LiteFold/GO · Datasets at Hugging Face

GO:0000253

253

3-beta-hydroxysteroid 3-dehydrogenase (NADP+) activity

molecular_function

Catalysis of the reaction: a 3-betahydroxyl sterol + NADP+ = a 3-oxosterol sterol + NADPH + H+.

[ "EC:1.1.1.270", "GOC:mah", "PMID:9811880" ]

null

[ "3-keto sterol reductase activity", "3-keto-steroid reductase activity", "3-KSR activity", "3beta-hydroxy-steroid:NADP+ 3-oxidoreductase" ]

[ "EXACT", "EXACT", "RELATED", "RELATED" ]

[ "GO:0050576" ]

[]

[ "EC:1.1.1.270", "MetaCyc:RXN-13686", "Reactome:R-HSA-194632 \"Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol)\"", "Reactome:R-HSA-194689 \"4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol\"", "Reactome:R-HSA-9945784 ...

[ "GO:0033764" ]

[]

[ "GO:0033764" ]

[]

[ "skos:exactMatch EC:1.1.1.270", "skos:exactMatch RHEA:34787", "skos:narrowMatch RHEA:18409", "skos:narrowMatch RHEA:33459", "skos:narrowMatch RHEA:36379", "skos:narrowMatch RHEA:46216", "skos:narrowMatch RHEA:46832", "skos:narrowMatch RHEA:46852", "skos:narrowMatch RHEA:56880", "skos:narrowMatch R...

null

false

true

5

GO:0000254

254

C-4 methylsterol oxidase activity

molecular_function

Catalysis of the reaction: 4,4-dimethyl-5alpha-cholest-7-en-3beta-ol + 6 Fe(II)-[cytochrome b5] + 5 H+ + 3 O2 = 4alpha-carboxy-4beta-methyl-5alpha-cholest-7-ene-3beta-ol + 6 Fe(III)-[cytochrome b5] + 4 H2O.

[ "PMID:9811880", "RHEA:55220" ]

null

[ "4-methylsterol oxidase activity", "methylsterol hydroxylase activity", "methylsterol monooxygenase activity" ]

[ "EXACT", "RELATED", "RELATED" ]

[]

[ "EC:1.14.18.9", "MetaCyc:RXN-13188", "Reactome:R-HSA-194641 \"4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol\"", "Reactome:R-HSA-194669 \"4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol\"", "Reactome:R-...

[ "GO:0016716" ]

[]

[ "GO:0016716" ]

[]

[ "skos:exactMatch EC:1.14.18.9", "skos:exactMatch RHEA:55220", "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/23278\" xsd:anyURI", "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/25815\" xsd:anyURI", "term_tracker_item \"https://github.com/geneontology/go-onto...

null

false

true

4

GO:0000255

255

allantoin metabolic process

biological_process

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" ]

null

[ "allantoin metabolism" ]

[ "EXACT" ]

[]

[ "GO:0008152" ]

[]

[ "GO:0008152" ]

[]

null

false

true

7

GO:0000256

256

allantoin catabolic process

biological_process

The chemical reactions and pathways resulting in the breakdown of allantoin, (2,5-dioxo-4-imidazolidinyl)urea.

[ "GOC:mah", "ISBN:0198547684" ]

null

[ "allantoin breakdown", "allantoin catabolism", "allantoin degradation" ]

[ "EXACT", "EXACT", "EXACT" ]

[]

[ "GO:0000255", "GO:0009056" ]

[]

[ "GO:0000255", "GO:0009056" ]

[]

null

false

true

4

GO:0000257

257

nitrilase activity

molecular_function

Catalysis of the reaction: a nitrile + H2O = a carboxylate + NH4+. Acts on a wide range of aromatic nitriles including (indole-3-yl)-acetonitrile and some aliphatic nitriles, and on the corresponding acid amides.

[ "RHEA:21724" ]

null

[ "acetonitrilase activity", "benzonitrilase activity", "nitrile aminohydrolase activity" ]

[ "RELATED", "RELATED", "RELATED" ]

[]

[ "EC:3.5.5.1", "KEGG_REACTION:R00540", "MetaCyc:3.5.5.1-RXN", "RHEA:21724", "RHEA:40775", "RHEA:45784", "UM-BBD_reactionID:r0377", "UM-BBD_reactionID:r0701" ]

[ "GO:0016815" ]

[]

[ "GO:0016815" ]

[]

[ "skos:exactMatch EC:3.5.5.1", "skos:exactMatch RHEA:21724", "skos:narrowMatch RHEA:40775", "skos:narrowMatch RHEA:45784" ]

null

false

true

1

GO:0000258

258

obsolete isoleucine/valine:sodium symporter activity

molecular_function

OBSOLETE. Catalysis of the reaction: (isoleucine or valine)(out) + Na+(out) = (isoleucine or valine)(in) + Na+(in).

[ "TC:2.A.26.1.1" ]

This term was made obsolete because it represents a multifunctional gene product.

[ "isoleucine/valine:sodium symporter activity" ]

[ "EXACT" ]

[]

[ "GO:0005283", "GO:0005304", "GO:0015188" ]

[]

null

true

4

GO:0000259

259

obsolete intracellular nucleoside transmembrane transporter activity

molecular_function

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" ]

This term was made obsolete because it contains component and function information.

[ "intracellular nucleoside transmembrane transporter activity" ]

[ "EXACT" ]

[]

[ "GO:0005337", "GO:0005622" ]

[]

null

true

1

GO:0000260

260

obsolete hydrogen-translocating V-type ATPase activity

molecular_function

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" ]

This term was made obsolete because it represents a gene product.

[ "hydrogen-translocating V-type ATPase activity" ]

[ "EXACT" ]

[]

[ "GO:0046961" ]

[]

null

true

7

GO:0000261

261

obsolete sodium-translocating V-type ATPase activity

molecular_function

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" ]

This term was made obsolete because it represents a gene product.

[ "sodium-translocating V-type ATPase activity" ]

[ "EXACT" ]

[]

[ "GO:0046962" ]

[]

null

true

8

GO:0000262

262

mitochondrial chromosome

cellular_component

A chromosome found in the mitochondrion of a eukaryotic cell.

