the receptor is ready to receive a signal." [GOC:dph] is_a: GO:0043112 ! receptor metabolic process relationship: part_of GO:0023051 ! regulation of signaling [Term] id: GO:0001882 name: nucleoside binding namespace: molecular_function def: "Interacting selectively and non-covalently with a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose." [GOC:hjd] subset: goslim_pir subset: gosubset_prok is_a: GO:0036094 ! small molecule binding is_a: GO:0097159 ! organic cyclic compound binding is_a: GO:0097367 ! carbohydrate derivative binding is_a: GO:1901363 ! heterocyclic compound binding [Term] id: GO:0001883 name: purine nucleoside binding namespace: molecular_function def: "Interacting selectively and non-covalently with a purine nucleoside, a compound consisting of a purine base linked either to ribose or deoxyribose." [GOC:hjd] is_a: GO:0001882 ! nucleoside binding [Term] id: GO:0001884 name: pyrimidine nucleoside binding namespace: molecular_function def: "Interacting selectively and non-covalently with a pyrimidine nucleoside, a compound consisting of a pyrimidine base linked either to ribose or deoxyribose." [GOC:hjd] is_a: GO:0001882 ! nucleoside binding [Term] id: GO:0001885 name: endothelial cell development namespace: biological_process def: "The progression of an endothelial cell over time, from its formation to the mature structure." [GOC:dph] is_a: GO:0002064 ! epithelial cell development relationship: part_of GO:0003158 ! endothelium development relationship: part_of GO:0045446 ! endothelial cell differentiation [Term] id: GO:0001886 name: endothelial cell morphogenesis namespace: biological_process def: "The change in form (cell shape and size) that occurs during the differentiation of an endothelial cell." [GOC:ascb_2009, GOC:dph, GOC:tb] is_a: GO:0003382 ! epithelial cell morphogenesis relationship: part_of GO:0001885 ! endothelial cell development [Term] id: GO:0001887 name: selenium compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving compounds that contain selenium, such as selenocysteine." [PMID:12730456] subset: gosubset_prok synonym: "selenium compound metabolism" EXACT [] synonym: "selenium metabolic process" EXACT [] synonym: "selenium metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0001888 name: glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity namespace: molecular_function def: "Catalysis of the reaction: UDP-N-acetyl-D-glucosamine + beta-D-glucuronosyl-(1->3)-beta-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-xylosyl-proteoglycan = UDP + alpha-N-acetyl-D-glucosaminyl-(1->4)-beta-D-glucuronosyl-(1->3)-beta-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-xylosyl-proteoglycan." [EC:2.4.1.223] synonym: "alpha-1,4-N-acetylglucosaminyltransferase activity" EXACT [EC:2.4.1.223] synonym: "alpha-N-acetylglucosaminyltransferase I activity" EXACT [EC:2.4.1.223] synonym: "alpha1,4-N-acetylglucosaminyltransferase activity" EXACT [EC:2.4.1.223] synonym: "glucuronosylgalactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity" EXACT [EC:2.4.1.223] synonym: "UDP-N-acetyl-D-glucosamine:beta-D-glucuronosyl-(1,3)-beta-D-galactosyl-(1,3)-beta-D-galactosyl-(1,4)-beta-D-xylosyl-proteoglycan 4IV-alpha-N-acetyl-D-glucosaminyltransferase activity" EXACT [EC:2.4.1.223] synonym: "UDP-N-acetyl-D-glucosamine:beta-D-glucuronosyl-(1->3)-beta-D-galactosyl-(1->3)-beta-D-galactosyl-(1->4)-beta-D-xylosyl-proteoglycan 4IV-alpha-N-acetyl-D-glucosaminyltransferase activity" EXACT [EC:2.4.1.223] xref: EC:2.4.1.223 xref: MetaCyc:2.4.1.223-RXN is_a: GO:0008375 ! acetylglucosaminyltransferase activity [Term] id: GO:0001889 name: liver development namespace: biological_process def: "The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes." [GOC:add, ISBN:068340007X] is_a: GO:0048732 ! gland development relationship: part_of GO:0061008 ! hepaticobiliary system development [Term] id: GO:0001890 name: placenta development namespace: biological_process def: "The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin." [GOC:add, ISBN:068340007X] synonym: "placental development" EXACT [] synonym: "placentation" EXACT [GOC:dph, GOC:tb] is_a: GO:0044702 ! single organism reproductive process is_a: GO:0044767 ! single-organism developmental process is_a: GO:0048513 ! animal organ development is_a: GO:0048608 ! reproductive structure development [Term] id: GO:0001891 name: phagocytic cup namespace: cellular_component def: "An invagination of the cell membrane formed by an actin dependent process during phagocytosis. Following internalization it is converted into a phagosome." [PMID:10358769] is_a: GO:0044459 ! plasma membrane part [Term] id: GO:0001892 name: embryonic placenta development namespace: biological_process def: "The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin." [GOC:add, ISBN:068340007X] synonym: "fetal placenta development" EXACT [GOC:dph] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0044702 ! single organism reproductive process is_a: GO:0048568 ! embryonic organ development relationship: part_of GO:0001701 ! in utero embryonic development relationship: part_of GO:0001890 ! placenta development [Term] id: GO:0001893 name: maternal placenta development namespace: biological_process def: "Maternally driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin." [GOC:add, ISBN:068340007X] synonym: "decidua development" RELATED [GOC:dph] is_a: GO:0044767 ! single-organism developmental process is_a: GO:0048608 ! reproductive structure development is_a: GO:0060135 ! maternal process involved in female pregnancy relationship: part_of GO:0001890 ! placenta development [Term] id: GO:0001894 name: tissue homeostasis namespace: biological_process def: "A homeostatic process involved in the maintenance of an internal steady state within a defined tissue of an organism, including control of cellular proliferation and death and control of metabolic function." [GOC:add, GOC:isa_complete] synonym: "tissue maintenance" NARROW [GOC:add] is_a: GO:0060249 ! anatomical structure homeostasis relationship: part_of GO:0048871 ! multicellular organismal homeostasis [Term] id: GO:0001895 name: retina homeostasis namespace: biological_process def: "A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function." [GOC:add, GOC:dph, GOC:tb, PMID:15365173, PMID:15365178] is_a: GO:0001894 ! tissue homeostasis [Term] id: GO:0001896 name: autolysis namespace: biological_process def: "A programmed cell death process observed in bacteria and filamentous fungi and leading to spontaneous death by lysis. Examples are lysis of the mother cell during sporulation of Bacillus subtilis and self-degradation of fungal cells in Aspergillus nidulans. Autolysis is also involved in bacterial biofilm formation." [GOC:add, GOC:jh2, GOC:mtg_apoptosis, PMID:10974124, PMID:19286987, PMID:26811896] subset: gosubset_prok xref: Wikipedia:Autolysis is_a: GO:0012501 ! programmed cell death [Term] id: GO:0001897 name: cytolysis by symbiont of host cells namespace: biological_process def: "The killing by an organism of a cell in its host organism by means of the rupture of cell membranes and the loss of cytoplasm. