LiteFold/GO huggingface dataset:
mitochondrion inheritance (GO:0000001)
Namespace: biological_process
Definition: The distribution of mitochondria, including the mitochondrial genome, into daughter cells after mitosis or meiosis, mediated by interactions between mitochondria and the cytoskeleton.
Synonyms: mitochondrial inheritance
obsolete ribosomal chaperone activity (GO:0000005)
Namespace: molecular_function
Definition: 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.
Synonyms: ribosomal chaperone activity
Comment: This term was made obsolete because it refers to a class of gene products and a biological process rather than a molecular function.
adenine deaminase activity (GO:0000034)
Namespace: molecular_function
Definition: Catalysis of the reaction: adenine + H+ + H2O = hypoxanthine + NH4+.
Synonyms: ADase activity; adenase activity; adenine aminase activity; adenine aminohydrolase activity
urea cycle (GO:0000050)
Namespace: biological_process
Definition: 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.
Synonyms: ornithine cycle; urea biosynthesis; urea biosynthetic process
mitotic G2 phase (GO:0000085)
Namespace: biological_process
Definition: The cell cycle 'gap' phase which is the interval between the completion of DNA synthesis and the beginning of DNA segregation by mitosis.
Synonyms: G2 phase of mitotic 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).
S-methylmethionine transmembrane transporter activity (GO:0000100)
Namespace: molecular_function
Definition: Enables the transfer of S-methylmethionine from one side of a membrane to the other.
Synonyms: S-methylmethionine permease activity; S-methylmethionine transporter activity
L-methionine secondary active transmembrane transporter activity (GO:0000102)
Namespace: molecular_function
Definition: Enables 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. Secondary active transporters include symporters and antiporters.
Synonyms: L-methionine porter activity
sulfate assimilation (GO:0000103)
Namespace: biological_process
Definition: The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
Synonyms: sulfate assimilation, phosphoadenylyl sulfate reduction by an oxidoreductase, acting on sulfur group of donors, NAD or NADP as acceptor; sulphate assimilation; sulphate assimilation, phosphoadenylyl sulphate reduction by an oxidoreductase, acting on sulphur group of donors, NAD or NADP as acceptor
obsolete regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)
Namespace: biological_process
Definition: OBSOLETE. Any process that regulates transcription such that the target genes are transcribed as part of the G2/M transition of the mitotic cell cycle.
Synonyms: G2/M-specific transcription in mitotic cell cycle; regulation of transcription from RNA polymerase II promoter during G2/M transition of mitotic cell cycle
Comment: This term was obsoleted because it represents a GO-CAM model.
sn-glycerol 1-phosphatase activity (GO:0000121)
Namespace: molecular_function
Definition: Catalysis of the reaction: H2O + sn-glycerol 1-phosphate = glycerol + phosphate.
Synonyms: alpha-glycerol phosphatase activity; alpha-glycerophosphatase activity; glycerol 3-phosphatase activity; glycerol 3-phosphate phosphohydrolase activity; glycerol-1-phosphatase activity; glycerol-1-phosphate phosphohydrolase activity; glycerol-3-phosphate phosphatase activity
flocculation (GO:0000128)
Namespace: biological_process
Definition: The reversible, non-sexual aggregation of single-celled organisms in suspension to form aggregates of many cells known as flocs.
Synonyms: cell-cell adhesion involved in flocculation; cell-cell adhesion involved in flocculation via cell wall protein-carbohydrate interaction; co-flocculation; coflocculation; coflocculation via lectin-mannose interaction; coflocculation via protein-carbohydrate interaction; flocculation via cell wall protein-carbohydrate interaction; flocculation via extracellular polymer
Comment: The word floc derives from the Latin word floccus, which means a tuft of wool.
phosphorelay signal transduction system (GO:0000160)
Namespace: biological_process
Definition: 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.