[ "GOC:mah" ]

null

[ "mitochondrial DNA", "mitochondrial genome", "mtDNA" ]

[ "NARROW", "RELATED", "NARROW" ]

[]

[ "NIF_Subcellular:sao1186327184" ]

[ "GO:0005694" ]

[ "part_of GO:0042645" ]

[ "part_of" ]

[ "GO:0042645" ]

[ "GO:0005694", "GO:0042645" ]

[ "GO:0005694", "part_of GO:0005739" ]

[]

null

false

true

6

GO:0000263

263

obsolete heterotrimeric G-protein GTPase, alpha-subunit

molecular_function

OBSOLETE. Subunit of a heterotrimeric G-protein GTPase that contains the guanine nucleotide binding site and possesses GTPase activity.

[ "GOC:mah", "ISBN:0198547684" ]

This term was made obsolete because it does not represent a molecular function.

[ "heterotrimeric G-protein GTPase, alpha-subunit" ]

[ "EXACT" ]

[]

[ "GO:0003924", "GO:0005834" ]

[]

null

true

6

GO:0000264

264

obsolete heterotrimeric G-protein GTPase, beta-subunit

molecular_function

OBSOLETE. Subunit of a heterotrimeric G-protein GTPase; associates tightly with the gamma subunit.

[ "GOC:mah", "ISBN:0198547684" ]

This term was made obsolete because it does not represent a molecular function.

[ "heterotrimeric G-protein GTPase, beta-subunit" ]

[ "EXACT" ]

[]

[ "GO:0003924", "GO:0005834" ]

[]

null

true

8

GO:0000265

265

obsolete heterotrimeric G-protein GTPase, gamma-subunit

molecular_function

OBSOLETE. Smallest subunit of a heterotrimeric G-protein GTPase; associates tightly with the beta subunit.

[ "GOC:mah", "ISBN:0198547684" ]

This term was made obsolete because it does not represent a molecular function.

[ "heterotrimeric G-protein GTPase, gamma-subunit" ]

[ "EXACT" ]

[]

[ "GO:0003924", "GO:0005834" ]

[]

null

true

3

GO:0000266

266

mitochondrial fission

biological_process

The division of a mitochondrion within a cell to form two or more separate mitochondrial compartments.

[ "PMID:11038192" ]

null

[ "mitochondrial division", "mitochondrial proliferation" ]

[ "EXACT", "RELATED" ]

[]

[ "GO:0007005", "GO:0048285" ]

[]

[ "GO:0007005", "GO:0048285" ]

[]

null

false

true

8

GO:0000267

267

obsolete cell fraction

cellular_component

OBSOLETE. A generic term for parts of cells prepared by disruptive biochemical techniques.

[ "GOC:ma" ]

This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component.

[ "cell fraction" ]

[ "EXACT" ]

[]

[ "GO:0005575" ]

[]

null

true

5

GO:0000268

268

peroxisome targeting sequence binding

molecular_function

Binding to a peroxisomal targeting sequence, a sequence of amino acids within a protein that acts as a signal for the localization of a protein into the peroxisome.

[ "GOC:mah", "ISBN:0879693568" ]

null

[ "peroxisome targeting signal receptor", "PTS binding", "PTS receptor" ]

[ "NARROW", "EXACT", "NARROW" ]

[ "GO:0005051" ]

[]

[ "GO:0005048" ]

[]

[ "GO:0005048" ]

[]

null

false

true

1

GO:0000269

269

toxin export channel activity

molecular_function

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 pos...

[ "GOC:mtg_transport" ]

null

[]

[ "GO:0015288", "GO:0019534" ]

[]

[ "GO:0015288", "GO:0019534" ]

[]

null

false

true

7

GO:0000270

270

peptidoglycan metabolic process

biological_process

The chemical reactions and pathways involving peptidoglycans, any of a class of glycoconjugates found only in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.

[ "PMID:33139480" ]

null

[ "murein metabolic process", "murein metabolism", "peptidoglycan metabolism" ]

[ "EXACT", "EXACT", "EXACT" ]

[ "GO:0009284" ]

[]

[ "GO:0030203" ]

[]

[ "GO:0030203" ]

[]

[ "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/29745\" xsd:anyURI" ]

null

false

true

7

GO:0000271

271

polysaccharide biosynthetic process

biological_process

The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

[ "GOC:curators" ]

null

[ "glycan biosynthesis", "glycan biosynthetic process", "polysaccharide anabolism", "polysaccharide biosynthesis", "polysaccharide formation", "polysaccharide synthesis" ]

[ "EXACT", "EXACT", "EXACT", "EXACT", "EXACT", "EXACT" ]

[]

[ "GO:0005976", "GO:0009059", "GO:0016051" ]

[]

[ "GO:0005976", "GO:0009059", "GO:0016051" ]

[]

null

false

true

6

GO:0000272

272

polysaccharide catabolic process

biological_process

The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.

[ "PMID:33139480" ]

null

[ "multicellular organismal polysaccharide catabolic process", "polysaccharide breakdown", "polysaccharide catabolism", "polysaccharide degradation" ]

[ "NARROW", "EXACT", "EXACT", "EXACT" ]

[ "GO:0044244" ]

[]

[ "GO:0005976", "GO:0009057", "GO:0016052" ]

[]

[ "GO:0005976", "GO:0009057", "GO:0016052" ]

[]

null

false

true

8

GO:0000274

274

obsolete mitochondrial proton-transporting ATP synthase, stator stalk

cellular_component

OBSOLETE. 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" ]

The reason for obsoletion is that this term unnecssarily specified a cellular compartment.

[ "mitochondrial proton-transporting ATP synthase, peripheral stalk" ]

[ "EXACT" ]

[]

[ "GO:0045259" ]

[]

[ "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/27253\" xsd:anyURI" ]

null

true

7

GO:0000275

275

obsolete mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1)

cellular_component

OBSOLETE. 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" ]

See also the cellular component term 'mitochondrial inner membrane ; GO:0005743'.\nThe reason for obsoletion is that this term unnecssarily specified a cellular compartment

[ "hydrogen-transporting ATP synthase, F1 sector", "proton-transporting ATP synthase complex, catalytic core F(1)" ]

[ "BROAD", "BROAD" ]

[]

[ "GO:0045259" ]

[]

[ "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/27253\" xsd:anyURI" ]

null

true

3

GO:0000276

276

obsolete mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)

cellular_component

OBSOLETE. All non-F1 subunits of the mitochondrial hydrogen-transporting ATP synthase, including integral and peripheral mitochondrial inner membrane proteins.