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add] subset: gosubset_prok synonym: "cytolysis by organism of host cells" EXACT [] is_a: GO:0001907 ! killing by symbiont of host cells is_a: GO:0051801 ! cytolysis in other organism involved in symbiotic interaction relationship: has_part GO:0052025 ! modification by symbiont of host cell membrane [Term] id: GO:0001898 name: regulation of cytolysis by symbiont of host cells namespace: biological_process def: "Any process in which an organism modulates the frequency, rate or extent of the cytolysis by that organism of cells in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add, GOC:dph, GOC:tb] subset: gosubset_prok synonym: "regulation by symbiont of cytolysis of host cells" EXACT [GOC:dph, GOC:tb] is_a: GO:0051802 ! regulation of cytolysis in other organism involved in symbiotic interaction intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001897 ! cytolysis by symbiont of host cells relationship: regulates GO:0001897 ! cytolysis by symbiont of host cells [Term] id: GO:0001899 name: negative regulation of cytolysis by symbiont of host cells namespace: biological_process def: "Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of cytolysis by that organism of cells in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add, GOC:dph, GOC:tb] subset: gosubset_prok synonym: "down regulation by symbiont of cytolysis of host cells" EXACT [] synonym: "down-regulation by symbiont of cytolysis of host cells" EXACT [] synonym: "downregulation by symbiont of cytolysis of host cells" EXACT [] synonym: "inhibition by symbiont of cytolysis of host cells" NARROW [] synonym: "negative regulation by symbiont of cytolysis of host cells" EXACT [GOC:dph, GOC:tb] is_a: GO:0001898 ! regulation of cytolysis by symbiont of host cells is_a: GO:0051803 ! negative regulation of cytolysis in other organism involved in symbiotic interaction intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001897 ! cytolysis by symbiont of host cells relationship: negatively_regulates GO:0001897 ! cytolysis by symbiont of host cells [Term] id: GO:0001900 name: positive regulation of cytolysis by symbiont of host cells namespace: biological_process def: "Any process in which an organism activates or increases the frequency, rate or extent of cytolysis by that organism of cells in its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add, GOC:dph, GOC:tb] subset: gosubset_prok synonym: "activation by symbiont of cytolysis of host cells" NARROW [] synonym: "positive regulation by symbiont of cytolysis of host cells" EXACT [GOC:dph, GOC:tb] synonym: "stimulation by symbiont of cytolysis of host cells" NARROW [] synonym: "up regulation by symbiont of cytolysis of host cells" EXACT [] synonym: "up-regulation by symbiont of cytolysis of host cells" EXACT [] synonym: "upregulation by symbiont of cytolysis of host cells" EXACT [] is_a: GO:0001898 ! regulation of cytolysis by symbiont of host cells is_a: GO:0051804 ! positive regulation of cytolysis in other organism involved in symbiotic interaction intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001897 ! cytolysis by symbiont of host cells relationship: positively_regulates GO:0001897 ! cytolysis by symbiont of host cells [Term] id: GO:0001905 name: activation of membrane attack complex namespace: biological_process def: "The activation of the membrane attack complex components of the complement cascade which can result in death of a target cell through cytolysis." [GOC:add, ISBN:0781735149] synonym: "activation of MAC" EXACT [] synonym: "activation of TCC" NARROW [] synonym: "activation of terminal complement complex" NARROW [GOC:add] synonym: "activation of the terminal complement cascade" NARROW [] synonym: "MAC assembly" EXACT [GOC:rl] synonym: "MAC formation" EXACT [GOC:rl] synonym: "membrane attack complex assembly" EXACT [GOC:rl] synonym: "membrane attack complex formation" EXACT [GOC:rl] is_a: GO:0006956 ! complement activation [Term] id: GO:0001906 name: cell killing namespace: biological_process def: "Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions." [GOC:add] subset: goslim_pir subset: gosubset_prok synonym: "necrosis" RELATED [] is_a: GO:0008150 ! biological_process disjoint_from: GO:0044848 ! biological phase [Term] id: GO:0001907 name: killing by symbiont of host cells namespace: biological_process def: "Any process mediated by an organism that results in the death of cells in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add] subset: gosubset_prok is_a: GO:0044004 ! disruption by symbiont of host cell is_a: GO:0051883 ! killing of cells in other organism involved in symbiotic interaction [Term] id: GO:0001909 name: leukocyte mediated cytotoxicity namespace: biological_process def: "The directed killing of a target cell by a leukocyte." [GO_REF:0000022, GOC:add, GOC:mtg_15nov05, ISBN:0781735149, PMID:11911826] comment: This term was improved by GO_REF:0000022. It was moved. Note that this term and its children describe contact-dependent killing of target cells by lymphocytes and myeloid cells of the immune system. synonym: "immune cell mediated cell death" EXACT [] synonym: "immune cell mediated cell killing" EXACT [] synonym: "immune cell mediated cytotoxicity" EXACT [] synonym: "leucocyte mediated cytotoxicity" EXACT [] is_a: GO:0001906 ! cell killing [Term] id: GO:0001910 name: regulation of leukocyte mediated cytotoxicity namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of leukocyte mediated cytotoxicity." [GOC:add, ISBN:0781735149, PMID:11911826] synonym: "regulation of immune cell mediated cell death" EXACT [] synonym: "regulation of immune cell mediated cell killing" EXACT [] synonym: "regulation of immune cell mediated cytotoxicity" EXACT [] synonym: "regulation of leucocyte mediated cytotoxicity" EXACT [] is_a: GO:0031341 ! regulation of cell killing intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001909 ! leukocyte mediated cytotoxicity relationship: regulates GO:0001909 ! leukocyte mediated cytotoxicity [Term] id: GO:0001911 name: negative regulation of leukocyte mediated cytotoxicity namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of leukocyte mediated cytotoxicity." [GOC:add, ISBN:0781735149, PMID:11911826] synonym: "down regulation of leukocyte mediated cytotoxicity" EXACT [] synonym: "down-regulation of leukocyte mediated cytotoxicity" EXACT [] synonym: "downregulation of leukocyte mediated cytotoxicity" EXACT [] synonym: "inhibition of leukocyte mediated cytotoxicity" NARROW [] synonym: "negative regulation of immune cell mediated cytotoxicity" EXACT [] synonym: "negative regulation of leucocyte mediated cytotoxicity" EXACT [] is_a: GO:0001910 ! regulation of leukocyte mediated cytotoxicity is_a: GO:0031342 ! negative regulation of cell killing intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001909 ! leukocyte mediated cytotoxicity relationship: negatively_regulates GO:0001909 ! leukocyte mediated cytotoxicity [Term] id: GO:0001912 name: positive regulation of leukocyte mediated cytotoxicity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of leukocyte mediated cytotoxicity." [GOC:add, ISBN:0781735149, PMID:11911826] synonym: "activation of leukocyte mediated cytotoxicity" NARROW [] synonym: "positive regulation of immune cell mediated cytotoxicity" EXACT [] synonym: "positive regulation of leucocyte mediated cytotoxicity" EXACT [] synonym: "stimulation of leukocyte mediated cytotoxicity" NARROW [] synonym: "up regulation of leukocyte mediated cytotoxicity" EXACT [] synonym: "up-regulation of leukocyte mediated cytotoxicity" EXACT [] synonym: "upregulation of leukocyte mediated cytotoxicity" EXACT [] is_a: GO:0001910 ! regulation of leukocyte mediated cytotoxicity is_a: GO:0031343 ! positive regulation of cell killing intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001909 ! leukocyte mediated cytotoxicity relationship: positively_regulates GO:0001909 ! leukocyte mediated cytotoxicity [Term] id: GO:0001913 name: T cell mediated cytotoxicity namespace: biological_process def: "The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors." [GOC:add, GOC:pr, ISBN:0781735149, PMID:11911826] comment: Note that either or both mechanisms mentioned in the definition may be used in this process. Note that both granule release and the engagement of death receptors on target cells result in the induction of apoptosis in the target cell. Note that both CD4 and CD8 positive T cells can mediate apoptosis of target cells, independently of their definition as 'helper' T cells or not. synonym: "T cell mediated apoptosis" EXACT [] synonym: "T cell mediated cell death" EXACT [] synonym: "T cell mediated cell killing" EXACT [] synonym: "T cell mediated cytolysis" RELATED [] synonym: "T lymphocyte mediated cytotoxicity" EXACT [] synonym: "T-cell mediated apoptosis" EXACT [] synonym: "T-cell mediated cell death" EXACT [] synonym: "T-cell mediated cell killing" EXACT [] synonym: "T-cell mediated cytotoxicity" EXACT [] synonym: "T-lymphocyte mediated cytotoxicity" EXACT [] is_a: GO:0001909 ! leukocyte mediated cytotoxicity is_a: GO:0002456 ! T cell mediated immunity is_a: GO:0044699 ! single-organism process [Term] id: GO:0001914 name: regulation of T cell mediated cytotoxicity namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of T cell mediated cytotoxicity." [GOC:add, ISBN:0781735149] synonym: "regulation of T cell mediated apoptosis" EXACT [] synonym: "regulation of T cell mediated cell death" EXACT [] synonym: "regulation of T cell mediated cell killing" EXACT [] synonym: "regulation of T cell mediated cytolysis" RELATED [] synonym: "regulation of T lymphocyte mediated cytotoxicity" EXACT [] synonym: "regulation of T-cell mediated apoptosis" EXACT [] synonym: "regulation of T-cell mediated cell death" EXACT [] synonym: "regulation of T-cell mediated cell killing" EXACT [] synonym: "regulation of T-cell mediated cytolysis" RELATED [] synonym: "regulation of T-cell mediated cytotoxicity" EXACT [] synonym: "regulation of T-lymphocyte mediated cytotoxicity" EXACT [] is_a: GO:0001910 ! regulation of leukocyte mediated cytotoxicity is_a: GO:0002709 ! regulation of T cell mediated immunity intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001913 ! T cell mediated cytotoxicity relationship: regulates GO:0001913 ! T cell mediated cytotoxicity [Term] id: GO:0001915 name: negative regulation of T cell mediated cytotoxicity namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of T cell mediated cytotoxicity." [GOC:add, ISBN:0781735149] synonym: "down regulation of T cell mediated cytotoxicity" EXACT [] synonym: "down-regulation of T cell mediated cytotoxicity" EXACT [] synonym: "downregulation of T cell mediated cytotoxicity" EXACT [] synonym: "inhibition of T cell mediated cytotoxicity" NARROW [] synonym: "negative regulation of T cell mediated apoptosis" EXACT [] synonym: "negative regulation of T cell mediated cell death" EXACT [] synonym: "negative regulation of T cell mediated cell killing" EXACT [] synonym: "negative regulation of T cell mediated cytolysis" RELATED [] synonym: "negative regulation of T lymphocyte mediated cytotoxicity" EXACT [] synonym: "negative regulation of T-cell mediated apoptosis" EXACT [] synonym: "negative regulation of T-cell mediated cell death" EXACT [] synonym: "negative regulation of T-cell mediated cell killing" EXACT [] synonym: "negative regulation of T-cell mediated cytolysis" RELATED [] synonym: "negative regulation of T-cell mediated