Synonyms: histidyl-aspartyl phosphorelay
obsolete nuclear translocation of MAPK during sporulation (sensu Saccharomyces) (GO:0000207)
Namespace: biological_process
Definition: 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).
Synonyms: nuclear translocation of MAPK during sporulation (sensu Saccharomyces)
Comment: This term was made obsolete because it is a gene product specific term.
nuclear chromosome (GO:0000228)
Namespace: cellular_component
Definition: 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.
Synonyms: nuclear interphase chromosome
3-beta-hydroxysteroid dehydrogenase [NAD(P)+]/C4-decarboxylase activity (GO:0000252)
Namespace: molecular_function
Definition: Catalysis of the reaction: a 3-beta-hydroxysteroid-4-alpha-carboxylate + NADP+ = a 3-oxosteroid + CO2 + NADPH.
Synonyms: 3beta-hydroxy-4alpha-methylcholestenecarboxylate 3-dehydrogenase (decarboxylating); 3beta-hydroxy-4beta-methyl-5alpha-cholest-7-ene-4alpha-carboxylate:NAD(P)+ 3-oxidoreductase (decarboxylating); 3beta-hydroxy-4beta-methylcholestenecarboxylate 3-dehydrogenase (decarboxylating); 3beta-hydroxy-4beta-methylcholestenoate dehydrogenase activity; C-3 sterol dehydrogenase (C-4 decarboxylase) activity; C-3 sterol dehydrogenase (C-4 sterol decarboxylase) activity; C-3 sterol dehydrogenase activity; sterol 4alpha-carboxylic decarboxylase activity; sterol-4-carboxylate 3-dehydrogenase (decarboxylating) activity; sterol-4alpha-carboxylate 3-dehydrogenase (decarboxylating)
mitotic cell cycle (GO:0000278)
Namespace: biological_process
Definition: 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.
Synonyms: mitosis
Comment: Note that this term should not be confused with 'GO:0140014 ; mitotic nuclear division'. 'GO:0000278 ; mitotic cell cycle represents the entire mitotic cell cycle, while 'GO:0140014 ; mitotic nuclear division' specifically represents the actual nuclear division step of the mitotic cell cycle.
nicotinamide-nucleotide adenylyltransferase activity (GO:0000309)
Namespace: molecular_function
Definition: Catalysis of the reaction: beta-nicotinamide D-ribonucleotide + ATP + H+ = diphosphate + NAD+.
Synonyms: adenosine triphosphate-nicotinamide mononucleotide transadenylase activity; ATP:nicotinamide-nucleotide adenylyltransferase activity; ATP:NMN adenylyltransferase activity; diphosphopyridine nucleotide pyrophosphorylase activity; NAD(+) diphosphorylase activity; NAD(+) pyrophosphorylase activity; NAD+ diphosphorylase activity; NAD+ pyrophosphorylase activity; nicotinamide adenine dinucleotide pyrophosphorylase activity; nicotinamide mononucleotide adenylyltransferase activity; NMN adenylyltransferase activity; NMNAT activity
organellar ribosome (GO:0000313)
Namespace: cellular_component
Definition: A ribosome contained within a subcellular membrane-bounded organelle.
storage vacuole (GO:0000322)
Namespace: cellular_component
Definition: A vacuole that functions primarily in the storage of materials, including nutrients, pigments, waste products, and small molecules.
lytic vacuole (GO:0000323)
Namespace: cellular_component
Definition: A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases.
obsolete positive regulation of transposition, DNA-mediated (GO:0000336)
Namespace: biological_process
Definition: OBSOLETE. Any process that activates or increases the frequency, rate or extent of DNA transposition.
Synonyms: activation of DNA transposition; positive regulation of DNA transposition; stimulation of DNA transposition; up regulation of DNA transposition; up-regulation of DNA transposition; upregulation of DNA transposition
Comment: This term was obsoleted because there is no evidence that this process exists.
plastid-encoded plastid RNA polymerase complex A (GO:0000343)
Namespace: cellular_component
Definition: 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.