[ "GOC:mtg_sensu", "PMID:10838056" ]

The reason for obsoletion is that this term unnecssarily specified a cellular compartment.

[]

[ "GO:0045259" ]

[]

[ "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/27253\" xsd:anyURI" ]

null

true

5

GO:0000277

277

[cytochrome c]-lysine N-methyltransferase activity

molecular_function

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" ]

null

[ "cytochrome c (lysine) methyltransferase activity", "cytochrome c methyltransferase activity", "cytochrome c-lysine N-methyltransferase activity", "cytochrome c-specific protein methylase III activity", "cytochrome c-specific protein-lysine methyltransferase activity", "S-adenosyl-L-methionine:cytochrome ...

[ "RELATED", "RELATED", "RELATED", "RELATED", "RELATED", "RELATED", "RELATED" ]

[]

[ "EC:2.1.1.59", "MetaCyc:2.1.1.59-RXN", "RHEA:24312" ]

[ "GO:0016279" ]

[]

[ "GO:0016279" ]

[]

[ "skos:exactMatch EC:2.1.1.59", "skos:exactMatch RHEA:24312", "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/30193\" xsd:anyURI" ]

null

false

true

3

GO:0000279

279

M phase

biological_process

A cell cycle phase during which nuclear division occurs, and which is comprises the phases: prophase, metaphase, anaphase and telophase.

[ "GOC:mtg_cell_cycle" ]

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 phas...

[ "M-phase" ]

[ "EXACT" ]

[]

[ "gocheck_do_not_annotate" ]

[ "Wikipedia:M_phase" ]

[ "GO:0022403" ]

[]

[ "GO:0022403" ]

[]

null

false

true

1

GO:0000280

280

nuclear division

biological_process

The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei.

[ "GOC:mah" ]

null

[ "karyokinesis" ]

[ "RELATED" ]

[]

[ "goslim_pir" ]

[]

[ "GO:0048285" ]

[]

[ "GO:0048285" ]

[]

null

false

true

9

GO:0000281

281

mitotic cytokinesis

biological_process

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" ]

null

[ "cytokinesis after mitosis" ]

[ "EXACT" ]

[]

[ "goslim_pombe" ]

[ "Reactome:R-HSA-68884 \"Mitotic Telophase/Cytokinesis\"" ]

[ "GO:0061640", "GO:1903047" ]

[]

[ "GO:0061640", "GO:1903047" ]

[ "GO:0061640", "part_of GO:0000278" ]

[]

null

false

true

4

GO:0000282

282

cellular bud site selection

biological_process

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" ]

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).

[ "bud site selection/establishment of cell polarity" ]

[ "BROAD" ]

[]

[ "GO:0030010", "GO:1903047" ]

[ "part_of GO:0000281" ]

[ "part_of" ]

[ "GO:0000281" ]

[ "GO:0000281", "GO:0030010", "GO:1903047" ]

[]

null

false

true

8

GO:0000284

284

obsolete shmoo orientation

biological_process

OBSOLETE. (Was not defined before being made obsolete).

[ "GOC:elh" ]

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.

[ "shmoo orientation" ]

[ "EXACT" ]

[]

[ "GO:0000753" ]

[]

null

true

5

GO:0000285

285

1-phosphatidylinositol-3-phosphate 5-kinase activity

molecular_function

Catalysis of the reaction: a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate + ADP + H+.

[ "EC:2.7.1.150", "RHEA:13609" ]

null

[ "ATP:1-phosphatidyl-1D-myo-inositol-3-phosphate 5-phosphotransferase activity", "phosphatidylinositol 3-phosphate 5-kinase activity", "phosphatidylinositol-3-phosphate 5-kinase activity", "type III PIP kinase activity" ]

[ "RELATED", "RELATED", "EXACT", "RELATED" ]

[]

[ "EC:2.7.1.150", "KEGG_REACTION:R05802", "MetaCyc:2.7.1.150-RXN", "Reactome:R-HSA-1675910 \"PI3P is phosphorylated to PI(3,5)P2 by PIKFYVE at the late endosome membrane\"", "Reactome:R-HSA-1675921 \"PI3P is phosphorylated to PI(3,5)P2 by PIKFYVE at the Golgi membrane\"", "Reactome:R-HSA-1676134 \"PI3P is p...

[ "GO:0052742" ]

[]

[ "GO:0052742" ]

[]

[ "skos:exactMatch EC:2.7.1.150", "skos:exactMatch RHEA:13609", "skos:narrowMatch RHEA:42348", "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/28336\" xsd:anyURI", "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/30193\" xsd:anyURI" ]

null

false

true

9

GO:0000286

286

L-alanine dehydrogenase (NAD+) activity

molecular_function

Catalysis of the reaction: L-alanine + NAD+ + H2O = pyruvate + NH4+ + NADH + H+.

[ "RHEA:18405" ]

null

[ "AlaDH", "alanine dehydrogenase activity", "alanine oxidoreductase activity", "alpha-alanine dehydrogenase activity", "L-alanine dehydrogenase activity", "L-alanine:NAD+ oxidoreductase (deaminating)", "NAD-dependent alanine dehydrogenase activity", "NAD-linked alanine dehydrogenase activity", "NADH-...

[ "RELATED", "BROAD", "RELATED", "RELATED", "RELATED", "RELATED", "RELATED", "RELATED", "RELATED" ]

[]

[ "EC:1.4.1.1", "MetaCyc:ALANINE-DEHYDROGENASE-RXN", "RHEA:18405" ]

[ "GO:0050018" ]

[]

[ "GO:0050018" ]

[]

[ "skos:exactMatch EC:1.4.1.1", "skos:exactMatch RHEA:18405", "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/30193\" xsd:anyURI", "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/30646\" xsd:anyURI" ]

null

false

true

9

GO:0000287

287

magnesium ion binding

molecular_function

Binding to a magnesium (Mg) ion.