cytotoxicity" EXACT [] synonym: "negative regulation of T-lymphocyte mediated cytotoxicity" EXACT [] is_a: GO:0001911 ! negative regulation of leukocyte mediated cytotoxicity is_a: GO:0001914 ! regulation of T cell mediated cytotoxicity is_a: GO:0002710 ! negative regulation of T cell mediated immunity intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001913 ! T cell mediated cytotoxicity relationship: negatively_regulates GO:0001913 ! T cell mediated cytotoxicity [Term] id: GO:0001916 name: positive regulation of T cell mediated cytotoxicity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of T cell mediated cytotoxicity." [GOC:add, ISBN:0781735149] synonym: "activation of T cell mediated cytotoxicity" NARROW [] synonym: "positive regulation of T cell mediated apoptosis" EXACT [] synonym: "positive regulation of T cell mediated cell death" EXACT [] synonym: "positive regulation of T cell mediated cell killing" EXACT [] synonym: "positive regulation of T cell mediated cytolysis" RELATED [] synonym: "positive regulation of T lymphocyte mediated cytotoxicity" EXACT [] synonym: "positive regulation of T-cell mediated apoptosis" EXACT [] synonym: "positive regulation of T-cell mediated cell death" EXACT [] synonym: "positive regulation of T-cell mediated cell killing" EXACT [] synonym: "positive regulation of T-cell mediated cytolysis" RELATED [] synonym: "positive regulation of T-cell mediated cytotoxicity" EXACT [] synonym: "positive regulation of T-lymphocyte mediated cytotoxicity" EXACT [] synonym: "stimulation of T cell mediated cytotoxicity" NARROW [] synonym: "up regulation of T cell mediated cytotoxicity" EXACT [] synonym: "up-regulation of T cell mediated cytotoxicity" EXACT [] synonym: "upregulation of T cell mediated cytotoxicity" EXACT [] is_a: GO:0001912 ! positive regulation of leukocyte mediated cytotoxicity is_a: GO:0001914 ! regulation of T cell mediated cytotoxicity is_a: GO:0002711 ! positive regulation of T cell mediated immunity intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001913 ! T cell mediated cytotoxicity relationship: positively_regulates GO:0001913 ! T cell mediated cytotoxicity [Term] id: GO:0001917 name: photoreceptor inner segment namespace: cellular_component def: "The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs." [GOC:add, PMID:12019563] subset: goslim_pir is_a: GO:0097458 ! neuron part [Term] id: GO:0001918 name: farnesylated protein binding namespace: molecular_function def: "Interacting selectively and non-covalently with a farnesylated protein." [GOC:add, PMID:14555765] is_a: GO:0005515 ! protein binding [Term] id: GO:0001919 name: regulation of receptor recycling namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of receptor recycling." [GOC:add] is_a: GO:0023051 ! regulation of signaling is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001881 ! receptor recycling relationship: regulates GO:0001881 ! receptor recycling [Term] id: GO:0001920 name: negative regulation of receptor recycling namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of receptor recycling." [GOC:add] synonym: "down regulation of receptor recycling" EXACT [] synonym: "down-regulation of receptor recycling" EXACT [] synonym: "downregulation of receptor recycling" EXACT [] synonym: "inhibition of receptor recycling" NARROW [] is_a: GO:0001919 ! regulation of receptor recycling is_a: GO:0010605 ! negative regulation of macromolecule metabolic process is_a: GO:0023057 ! negative regulation of signaling is_a: GO:0031324 ! negative regulation of cellular metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001881 ! receptor recycling relationship: negatively_regulates GO:0001881 ! receptor recycling [Term] id: GO:0001921 name: positive regulation of receptor recycling namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of receptor recycling." [GOC:add] synonym: "activation of receptor recycling" NARROW [] synonym: "stimulation of receptor recycling" NARROW [] synonym: "up regulation of receptor recycling" EXACT [] synonym: "up-regulation of receptor recycling" EXACT [] synonym: "upregulation of receptor recycling" EXACT [] is_a: GO:0001919 ! regulation of receptor recycling is_a: GO:0010604 ! positive regulation of macromolecule metabolic process is_a: GO:0023056 ! positive regulation of signaling is_a: GO:0031325 ! positive regulation of cellular metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001881 ! receptor recycling relationship: positively_regulates GO:0001881 ! receptor recycling [Term] id: GO:0001922 name: B-1 B cell homeostasis namespace: biological_process def: "The process of regulating the proliferation and elimination of B cells of the B-1 subset such that the total number of B-1 B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. B-1 B cells are a distinct subset of B cells characterized as being CD5 positive, found predominantly in the peritoneum, pleural cavities, and spleen, and enriched for self-reactivity." [GOC:add, ISBN:0781735149] comment: Note that this term represents the return of B-1 B cell levels to stable numbers following an immune response, as well as the proliferation and elimination of B-1 B cells in a organism required to maintain stable numbers in the absence of an outside stimulus. synonym: "B-1 B lymphocyte homeostasis" EXACT [] synonym: "B-1 B-cell homeostasis" EXACT [] synonym: "B-1 B-lymphocyte homeostasis" EXACT [] is_a: GO:0001782 ! B cell homeostasis [Term] id: GO:0001923 name: B-1 B cell differentiation namespace: biological_process def: "The process in which a hemopoietic stem cell acquires the specialized features of a B-1 B cell. B-1 B cells are a distinct subset of B cells characterized as being CD5 positive, found predominantly in the peritoneum, pleural cavities, and spleen, and enriched for self-reactivity." [GOC:add, ISBN:0781735149] synonym: "B-1 B cell development" RELATED [GOC:add] synonym: "B-1 B lymphocyte differentiation" EXACT [] synonym: "B-1 B-cell differentiation" EXACT [] synonym: "B-1 B-lymphocyte differentiation" EXACT [] is_a: GO:0002335 ! mature B cell differentiation [Term] id: GO:0001924 name: regulation of B-1 B cell differentiation namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of