Synonyms: PEP-A
generation of catalytic spliceosome for second transesterification step (GO:0000350)
Namespace: biological_process
Definition: 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.
Synonyms: catalytic spliceosome assembly for second transesterification step; formation of catalytic spliceosome for second transesterification step; formation of catalytic U12-type spliceosome for second transesterification step; formation of catalytic U2-type spliceosome for second transesterification step; formation of spliceosomal A2-2 complex; formation of spliceosomal C1 complex; lariat formation, 5'-splice site cleavage; spliceosomal A2-3 complex biosynthesis; spliceosomal A2-3 complex formation; spliceosomal C2 complex biosynthesis; spliceosomal C2 complex formation
Comment: Note that this step represents formation of the A2-3 complex (yeast) or the C2 complex (mammalian).
obsolete first U2-type spliceosomal transesterification activity (GO:0000362)
Namespace: molecular_function
Definition: 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.
Synonyms: first U2-type spliceosomal transesterification activity; lariat formation, 5'-splice site cleavage
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.
obsolete first U12-type spliceosomal transesterification activity (GO:0000363)
Namespace: molecular_function
Definition: 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.
Synonyms: first U12-type spliceosomal transesterification activity; lariat formation, 5'-splice site cleavage
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.
Group I intron splicing (GO:0000372)
Namespace: biological_process
Definition: 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).
Synonyms: mRNA splicing
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).
mRNA 5'-splice site recognition (GO:0000395)
Namespace: biological_process
Definition: Recognition of the intron 5'-splice site by components of the assembling spliceosome.
Synonyms: nuclear mRNA 5' splice site recognition; nuclear mRNA 5'-splice site recognition; spliceosomal CC complex biosynthesis; spliceosomal CC complex formation; spliceosomal commitment complex biosynthesis; spliceosomal commitment complex formation; spliceosomal E complex biosynthesis; spliceosomal E complex formation; U12-type nuclear mRNA 5' splice site recognition; U12-type nuclear mRNA 5'-splice site recognition; U2-type nuclear mRNA 5' splice site recognition; U2-type nuclear mRNA 5'-splice site recognition
Comment: Note that this step represents formation of the Commitment Complex (CC, in yeast) or the E complex (mammalian).
autophagy of mitochondrion (GO:0000422)
Namespace: biological_process
Definition: The autophagic process in which mitochondria are delivered to a type of vacuole and degraded in response to changing cellular conditions.
Synonyms: mitochondrion degradation; mitochondrion disassembly; mitophagy
regulation of transcription from RNA polymerase II promoter by glucose (GO:0000430)
Namespace: biological_process
Definition: Any process involving glucose that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
core TFIIH complex portion of NEF3 complex (GO:0000440)
Namespace: cellular_component
Definition: The core TFIIH complex when it is part of the nucleotide-excision repair factor 3 (NEF3).
Synonyms: SSL2-core TFIIH complex portion of NEF3 complex
THO complex part of transcription export complex (GO:0000445)
Namespace: cellular_component
Definition: 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.
Synonyms: THO complex part of TREX complex
nucleoplasmic THO complex (GO:0000446)
Namespace: cellular_component
Definition: 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.
obsolete dimethylation involved in SSU-rRNA maturation (GO:0000456)
Namespace: biological_process
Definition: OBSOLETE. 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.
Comment: The reason for obsoletion is that this term can be captured as a GO-CAM model.
endonucleolytic cleavage between LSU-rRNA and 5S rRNA of tricistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 5S) (GO:0000458)
Namespace: biological_process
Definition: 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.
maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000466)
Namespace: biological_process
Definition: 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.
obsolete endonucleolytic cleavage involved in rRNA processing (GO:0000478)
Namespace: biological_process
Definition: OBSOLETE. 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.