[ "GOC:ai" ]

null

[ "magnesium binding", "Mg binding" ]

[ "EXACT", "EXACT" ]

[]

[ "GO:0046872" ]

[]

[ "GO:0046872" ]

[]

null

false

true

8

GO:0000288

288

nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay

biological_process

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" ]

null

[ "deadenylation-dependent mRNA decay", "mRNA breakdown, deadenylation-dependent decay", "mRNA catabolic process, deadenylation-dependent", "mRNA catabolic process, deadenylylation-dependent", "mRNA catabolism, deadenylation-dependent", "mRNA catabolism, deadenylylation-dependent", "mRNA degradation, dead...

[ "EXACT", "EXACT", "EXACT", "EXACT", "EXACT", "EXACT", "EXACT", "EXACT" ]

[]

[ "Reactome:R-HSA-429914 \"Deadenylation-dependent mRNA decay\"" ]

[ "GO:0000956", "GO:0061157" ]

[]

[ "GO:0000956", "GO:0061157" ]

[]

[ "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/20568\" xsd:anyURI" ]

null

false

true

3

GO:0000289

289

nuclear-transcribed mRNA poly(A) tail shortening

biological_process

Shortening of the poly(A) tail of a nuclear-transcribed mRNA from full length to an oligo(A) length.

[ "GOC:krc" ]

null

[ "3' to 5' mRNA deadenylation", "mRNA deadenylation", "nuclear mRNA poly(A) tail shortening" ]

[ "RELATED", "RELATED", "RELATED" ]

[]

[ "Reactome:R-HSA-429947 \"Deadenylation of mRNA\"" ]

[ "GO:0000956" ]

[ "part_of GO:0000288" ]

[ "part_of" ]

[ "GO:0000288" ]

[ "GO:0000288", "GO:0000956" ]

[]

null

false

true

1

GO:0000290

290

deadenylation-dependent decapping of nuclear-transcribed mRNA

biological_process

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" ]

null

[ "deadenylation-dependent decapping of nuclear mRNA", "deadenylylation-dependent decapping" ]

[ "EXACT", "EXACT" ]

[]

[ "GO:0000956", "GO:0110156" ]

[ "part_of GO:0000288" ]

[ "part_of" ]

[ "GO:0000288" ]

[ "GO:0000288", "GO:0000956", "GO:0110156" ]

[]

null

false

true

5

GO:0000291

291

obsolete nuclear-transcribed mRNA catabolic process, exonucleolytic

biological_process

OBSOLETE. 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" ]

The reason for obsoletion is that this represents an unnecessary grouping term

[ "exonucleolytic degradation of mRNA", "mRNA breakdown, exonucleolytic", "mRNA degradation, exonucleolytic", "nuclear mRNA catabolic process, exonucleolytic" ]

[ "EXACT", "EXACT", "EXACT", "EXACT" ]

[]

[ "GO:0000956" ]

[]

[ "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/27169\" xsd:anyURI" ]

null

true

5

GO:0000292

292

RNA fragment catabolic process

biological_process

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" ]

null

[ "group I intron catabolic process", "RNA fragment breakdown", "RNA fragment catabolism", "RNA fragment degradation" ]

[ "NARROW", "EXACT", "EXACT", "EXACT" ]

[ "GO:0030452" ]

[]

[ "GO:0006401" ]

[]

[ "GO:0006401" ]

[]

null

false

true

2

GO:0000293

293

ferric-chelate reductase activity

molecular_function

Catalysis of the reaction: 2 Fe3+-siderophore + electron donor = 2 Fe2+-siderophore + electron acceptor.

[ "PMID:33559753" ]

null

[ "ferric chelate reductase activity", "iron chelate reductase activity" ]

[ "EXACT", "EXACT" ]

[]

[ "GO:0016722" ]

[]

[ "GO:0016722" ]

[]

[ "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/21029\" xsd:anyURI", "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/26726\" xsd:anyURI", "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/30815\" xsd:anyURI" ]

null

false

true

5

GO:0000294

294

nuclear-transcribed mRNA catabolic process, RNase MRP-dependent

biological_process

A minor MRP-dependent nuclear-transcribed mRNA degradation pathway that begins with an endonucleolytic cleavage to generate unprotected ends.

[ "PMID:14729943" ]

null

[ "nuclear mRNA catabolic process, endonucleolytic cleavage-dependent decay", "nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay" ]

[ "EXACT", "RELATED" ]

[]

[ "GO:0000956" ]

[]

[ "GO:0000956" ]

[]

[ "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/24917\" xsd:anyURI" ]

null

false

true

4

GO:0000295

295

adenine nucleotide transmembrane transporter activity

molecular_function

Enables the transfer of adenine nucleotides (AMP, ADP, and ATP) from one side of a membrane to the other.

[ "PMID:11566870" ]

null

[]

[ "Reactome:R-HSA-389652 \"PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP\"" ]

[ "GO:0015216" ]

[ "part_of GO:0051503" ]

[ "part_of" ]

[ "GO:0051503" ]

[ "GO:0015216", "GO:0051503" ]

[]

null

false

true

2

GO:0000296

296

spermine transport

biological_process

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" ]

null

[]

[ "GO:0015846" ]

[]

[ "GO:0015846" ]

[]

null

false

true

1

GO:0000297

297

spermine transmembrane transporter activity

molecular_function

Enables the transfer of spermine from one side of a 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" ]

null

[]

[ "GO:0015203" ]

[ "part_of GO:1903710" ]

[ "part_of" ]

[ "GO:1903710" ]

[ "GO:0015203", "GO:1903710" ]

[]

null

false

true

2

GO:0000298

298

endopolyphosphatase activity

molecular_function

Catalysis of the reaction: polyphosphate + n H2O = (n+1) oligophosphate. The product contains 4 or 5 phosphate residues.

[ "EC:3.6.1.10" ]

null

[ "metaphosphatase activity", "polymetaphosphatase activity", "polyphosphatase activity", "polyphosphate depolymerase activity", "polyphosphate polyphosphohydrolase activity" ]

[ "BROAD", "RELATED", "BROAD", "BROAD", "RELATED" ]

[]

[ "EC:3.6.1.10", "MetaCyc:ENDOPOLYPHOSPHATASE-RXN", "RHEA:22452" ]

[ "GO:0016462" ]

[]

[ "GO:0016462" ]

[]

[ "skos:exactMatch EC:3.6.1.10", "skos:exactMatch RHEA:22452", "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/30193\" xsd:anyURI" ]

null

false

true

9

GO:0000299

299

obsolete integral to membrane of membrane fraction

cellular_component

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" ]

This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component.