B-1 B cell differentiation. B-1 B cells are a distinct subset of B cells characterized as being CD5 positive, found predominantly in the peritoneum, pleural cavities, and spleen, and enriched for self-reactivity." [GOC:add, ISBN:0781735149] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "regulation of B-1 B cell development" RELATED [GOC:add] synonym: "regulation of B-1 B lymphocyte differentiation" EXACT [] synonym: "regulation of B-1 B-cell differentiation" EXACT [] synonym: "regulation of B-1 B-lymphocyte differentiation" EXACT [] is_a: GO:0045577 ! regulation of B cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001923 ! B-1 B cell differentiation relationship: regulates GO:0001923 ! B-1 B cell differentiation [Term] id: GO:0001925 name: negative regulation of B-1 B cell differentiation namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of B-1 B cell differentiation." [GOC:add, ISBN:0781735149] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "down regulation of B-1 B cell differentiation" EXACT [] synonym: "down-regulation of B-1 B cell differentiation" EXACT [] synonym: "downregulation of B-1 B cell differentiation" EXACT [] synonym: "inhibition of B-1 B cell differentiation" NARROW [] synonym: "negative regulation of B-1 B cell development" RELATED [GOC:add] synonym: "negative regulation of B-1 B lymphocyte differentiation" EXACT [] synonym: "negative regulation of B-1 B-cell differentiation" EXACT [] synonym: "negative regulation of B-1 B-lymphocyte differentiation" EXACT [] is_a: GO:0001924 ! regulation of B-1 B cell differentiation is_a: GO:0045578 ! negative regulation of B cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001923 ! B-1 B cell differentiation relationship: negatively_regulates GO:0001923 ! B-1 B cell differentiation [Term] id: GO:0001926 name: positive regulation of B-1 B cell differentiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of B-1 B cell differentiation." [GOC:add, ISBN:0781735149] comment: Note that immunologists typically use the word 'development' to refer to cells of B or T cell lineages undergoing the process that GO describes as 'cell differentiation'. synonym: "activation of B-1 B cell differentiation" NARROW [] synonym: "positive regulation of B-1 B cell development" RELATED [GOC:add] synonym: "positive regulation of B-1 B lymphocyte differentiation" EXACT [] synonym: "positive regulation of B-1 B-cell differentiation" EXACT [] synonym: "positive regulation of B-1 B-lymphocyte differentiation" EXACT [] synonym: "stimulation of B-1 B cell differentiation" NARROW [] synonym: "up regulation of B-1 B cell differentiation" EXACT [] synonym: "up-regulation of B-1 B cell differentiation" EXACT [] synonym: "upregulation of B-1 B cell differentiation" EXACT [] is_a: GO:0001924 ! regulation of B-1 B cell differentiation is_a: GO:0045579 ! positive regulation of B cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001923 ! B-1 B cell differentiation relationship: positively_regulates GO:0001923 ! B-1 B cell differentiation [Term] id: GO:0001927 name: exocyst assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of various polypeptides into the exocyst complex." [GOC:hjd, PMID:9700152, Wikipedia:Exocyst] is_a: GO:0043623 ! cellular protein complex assembly relationship: part_of GO:0006904 ! vesicle docking involved in exocytosis [Term] id: GO:0001928 name: regulation of exocyst assembly namespace: biological_process def: "Any process that modulates the frequency, rate or extent of exocyst assembly." [GOC:hjd] comment: Note that the assembly is regulated by several small GTPases of the Rab and Rho families. is_a: GO:0017157 ! regulation of exocytosis is_a: GO:0043254 ! regulation of protein complex assembly intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001927 ! exocyst assembly relationship: regulates GO:0001927 ! exocyst assembly [Term] id: GO:0001929 name: negative regulation of exocyst assembly namespace: biological_process def: "Any process that stops, prevents, or reduces the rate or extent of exocyst assembly." [GOC:hjd] synonym: "down regulation of exocyst assembly" EXACT [] synonym: "down-regulation of exocyst assembly" EXACT [] synonym: "downregulation of exocyst assembly" EXACT [] synonym: "inhibition of exocyst assembly" NARROW [] is_a: GO:0001928 ! regulation of exocyst assembly is_a: GO:0031333 ! negative regulation of protein complex assembly is_a: GO:0045920 ! negative regulation of exocytosis intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001927 ! exocyst assembly relationship: negatively_regulates GO:0001927 ! exocyst assembly [Term] id: GO:0001930 name: positive regulation of exocyst assembly namespace: biological_process def: "Any process that increases the rate or extent of exocyst assembly." [GOC:hjd] synonym: "activation of exocyst assembly" NARROW [] synonym: "stimulation of exocyst assembly" NARROW [] synonym: "up regulation of exocyst assembly" EXACT [] synonym: "up-regulation of exocyst assembly" EXACT [] synonym: "upregulation of exocyst assembly" EXACT [] is_a: GO:0001928 ! regulation of exocyst assembly is_a: GO:0031334 ! positive regulation of protein complex assembly is_a: GO:0045921 ! positive regulation of exocytosis intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001927 ! exocyst assembly relationship: positively_regulates GO:0001927 ! exocyst assembly [Term] id: GO:0001931 name: uropod namespace: cellular_component def: "A membrane projection with related cytoskeletal components at the trailing edge of a cell in the process of migrating or being activated, found on the opposite side of the cell from the leading edge or immunological synapse, respectively." [GOC:add, ISBN:0781735149, PMID:12714569, PMID:12787750] synonym: "distal pole complex" RELATED [] synonym: "retractile pole" RELATED [] synonym: "uropodium" EXACT [] is_a: GO:0042995 ! cell projection intersection_of: GO:0042995 ! cell projection intersection_of: part_of GO:0031254 ! cell trailing edge relationship: part_of GO:0031254 ! cell trailing edge [Term] id: GO:0001932 name: regulation of protein phosphorylation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein." [GOC:hjd] subset: gosubset_prok synonym: "regulation of protein