Synonyms: endonucleolytic cleavage during rRNA processing
Comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)
Namespace: cellular_component
Definition: 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.
Synonyms: GPI-GlcNAc transferase complex; GPI-GnT complex; GPI-N-acetylglucosaminyltransferase complex
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.
H3-H4 histone complex chaperone activity (GO:0000510)
Namespace: molecular_function
Definition: A histone chaperone that carries a H3-H4 histone complex.
Synonyms: H3-H4 histone carrier activity; H3.1-H4 histone complex chaperone activity; H3.2-H4 histone complex chaperone activity; H3.3-H4 histone complex chaperone activity
Comment: Mammalian cells have seven known sequence variants of histone H3. These are denoted as Histone H3.1, Histone H3.2, Histone H3.3, Histone H3.4 (H3T), Histone H3.5, Histone H3.X and Histone H3.Y (https://en.wikipedia.org/wiki/Histone_H3).
meiotic mismatch repair (GO:0000710)
Namespace: biological_process
Definition: 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.
obsolete nucleotide-excision repair, DNA duplex unwinding (GO:0000717)
Namespace: biological_process
Definition: OBSOLETE. The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage.
Comment: The reason for obsoletion is that the term represents a molecular function.
telomere maintenance (GO:0000723)
Namespace: biological_process
Definition: 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.
Synonyms: regulation of telomere length
recombinational repair (GO:0000725)
Namespace: biological_process
Definition: A DNA repair process that involves the exchange, reciprocal or nonreciprocal, of genetic material between the broken DNA molecule and a homologous DNA region.
DNA synthesis involved in DNA repair (GO:0000731)
Namespace: biological_process
Definition: Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template.
Synonyms: DNA repair synthesis; DNA synthesis during DNA repair; mitotic DNA repair synthesis
obsolete DNA strand renaturation (GO:0000733)
Namespace: biological_process
Definition: OBSOLETE. The identification and annealing of complementary base pairs in single-strand DNA.
Comment: This term was obsoleted because it represents a molecular function.
mitotic cell cycle G1 arrest in response to pheromone (GO:0000751)
Namespace: biological_process
Definition: The cell cycle regulatory process in which the mitotic cell cycle is halted during G1 as a result of a pheromone stimulus. An example of this process is found in Saccharomyces cerevisiae.
Synonyms: cell cycle arrest in response to pheromone
obsolete negative adaptation of signaling pathway by response to pheromone involved in pheromone-induced unidirectional conjugation (GO:0000766)
Namespace: biological_process
Definition: OBSOLETE. 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.
Synonyms: adaptation to pheromone during pheromone-induced unidirectional conjugation; desensitization to pheromone during pheromone-induced unidirectional conjugation; negative adaptation of signalling pathway by response to pheromone involved in pheromone-induced unidirectional conjugation
Comment: This term was obsoleted because it is a pre-composed term that should be captured as a GO-CAM model.
telomere cap complex (GO:0000782)
Namespace: cellular_component
Definition: A complex of DNA and protein located at the end of a linear chromosome that protects and stabilizes a linear chromosome.
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.
origin recognition complex (GO:0000808)
Namespace: cellular_component
Definition: A multisubunit complex that is located at the replication origins of a chromosome.
Synonyms: ORC; origin of replication recognition complex
inositol hexakisphosphate 4-kinase activity (GO:0000830)
Namespace: molecular_function
Definition: Catalysis of the reaction: ATP + 1D-myo-inositol hexakisphosphate = ADP + 4-diphospho-1D-myo-inositol (1,2,3,5,6)pentakisphosphate.
5-diphosphoinositol pentakisphosphate 6-kinase activity (GO:0000834)
Namespace: molecular_function
Definition: Catalysis of the reaction: ATP + 5-diphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate = ADP + 5,6-bisdiphosphoinositol-1D-myo-inositol (1,2,3,4)tetrakisphosphate.
Synonyms: inositol heptakisphosphate 6-kinase activity