[ "integral to membrane of membrane fraction" ]

[ "EXACT" ]

[]

null

true

4

GO:0000300

300

obsolete peripheral to membrane of membrane fraction

cellular_component

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" ]

This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component.

[ "peripheral to membrane of membrane fraction" ]

[ "EXACT" ]

[]

[ "GO:0019898" ]

[]

null

true

6

GO:0000301

301

retrograde transport, vesicle recycling within Golgi

biological_process

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-Gol...

[ "ISBN:0716731363" ]

null

[ "retrograde (vesicle recycling within Golgi) transport" ]

[ "EXACT" ]

[]

[ "GO:0006891" ]

[]

[ "GO:0006891" ]

[]

null

false

true

8

GO:0000302

302

response to reactive oxygen species

biological_process

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" ]

null

[ "response to active oxygen species", "response to AOS", "response to reactive oxidative species", "response to reactive oxygen intermediate", "response to ROI", "response to ROS" ]

[ "EXACT", "EXACT", "EXACT", "EXACT", "EXACT", "EXACT" ]

[]

[ "GO:0006979", "GO:1901700" ]

[]

[ "GO:0006979", "GO:1901700" ]

[]

null

false

true

4

GO:0000303

303

response to superoxide

biological_process

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 supero...

[ "GOC:krc", "ISBN:0198506732" ]

null

[]

[ "GO:0000305" ]

[]

[ "GO:0000305" ]

[]

null

false

true

8

GO:0000304

304

response to singlet oxygen

biological_process

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 r...

[ "GOC:krc", "ISBN:0124325653", "ISBN:0198506732" ]

null

[]

[ "GO:0000302" ]

[]

[ "GO:0000302" ]

[]

null

false

true

6

GO:0000305

305

response to oxygen radical

biological_process

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 super...

[ "GOC:krc", "ISBN:0124325653" ]

null

[]

[ "GO:0000302" ]

[]

[ "GO:0000302" ]

[]

null

false

true

1

GO:0000306

306

obsolete extrinsic component of vacuolar membrane

cellular_component

OBSOLETE. 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" ]

This term was obsoleted because it represents protein topology, not a cellular component.

[ "extrinsic to vacuolar membrane" ]

[ "EXACT" ]

[]

[ "GO:0005774" ]

[ "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/23424\" xsd:anyURI" ]

null

true

3

GO:0000307

307

cyclin-dependent protein kinase holoenzyme complex

cellular_component

Cyclin-dependent protein kinases (CDKs) are enzyme complexes that contain a kinase catalytic subunit associated with a regulatory cyclin partner.

[ "GOC:krc", "PMID:11602261" ]

null

[ "CDK holoenzyme" ]

[ "EXACT" ]

[]

[ "goslim_pir" ]

[]

[ "GO:1902554" ]

[]

[ "GO:1902554" ]

[]

null

false

true

9

GO:0000308

308

cytoplasmic cyclin-dependent protein kinase holoenzyme complex

cellular_component

Cyclin-dependent protein kinase (CDK) complex found in the cytoplasm.

[ "GOC:krc" ]

null

[ "CDK holoenzyme" ]

[ "BROAD" ]

[]

[ "GO:0000307" ]

[ "part_of GO:0005737" ]

[ "part_of" ]

[ "GO:0005737" ]

[ "GO:0000307", "GO:0005737" ]

[ "GO:0000307", "part_of GO:0005737" ]

[]

null

false

true

9

GO:0000310

310

xanthine phosphoribosyltransferase activity

molecular_function

Catalysis of the reaction: diphosphate + XMP = 5-phospho-alpha-D-ribose 1-diphosphate + xanthine.

[ "RHEA:10800" ]

null

[ "5-phospho-alpha-D-ribose-1-diphosphate:xanthine phospho-D-ribosyltransferase activity", "Xan phosphoribosyltransferase activity", "xanthine-guanine phosphoribosyltransferase activity", "xanthosine 5'-phosphate pyrophosphorylase activity", "xanthylate pyrophosphorylase activity", "xanthylic pyrophosphoryl...

[ "RELATED", "RELATED", "EXACT", "RELATED", "RELATED", "RELATED", "RELATED", "RELATED" ]

[ "GO:0009043" ]

[]

[ "EC:2.4.2.22", "MetaCyc:XANPRIBOSYLTRAN-RXN", "RHEA:10800" ]

[ "GO:0106130" ]

[]

[ "GO:0106130" ]

[]

[ "skos:exactMatch EC:2.4.2.22", "skos:exactMatch RHEA:10800" ]

null

false

true

6

GO:0000311

311

plastid large ribosomal subunit

cellular_component

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" ]

null

[]

[ "GO:0000315" ]

[ "part_of GO:0009547" ]

[ "part_of" ]

[ "GO:0009547" ]

[ "GO:0000315", "GO:0009547" ]

[ "GO:0015934", "part_of GO:0009547" ]

[]

null

false

true

2

GO:0000312

312

plastid small ribosomal subunit

cellular_component

The smaller of the two subunits of a plastid ribosome.

[ "GOC:mcc" ]

null

[]

[ "GO:0000314" ]

[ "part_of GO:0009547" ]

[ "part_of" ]

[ "GO:0009547" ]

[ "GO:0000314", "GO:0009547" ]

[ "GO:0015935", "part_of GO:0009547" ]

[]

null

false

true

1

GO:0000314

314

organellar small ribosomal subunit

cellular_component

The smaller of the two subunits of an organellar ribosome.

[ "GOC:mcc" ]

null

[]

[ "GO:0015935" ]

[ "part_of GO:0000313" ]

[ "part_of" ]

[ "GO:0000313" ]

[ "GO:0000313", "GO:0015935" ]

[ "GO:0015935", "part_of GO:0000313" ]

[]

null

false

true

9

GO:0000315

315

organellar large ribosomal subunit

cellular_component

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" ]

null

[]

[ "GO:0015934" ]

[ "part_of GO:0000313" ]

[ "part_of" ]

[ "GO:0000313" ]

[ "GO:0000313", "GO:0015934" ]

[ "GO:0015934", "part_of GO:0000313" ]

[]

null

false

true

6

GO:0000316

316

sulfite transmembrane transport

biological_process

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" ]

null

[ "sulphite transport" ]

[ "EXACT" ]

[]

[ "GO:0015698", "GO:0055085", "GO:0072348" ]

[]

[ "GO:0015698", "GO:0055085", "GO:0072348" ]

[]

[ "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/28653\" xsd:anyURI" ]

null

false

true

7

GO:0000319

319

sulfite transmembrane transporter activity

molecular_function

Enables the transfer of sulfite ions from one side of a membrane to the other.