amino acid phosphorylation" EXACT [GOC:bf] is_a: GO:0031399 ! regulation of protein modification process is_a: GO:0042325 ! regulation of phosphorylation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006468 ! protein phosphorylation relationship: regulates GO:0006468 ! protein phosphorylation [Term] id: GO:0001933 name: negative regulation of protein phosphorylation namespace: biological_process def: "Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein." [GOC:hjd] subset: gosubset_prok synonym: "down regulation of protein amino acid phosphorylation" EXACT [] synonym: "down-regulation of protein amino acid phosphorylation" EXACT [] synonym: "downregulation of protein amino acid phosphorylation" EXACT [] synonym: "inhibition of protein amino acid phosphorylation" NARROW [] synonym: "negative regulation of protein amino acid phosphorylation" EXACT [GOC:bf] is_a: GO:0001932 ! regulation of protein phosphorylation is_a: GO:0031400 ! negative regulation of protein modification process is_a: GO:0042326 ! negative regulation of phosphorylation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006468 ! protein phosphorylation relationship: negatively_regulates GO:0006468 ! protein phosphorylation [Term] id: GO:0001934 name: positive regulation of protein phosphorylation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein." [GOC:hjd] subset: gosubset_prok synonym: "activation of protein amino acid phosphorylation" NARROW [] synonym: "positive regulation of protein amino acid phosphorylation" EXACT [GOC:bf] synonym: "stimulation of protein amino acid phosphorylation" NARROW [] synonym: "up regulation of protein amino acid phosphorylation" EXACT [] synonym: "up-regulation of protein amino acid phosphorylation" EXACT [] synonym: "upregulation of protein amino acid phosphorylation" EXACT [] is_a: GO:0001932 ! regulation of protein phosphorylation is_a: GO:0031401 ! positive regulation of protein modification process is_a: GO:0042327 ! positive regulation of phosphorylation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006468 ! protein phosphorylation relationship: positively_regulates GO:0006468 ! protein phosphorylation [Term] id: GO:0001935 name: endothelial cell proliferation namespace: biological_process def: "The multiplication or reproduction of endothelial cells, resulting in the expansion of a cell population. Endothelial cells are thin flattened cells which line the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium." [GOC:add, ISBN:0781735149] is_a: GO:0050673 ! epithelial cell proliferation [Term] id: GO:0001936 name: regulation of endothelial cell proliferation namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of endothelial cell proliferation." [GOC:add] is_a: GO:0050678 ! regulation of epithelial cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001935 ! endothelial cell proliferation relationship: regulates GO:0001935 ! endothelial cell proliferation [Term] id: GO:0001937 name: negative regulation of endothelial cell proliferation namespace: biological_process def: "Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation." [GOC:add] synonym: "down regulation of endothelial cell proliferation" EXACT [] synonym: "down-regulation of endothelial cell proliferation" EXACT [] synonym: "downregulation of endothelial cell proliferation" EXACT [] synonym: "inhibition of endothelial cell proliferation" NARROW [] is_a: GO:0001936 ! regulation of endothelial cell proliferation is_a: GO:0050680 ! negative regulation of epithelial cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0001935 ! endothelial cell proliferation relationship: negatively_regulates GO:0001935 ! endothelial cell proliferation [Term] id: GO:0001938 name: positive regulation of endothelial cell proliferation namespace: biological_process def: "Any process that activates or increases the rate or extent of endothelial cell proliferation." [GOC:add] synonym: "activation of endothelial cell proliferation" NARROW [] synonym: "stimulation of endothelial cell proliferation" NARROW [] synonym: "up regulation of endothelial cell proliferation" EXACT [] synonym: "up-regulation of endothelial cell proliferation" EXACT [] synonym: "upregulation of endothelial cell proliferation" EXACT [] is_a: GO:0001936 ! regulation of endothelial cell proliferation is_a: GO:0050679 ! positive regulation of epithelial cell proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0001935 ! endothelial cell proliferation relationship: positively_regulates GO:0001935 ! endothelial cell proliferation [Term] id: GO:0001939 name: female pronucleus namespace: cellular_component def: "The pronucleus originating from the ovum that is being fertilized." [GOC:hjd, ISBN:0198506732] is_a: GO:0045120 ! pronucleus [Term] id: GO:0001940 name: male pronucleus namespace: cellular_component def: "The pronucleus originating from the spermatozoa that was involved in fertilization." [GOC:hjd, ISBN:0198506732] is_a: GO:0045120 ! pronucleus [Term] id: GO:0001941 name: postsynaptic membrane organization namespace: biological_process def: "A process which results in the assembly, arrangement of constituent parts, or disassembly of a postsynaptic membrane, the specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft)." [GOC:dph, GOC:pr] synonym: "post-synaptic membrane organization" EXACT [] synonym: "postsynaptic membrane organisation" EXACT [GOC:curators] is_a: GO:0044802 ! single-organism membrane organization relationship: part_of GO:0050808 ! synapse organization [Term] id: GO:0001942 name: hair follicle development namespace: biological_process alt_id: GO:0001943 def: "The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open." [GOC:dph, UBERON:0002073] is_a: GO:0022405 ! hair cycle process is_a: GO:0044767 ! single-organism developmental process is_a: GO:0048856 ! anatomical structure development relationship: part_of GO:0098773 ! skin epidermis development [Term] id: GO:0001944 name: vasculature development namespace: biological_process def: "The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism." [GOC:dph, UBERON:0002409] synonym: "vascular system development" RELATED [GOC:curators] is_a: GO:0048731 ! system development relationship: part_of GO:0072358 ! cardiovascular system development [Term] id: GO:0001945 name: lymph vessel development namespace: biological_process def: "The process whose specific outcome is the progression of a lymph vessel over time, from its formation to the mature structure." [GOC:dph, UBERON:0001473] is_a: GO:0044767 ! single-organism developmental process is_a: GO:0048856 ! anatomical structure development relationship: part_of GO:0001944 ! vasculature development [Term] id: GO:0001946 name: lymphangiogenesis namespace: biological_process def: "Lymph vessel formation when new vessels emerge from the proliferation of pre-existing vessels." [GOC:dph, PMID:11596157] synonym: "lymph vessel formation" EXACT systematic_synonym [] xref: Wikipedia:Lymphangiogenesis is_a: GO:0009653 ! anatomical structure morphogenesis is_a: GO:0044767 ! single-organism developmental process is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis relationship: part_of GO:0036303 ! lymph vessel morphogenesis [Term] id: GO:0001947 name: heart looping namespace: biological_process def: "The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation." [GOC:dph, PMID:12094232] synonym: "cardiac looping" EXACT [] is_a: GO:0003143 ! embryonic heart tube morphogenesis relationship: part_of GO:0061371 ! determination of heart left/right asymmetry [Term] id: GO:0001948 name: glycoprotein binding namespace: molecular_function def: "Interacting selectively and non-covalently with a glycoprotein, a protein that contains covalently bound glycose (monosaccharide) residues. These also include proteoglycans." [GOC:hjd, ISBN:0198506732] is_a: GO:0097367 ! carbohydrate derivative binding [Term] id: GO:0001949 name: sebaceous gland cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized epidermal cell acquires the specialized features of a sebaceous gland cell." [GOC:mgi_curators, PMID:15737203] synonym: "sebocytes differentiation" NARROW [GOC:mgi_curators] is_a: GO:0009913 ! epidermal cell differentiation relationship: part_of GO:0048733 ! sebaceous gland development [Term] id: GO:0001950 name: obsolete plasma membrane enriched fraction namespace: cellular_component def: "OBSOLETE: The fraction of cells, prepared by disruptive biochemical methods, that is enriched for plasma membranes." [GOC:mgi_curators, PMID:11562363, PMID:15601832] comment: This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component. synonym: "plasma membrane enriched fraction" EXACT [] synonym: "PME fraction" RELATED [GOC:mah] is_obsolete: true consider: GO:0005886 [Term] id: GO:0001951 name: intestinal D-glucose absorption namespace: biological_process def: "Uptake of D-glucose into the blood by absorption from the small intestine." [GOC:mgi_curators, PMID:5601832] is_a: GO:0015758 ! glucose transport is_a: GO:0044707 ! single-multicellular organism process is_a: GO:0050892 ! intestinal absorption [Term] id: GO:0001952 name: regulation of cell-matrix adhesion namespace: biological_process def: "Any process that modulates the frequency, rate or extent of attachment of a cell to the extracellular matrix." [GOC:hjd] is_a: GO:0010810 ! regulation of cell-substrate adhesion intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0007160 ! cell-matrix adhesion relationship: regulates GO:0007160 ! cell-matrix adhesion [Term] id: GO:0001953 name: negative regulation of cell-matrix adhesion namespace: biological_process def: "Any process that stops, prevents, or reduces the rate or extent of cell adhesion to the extracellular matrix." [GOC:hjd] synonym: "down regulation of cell-matrix adhesion" EXACT [] synonym: "down-regulation of cell-matrix adhesion" EXACT [] synonym: "downregulation of cell-matrix adhesion" EXACT [] synonym: "inhibition of cell-matrix adhesion" NARROW [] is_a: GO:0001952 ! regulation of cell-matrix adhesion is_a: GO:0010812 ! negative regulation of cell-substrate adhesion intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0007160 ! cell-matrix adhesion relationship: negatively_regulates GO:0007160 ! cell-matrix adhesion [Term] id: GO:0001954 name: positive regulation of cell-matrix adhesion namespace: biological_process def: "Any process that activates or increases the rate or extent of cell adhesion to an extracellular matrix." [GOC:hjd] synonym: "activation of cell-matrix adhesion" NARROW [] synonym: "stimulation of cell-matrix adhesion" NARROW [] synonym: "up regulation of cell-matrix adhesion" EXACT [] synonym: "up-regulation of cell-matrix adhesion" EXACT [] synonym: "upregulation of cell-matrix adhesion" EXACT [] is_a: GO:0001952 ! regulation of cell-matrix adhesion is_a: GO:0010811 ! positive regulation of cell-substrate adhesion intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007160 ! cell-matrix adhesion relationship: positively_regulates GO:0007160 ! cell-matrix adhesion [Term] id: GO:0001955 name: blood vessel maturation namespace: biological_process def: "A developmental process, independent of morphogenetic (shape) change, that is required for a blood vessel to attain its fully functional state." [GOC:dph] is_a: GO:0071695 ! anatomical structure maturation relationship: part_of GO:0001568 ! blood vessel development [Term] id: GO:0001956 name: positive regulation of neurotransmitter secretion namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the regulated release of a neurotransmitter." [GOC:hjd] synonym: "activation of neurotransmitter secretion" NARROW [] synonym: "stimulation of neurotransmitter secretion" NARROW [] synonym: "up regulation of neurotransmitter secretion" EXACT [] synonym: "up-regulation of neurotransmitter secretion" EXACT [] synonym: "upregulation of neurotransmitter secretion" EXACT [] is_a: GO:0046928 ! regulation of neurotransmitter secretion is_a: GO:0050806 ! positive regulation of synaptic transmission is_a: GO:0051590 ! positive regulation of neurotransmitter transport is_a: GO:1903532 ! positive regulation of secretion by cell intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0007269 ! neurotransmitter secretion relationship: positively_regulates GO:0007269 ! neurotransmitter secretion [Term] id: GO:0001957 name: intramembranous ossification namespace: biological_process def: "Direct ossification that occurs