[ "GOC:as" ]

null

[ "sulphite transporter activity" ]

[ "EXACT" ]

[]

[ "GO:1901682" ]

[ "part_of GO:0000316" ]

[ "part_of" ]

[ "GO:0000316" ]

[ "GO:0000316", "GO:1901682" ]

[]

null

false

true

4

GO:0000320

320

re-entry into mitotic cell cycle

biological_process

The resumption of the mitotic cell division cycle by cells that were in a quiescent or other non-dividing state.

[ "GOC:krc" ]

null

[]

[ "GO:0022402" ]

[]

[ "GO:0022402" ]

[]

null

false

true

4

GO:0000321

321

re-entry into mitotic cell cycle after pheromone arrest

biological_process

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" ]

null

[]

[ "GO:0000320" ]

[]

[ "GO:0000320" ]

[]

null

false

true

1

GO:0000324

324

fungal-type vacuole

cellular_component

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 prim...

[ "GOC:mah", "GOC:mtg_sensu", "ISBN:0879693649" ]

null

[ "vacuole, cell cycle-correlated morphology" ]

[ "EXACT" ]

[]

[ "GO:0000322", "GO:0000323" ]

[]

[ "GO:0000322", "GO:0000323" ]

[]

null

false

true

3

GO:0000325

325

plant-type vacuole

cellular_component

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" ]

null

[ "vacuole, cell cycle-independent morphology" ]

[ "EXACT" ]

[]

[ "GO:0005773" ]

[]

[ "GO:0005773" ]

[]

null

false

true

8

GO:0000326

326

protein storage vacuole

cellular_component

A storage vacuole that contains a lytic vacuole; identified in plants.

[ "PMID:11739409" ]

null

[]

[ "GO:0000322", "GO:0000325" ]

[]

[ "GO:0000322", "GO:0000325" ]

[]

null

false

true

4

GO:0000327

327

lytic vacuole within protein storage vacuole

cellular_component

A membrane-bounded compartment containing crystals of phytic acid and proteins characteristic of a lytic vacuole, found within a storage vacuole.

[ "PMID:11739490" ]

null

[]

[ "GO:0000323" ]

[ "part_of GO:0000326" ]

[ "part_of" ]

[ "GO:0000326" ]

[ "GO:0000323", "GO:0000326" ]

[ "GO:0000323", "part_of GO:0000326" ]

[]

null

false

true

5

GO:0000328

328

fungal-type vacuole lumen

cellular_component

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" ]

null

[ "lumen of vacuole with cell cycle-correlated morphology" ]

[ "EXACT" ]

[]

[ "GO:0005775" ]

[ "part_of GO:0000324" ]

[ "part_of" ]

[ "GO:0000324" ]

[ "GO:0000324", "GO:0005775" ]

[]

null

false

true

9

GO:0000329

329

fungal-type vacuole membrane

cellular_component

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" ]

null

[ "fungal-type vacuolar membrane", "membrane of vacuole with cell cycle-correlated morphology" ]

[ "RELATED", "EXACT" ]

[]

[ "GO:0098852" ]

[ "part_of GO:0000324" ]

[ "part_of" ]

[ "GO:0000324" ]

[ "GO:0000324", "GO:0098852" ]

[]

null

false

true

2

GO:0000330

330

plant-type vacuole lumen

cellular_component

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" ]

null

[ "lumen of vacuole with cell cycle-independent morphology" ]

[ "EXACT" ]

[]

[ "GO:0005775" ]

[ "part_of GO:0000325" ]

[ "part_of" ]

[ "GO:0000325" ]

[ "GO:0000325", "GO:0005775" ]

[]

null

false

true

7

GO:0000331

331

contractile vacuole

cellular_component

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. One of its functions is osmoregulatory.

[ "GOC:jl", "PMID:10503189", "PMID:23890380" ]

null

[ "central bladder", "central vacuole" ]

[ "RELATED", "RELATED" ]

[]

[ "Wikipedia:Contractile_vacuole" ]

[ "GO:0005773", "GO:0031410" ]

[ "part_of GO:0062159" ]

[ "part_of" ]

[ "GO:0062159" ]

[ "GO:0005773", "GO:0031410", "GO:0062159" ]

[]

null

false

true

5

GO:0000332

332

template for synthesis of G-rich strand of telomere DNA activity

molecular_function

Provision of the template used by reverse transcriptase to synthesize the G-rich strand of telomeric DNA.

[ "PMID:11812242", "PMID:7958872" ]

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.

[ "telomerase RNA", "telomerase, template" ]

[ "EXACT", "EXACT" ]

[]

[ "GO:0000497" ]

[ "part_of GO:0003720" ]

[ "part_of" ]

[ "GO:0003720" ]

[ "GO:0000497", "GO:0003720" ]

[]

null

false

true

2

GO:0000333

333

telomerase catalytic core complex

cellular_component

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" ]

null

[ "TERT-TERC complex" ]

[ "RELATED" ]

[]

[ "GO:0005697", "GO:0061695" ]

[]

[ "GO:0005697", "GO:0061695" ]

[]

null

false

true

2

GO:0000334

334

3-hydroxyanthranilate 3,4-dioxygenase activity

molecular_function

Catalysis of the reaction: 3-hydroxyanthranilate + O2 = cis,cis-2-amino-3-(3-oxoprop-1-enyl)but-2-enedioate + H+.

[ "EC:1.13.11.6", "RHEA:17953" ]

null

[ "3-hydroxyanthranilate oxygenase activity", "3-hydroxyanthranilate:oxygen 3,4-oxidoreductase (decyclizing)", "3-hydroxyanthranilic acid dioxygenase activity", "3-hydroxyanthranilic acid oxygenase activity", "3-hydroxyanthranilic oxygenase activity", "3HAO" ]

[ "RELATED", "RELATED", "RELATED", "RELATED", "RELATED", "RELATED" ]

[]

[ "EC:1.13.11.6", "KEGG_REACTION:R02665", "MetaCyc:1.13.11.6-RXN", "Reactome:R-HSA-71218 \"3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde\"", "RHEA:17953", "UM-BBD_reactionID:r1027" ]

[ "GO:0016702" ]

[]

[ "GO:0016702" ]

[]

[ "skos:exactMatch EC:1.13.11.6", "skos:exactMatch RHEA:17953", "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/30193\" xsd:anyURI" ]

null

false

true

3

GO:0000335

335

obsolete negative regulation of transposition, DNA-mediated

biological_process

OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of DNA transposition.