within mesenchyme or an accumulation of relatively unspecialized cells." [ISBN:0878932437] comment: An instance of intramembranous ossification may also be classified as metaplastic; the former classifies based on tissue type location, and the latter based on mechanism/cell division. synonym: "dermal ossification" NARROW [GO_REF:0000034] synonym: "intramembranous bone ossification" RELATED [GOC:cjm] xref: Wikipedia:Intramembranous_ossification is_a: GO:0036072 ! direct ossification [Term] id: GO:0001958 name: endochondral ossification namespace: biological_process def: "Replacement ossification wherein bone tissue replaces cartilage." [GO_REF:0000034, ISBN:0878932437] xref: Wikipedia:Endochondral_ossification is_a: GO:0036075 ! replacement ossification relationship: part_of GO:0060350 ! endochondral bone morphogenesis [Term] id: GO:0001959 name: regulation of cytokine-mediated signaling pathway namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the cytokine mediated signaling pathway." [GOC:hjd] synonym: "regulation of cytokine and chemokine mediated signaling pathway" EXACT [] synonym: "regulation of cytokine mediated signaling pathway" EXACT [GOC:dph, GOC:tb] synonym: "regulation of cytokine mediated signalling pathway" EXACT [] is_a: GO:0009966 ! regulation of signal transduction is_a: GO:0060759 ! regulation of response to cytokine stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0019221 ! cytokine-mediated signaling pathway relationship: regulates GO:0019221 ! cytokine-mediated signaling pathway [Term] id: GO:0001960 name: negative regulation of cytokine-mediated signaling pathway namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the cytokine mediated signaling pathway." [GOC:hjd] synonym: "down regulation of cytokine mediated signaling pathway" EXACT [] synonym: "down-regulation of cytokine mediated signaling pathway" EXACT [] synonym: "downregulation of cytokine mediated signaling pathway" EXACT [] synonym: "inhibition of cytokine mediated signaling pathway" NARROW [] synonym: "negative regulation of cytokine and chemokine mediated signaling pathway" EXACT [] synonym: "negative regulation of cytokine mediated signaling pathway" EXACT [GOC:dph, GOC:tb] synonym: "negative regulation of cytokine mediated signalling pathway" EXACT [] is_a: GO:0001959 ! regulation of cytokine-mediated signaling pathway is_a: GO:0009968 ! negative regulation of signal transduction is_a: GO:0060761 ! negative regulation of response to cytokine stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0019221 ! cytokine-mediated signaling pathway relationship: negatively_regulates GO:0019221 ! cytokine-mediated signaling pathway [Term] id: GO:0001961 name: positive regulation of cytokine-mediated signaling pathway namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of a cytokine mediated signaling pathway." [GOC:hjd] synonym: "activation of cytokine mediated signaling pathway" NARROW [] synonym: "positive regulation of cytokine and chemokine mediated signaling pathway" EXACT [] synonym: "positive regulation of cytokine mediated signaling pathway" EXACT [GOC:dph, GOC:tb] synonym: "positive regulation of cytokine mediated signalling pathway" EXACT [] synonym: "stimulation of cytokine mediated signaling pathway" NARROW [] synonym: "up regulation of cytokine mediated signaling pathway" EXACT [] synonym: "up-regulation of cytokine mediated signaling pathway" EXACT [] synonym: "upregulation of cytokine mediated signaling pathway" EXACT [] is_a: GO:0001959 ! regulation of cytokine-mediated signaling pathway is_a: GO:0009967 ! positive regulation of signal transduction is_a: GO:0060760 ! positive regulation of response to cytokine stimulus intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0019221 ! cytokine-mediated signaling pathway relationship: positively_regulates GO:0019221 ! cytokine-mediated signaling pathway [Term] id: GO:0001962 name: alpha-1,3-galactosyltransferase activity namespace: molecular_function def: "Catalysis of the transfer of a galactose residue from a donor molecule, such as GDP-galactose or UDP-galactose, to an oligosaccharide, forming an alpha-(1->3) linkage." [GOC:hjd, PMID:10854427] synonym: "isoglobotriaosylceramide synthase" NARROW [] xref: EC:2.4.1.- is_a: GO:0008378 ! galactosyltransferase activity [Term] id: GO:0001963 name: synaptic transmission, dopaminergic namespace: biological_process def: "The process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine." [GOC:dph] is_a: GO:0007270 ! neuron-neuron synaptic transmission [Term] id: GO:0001964 name: startle response namespace: biological_process def: "An action or movement due to the application of a sudden unexpected stimulus." [GOC:dph] xref: Wikipedia:Startle_reaction is_a: GO:0009605 ! response to external stimulus is_a: GO:0050905 ! neuromuscular process [Term] id: GO:0001965 name: G-protein alpha-subunit binding namespace: molecular_function def: "Interacting selectively and non-covalently with a G-protein alpha subunit. The alpha subunit binds a guanine nucleotide." [GOC:hjd] synonym: "G-alpha protein subunit binding" EXACT [] is_a: GO:0005515 ! protein binding [Term] id: GO:0001966 name: thigmotaxis namespace: biological_process def: "The directed movement of a motile cell or organism in response to touch." [GOC:dph] synonym: "stereotaxis" EXACT [] synonym: "taxis in response to mechanical stimulus" BROAD [] synonym: "taxis in response to touch stimulus" EXACT [] is_a: GO:0042330 ! taxis [Term] id: GO:0001967 name: suckling behavior namespace: biological_process def: "Specific behavior of a newborn or infant mammal that results in the derivation of nourishment from the breast." [GOC:dph, GOC:pr] synonym: "nursing behavior" EXACT [] is_a: GO:0007631 ! feeding behavior is_a: GO:0051705 ! multi-organism behavior [Term] id: GO:0001968 name: fibronectin binding namespace: molecular_function def: "Interacting selectively and non-covalently with a fibronectin, a group of related adhesive glycoproteins of high molecular weight found on the surface of animal cells, connective tissue matrices, and in extracellular fluids." [GOC:hjd] subset: goslim_chembl is_a: GO:0005515 ! protein binding [Term] id: GO:0001969 name: regulation of act