[ "GOC:dph", "GOC:krc", "GOC:tb" ]

This term was obsoleted because there is no evidence that this process exists.

[ "down regulation of DNA transposition", "down-regulation of DNA transposition", "downregulation of DNA transposition", "inhibition of DNA transposition", "negative regulation of DNA transposition" ]

[ "EXACT", "EXACT", "EXACT", "NARROW", "EXACT" ]

[]

[ "GO:0006313" ]

[ "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/23746\" xsd:anyURI" ]

null

true

4

GO:0000337

337

obsolete regulation of transposition, DNA-mediated

biological_process

OBSOLETE. 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" ]

This term was obsoleted because there is no evidence that this process exists.

[ "regulation of DNA transposition" ]

[ "EXACT" ]

[]

[ "GO:0006313" ]

[ "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/23746\" xsd:anyURI" ]

null

true

5

GO:0000338

338

protein deneddylation

biological_process

The removal of a ubiquitin-like protein of the NEDD8 type from a protein.

[ "GOC:krc" ]

null

[ "cullin deneddylation" ]

[ "NARROW" ]

[ "GO:0010388" ]

[]

[ "GO:0070646" ]

[]

[ "GO:0070646" ]

[]

null

false

true

1

GO:0000339

339

RNA cap binding

molecular_function

Binding to a 7-methylguanosine (m7G) group or derivative located at the 5' end of an RNA molecule.

[ "GOC:krc" ]

null

[ "binding to mRNA cap", "mRNA cap binding", "snRNA cap binding" ]

[ "NARROW", "NARROW", "NARROW" ]

[]

[ "GO:0003723" ]

[]

[ "GO:0003723" ]

[]

null

false

true

5

GO:0000340

340

RNA 7-methylguanosine cap binding

molecular_function

Binding to a 7-methylguanosine group added cotranscriptionally to the 5' end of RNA molecules transcribed by polymerase II.

[ "GOC:krc" ]

null

[ "RNA m7G cap binding" ]

[ "EXACT" ]

[]

[ "GO:0000339" ]

[]

[ "GO:0000339" ]

[]

null

false

true

4

GO:0000341

341

RNA trimethylguanosine cap binding

molecular_function

Binding to 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 s...

[ "GOC:krc" ]

null

[ "RNA m2,2,7G cap binding" ]

[ "EXACT" ]

[]

[ "GO:0000339" ]

[]

[ "GO:0000339" ]

[]

null

false

true

2

GO:0000342

342

RNA cap 4 binding

molecular_function

Binding to 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 t...

[ "GOC:krc", "PMID:10880518", "PMID:12121975" ]

null

[]

[ "GO:0000339" ]

[]

[ "GO:0000339" ]

[]

null

false

true

4

GO:0000344

344

plastid-encoded plastid RNA polymerase complex B

cellular_component

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 ...

[ "PMID:10946105" ]

null

[ "PEP-B" ]

[ "EXACT" ]

[]

[ "GO:0000427" ]

[]

[ "GO:0000427" ]

[]

null

false

true

4

GO:0000345

345

cytosolic DNA-directed RNA polymerase complex

cellular_component

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" ]

null

[]

[ "GO:0000428" ]

[ "part_of GO:0005829" ]

[ "part_of" ]

[ "GO:0005829" ]

[ "GO:0000428", "GO:0005829" ]

[]

null

false

true

1

GO:0000346

346

transcription export complex

cellular_component

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...

[ "GOC:krc", "PMID:11979277" ]

null

[ "TREX complex" ]

[ "EXACT" ]

[]

[ "goslim_pir" ]

[]

[ "GO:0140513" ]

[]

[ "GO:0140513" ]

[]

null

false

true

2

GO:0000347

347

THO complex

cellular_component

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 com...

[ "GOC:krc", "PMID:11060033", "PMID:11979277", "PMID:16983072" ]

null

[]

[ "goslim_pir" ]

[]

[ "GO:0140513" ]

[]

[ "GO:0140513" ]

[]

null

false

true

9

GO:0000348

348

mRNA branch site recognition

biological_process

Recognition of the pre-mRNA branch site sequence by components of the assembling spliceosome.

[ "GOC:krc", "ISBN:0879695897" ]

Note that this step represents the formation of the B complex (yeast) or the A complex (mammalian).

[ "nuclear mRNA branch site recognition", "spliceosomal A complex biosynthesis", "spliceosomal A complex formation", "spliceosomal B complex biosynthesis", "spliceosomal B complex formation", "U12-type nuclear mRNA branch site recognition", "U2-type nuclear mRNA branch site recognition" ]

[ "EXACT", "NARROW", "NARROW", "NARROW", "NARROW", "NARROW", "NARROW" ]

[ "GO:0000370", "GO:0000371" ]

[]

[ "GO:0022618" ]

[ "part_of GO:0000245" ]

[ "part_of" ]

[ "GO:0000245" ]

[ "GO:0000245", "GO:0022618" ]

[]

null

false

true

6

GO:0000349

349

generation of catalytic spliceosome for first transesterification step

biological_process

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" ]

Note that this step represents the formation of the A2-2 complex (yeast) or the C1 complex (mammalian).

[ "catalytic spliceosome assembly for first transesterification step", "formation of catalytic spliceosome for first transesterification step", "spliceosomal A2-2 complex biosynthesis", "spliceosomal A2-2 complex formation", "spliceosomal C1 complex biosynthesis", "spliceosomal C1 complex formation", "U12...

[ "RELATED", "EXACT", "NARROW", "NARROW", "NARROW", "NARROW", "NARROW", "NARROW" ]

[ "GO:0000356", "GO:0000357" ]

[]

[ "GO:0022618" ]

[ "part_of GO:0000393" ]

[ "part_of" ]

[ "GO:0000393" ]

[ "GO:0000393", "GO:0022618" ]

[]

null

false

true

4

GO:0000352

352

trans assembly of SL-containing precatalytic spliceosome

biological_process

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" ]

null

[ "trans assembly of spliced leader-containing precatalytic spliceosome" ]

[ "EXACT" ]

[]

[ "GO:0022618" ]

[ "part_of GO:0000245", "part_of GO:0045291" ]

[ "part_of", "part_of" ]

[ "GO:0000245", "GO:0045291" ]

[ "GO:0000245", "GO:0022618", "GO:0045291" ]

[]

null

false

true

8

GO:0000353

353

formation of quadruple SL/U4/U5/U6 snRNP

biological_process

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" ]

Note that this step is analogous to 5' splice site selection in cis-splicing.

[]

[ "GO:0022618" ]

[ "part_of GO:0045291" ]

[ "part_of" ]

[ "GO:0045291" ]

[ "GO:0022618", "GO:0045291" ]

[]

null

false

true

8

GO:0000354

354

cis assembly of pre-catalytic spliceosome

biological_process

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" ]

Note that this step represents formation of the A2-1 complex (yeast) or the B1 complex (mammals).

[ "cis assembly of U12-type pre-catalytic spliceosome", "cis assembly of U2-type pre-catalytic spliceosome", "formation of spliceosomal A2-1 complex", "formation of spliceosomal B1 complex", "spliceosomal A2-1 complex biosynthesis", "spliceosomal A2-1 complex formation", "spliceosomal B1 complex biosynthe...

[ "NARROW", "NARROW", "NARROW", "NARROW", "NARROW", "NARROW", "NARROW", "NARROW" ]

[ "GO:0000360", "GO:0000361" ]

[]

[ "GO:0022618" ]

[ "part_of GO:0000245", "part_of GO:0045292" ]

[ "part_of", "part_of" ]

[ "GO:0000245", "GO:0045292" ]

[ "GO:0000245", "GO:0022618", "GO:0045292" ]

[]

null

false

true

9

GO:0000364

364

obsolete second U2-type spliceosomal transesterification activity

molecular_function

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 exo...

[ "GOC:krc", "ISBN:0879695897" ]

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.

[ "3'-splice site cleavage, exon ligation", "second U2-type spliceosomal transesterification activity" ]

[ "BROAD", "EXACT" ]

[]

[ "GO:0000386" ]

[]

null

true

1

GO:0000365

365

mRNA trans splicing, via spliceosome

biological_process

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", "PMID:18458335" ]

null

[ "nuclear mRNA trans splicing, via spliceosome", "nuclear mRNA trans splicing, via U2-type spliceosome" ]

[ "EXACT", "NARROW" ]

[]

[ "GO:0000398" ]

[]

[ "GO:0000398" ]

[]

null

false

true

1

GO:0000366

366

mRNA alternative trans-splicing

biological_process

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" ]

null

[ "intergenic mRNA trans splicing", "intergenic nuclear mRNA trans splicing" ]

[ "EXACT", "EXACT" ]

[]

[ "GO:0000365", "GO:0000380" ]

[]

[ "GO:0000365", "GO:0000380" ]

[]

[ "term_tracker_item \"https://github.com/geneontology/go-ontology/issues/27611\" xsd:anyURI" ]

null

false

true

5

GO:0000367

367

obsolete second U12-type spliceosomal transesterification activity

molecular_function

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 ex...

[ "GOC:krc", "ISBN:0879695897" ]

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.

[ "3'-splice site cleavage, exon ligation", "second U12-type spliceosomal transesterification activity" ]

[ "BROAD", "EXACT" ]

[]

[ "GO:0000386" ]

[]

null

true

5

GO:0000373

373

Group II intron splicing

biological_process

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. Spli...

[ "GOC:krc", "PMID:11377794" ]

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.

[ "mRNA splicing" ]

[ "RELATED" ]

[]

[ "GO:0000377" ]

[]

[ "GO:0000377" ]

[]

null

false

true

1

GO:0000374

374

Group III intron splicing

biological_process

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 transesterific...

[ "GOC:krc", "PMID:11377794" ]

Note that Group III introns are known to be found in mRNA of plastids of euglenoid protists.

[ "mRNA splicing" ]

[ "RELATED" ]

[]

[ "GO:0000377" ]

[]

[ "GO:0000377" ]

[]

null

false

true

7

GO:0000375

375

RNA splicing, via transesterification reactions

biological_process

Splicing of RNA via a series of two transesterification reactions.

[ "GOC:krc" ]

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. N...

[ "pre-mRNA splicing factor activity", "RNA splicing factor activity, transesterification mechanism", "spliceosomal catalysis" ]

[ "RELATED", "RELATED", "RELATED" ]

[ "GO:0000385", "GO:0031202" ]

[ "goslim_pir" ]

[]

[ "GO:0008380" ]

[]

[ "GO:0008380" ]

[]

null

false

true

6

GO:0000376

376

RNA splicing, via transesterification reactions with guanosine as nucleophile

biological_process

Splicing of RNA via a series of two transesterification reactions with exogenous guanosine as the initiating nucleophile.

[ "GOC:krc", "PMID:11377794" ]

null

[]

[ "GO:0000375" ]

[]

[ "GO:0000375" ]

[]

null

false

true

5

GO:0000377

377

RNA splicing, via transesterification reactions with bulged adenosine as nucleophile

biological_process

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" ]

null

[ "lariat RNA biosynthesis", "lariat RNA formation" ]

[ "RELATED", "RELATED" ]

[]

[ "GO:0000375" ]

[]

[ "GO:0000375" ]

[]

null

false

true

7

GO:0000378

378

RNA exon ligation

biological_process

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" ]

Note that this is not a part of spliceosomal RNA splicing.

[]

[ "GO:0016070" ]

[ "part_of GO:0000394" ]

[ "part_of" ]

[ "GO:0000394" ]

[ "GO:0000394", "GO:0016070" ]

[]

null

false

true

9

GO:0000379

379

tRNA-type intron splice site recognition and cleavage

biological_process

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" ]

null

[]

[ "GO:0006396" ]

[ "part_of GO:0006388" ]

[ "part_of" ]

[ "GO:0006388" ]

[ "GO:0006388", "GO:0006396" ]

[]

null

false

true

3