LiteFold/GO huggingface dataset:
ATP-dependent DNA damage sensor activity (GO:0140664)
Namespace: molecular_function
Definition: A molecule that recognises toxic DNA structures, and initiates a signaling response, driven by ATP hydrolysis.
Synonyms: ATP-dependent DNA damage sensing activity
ATP-dependent H3-H4 histone complex chaperone activity (GO:0140665)
Namespace: molecular_function
Definition: A histone chaperone that carries a H3-H4 histone complex, driven by ATP hydrolysis.
Synonyms: ATP-dependent H3-H4 histone complex loader activity; H3-H4 dimer loading activity; H3-H4 histone chaperone; H3-H4 histone complex loader activity; histone chaperone; histone H3-H4 dimer loading activity
annealing activity (GO:0140666)
Namespace: molecular_function
Definition: An activity that facilitates the formation of a complementary double-stranded polynucleotide molecule.
Synonyms: renaturation
cohesin unloader activity (GO:0140670)
Namespace: molecular_function
Definition: Facilitating a conformational change to unload a cohesin complex from sister chromatids.
Synonyms: cohesin unloading activity
ADA complex (GO:0140671)
Namespace: cellular_component
Definition: A chromatin remodeling complex that regulates transcription via acetylation primarily of nucleosomal histones H3 and H2B. In budding yeast shares the histone acetylation (HAT) module of ADA2-GCN5-NGG1-SGF29 with the related SAGA complex.
Synonyms: ADA HAT complex; ADA histone acetyltransferase complex; Ada2/Gcn5/Ada3 transcription activator complex; scADA
ATAC complex (GO:0140672)
Namespace: cellular_component
Definition: A chromatin remodeling complex that regulates transcription via acetylation primarily of nucleosomal histones H3 and possibly H4. Shares the histone acetylation (HAT) module of GCN5/PCAF-ADA2-ADA3-SGF29 (or orthologs) with the related SAGA complex (GO:0000124). Contains HAT subunits GCN5 or PCAF in a mutually exclusive manner. In addition to the HAT module contains DR1/NC2B, KAT14, MBIP, WDR5, YEATS2 and ZZZ3 or orthologs. Also regulates the activity of non-histone targets and orchestrates mitotic progression by regulating Cyclin A degradation through acetylation.
Synonyms: Ada two A containing complex; Ada Two-A containing complex; Ada-Two-A-containing complex; ADA2A-containing complex; G-ATAC complex; KAT2A-containing ATAC complex; KAT2B-containing ATAC complex
transcription elongation-coupled chromatin remodeling (GO:0140673)
Namespace: biological_process
Definition: A chromatin remodeling process that reestablishes the chromatin structure following the passage of RNA polymerase II during transcription elongation, thus preventing cryptic transcription initiation.
Synonyms: chromatin maintenance during transcription elongation; co-transcriptional chromatin reassembly; DNA replication-independent chromatin organization; euchromatin maintenance during transcription elongation; maintenance of chromatin integrity during transcription elongation by RNAPII; maintenance of transcriptionally active chromatin during transcription elongation; transcription elongation coupled chromatin remodeling; transcriptional elongation-coupled chromatin remodeling
Comment: Note: Do not confuse with 'GO:0045815 transcriptional initiation-coupled chromatin remodeling', which describes the maintenance of chromatin in an open conformation, allowing the transcriptional machinery to access the DNA.
ATP-dependent histone chaperone activity (GO:0140674)
Namespace: molecular_function
Definition: Binding to and carrying a histone or a histone complex to unload or deposit it as a nucleosome, driven by ATP hydrolysis.
Synonyms: ATP-dependent histone loader activity; ATP-dependent histone unloader activity; histone loader activity; histone loading activity; histone unloader activity; histone unloading activity; nucleosome remodeling activity
oscillatory cAMP signaling (GO:0140676)
Namespace: biological_process
Definition: Fluctuation in the extracellular cAMP levels due to the alternate activation of adenylate cyclase, which produces cAMP, and phosphodiesterase, which degrades it. Occurs in Dictyostelium during early sorocarp development. Oscillation in signaling result is directional chemotaxis of cells towards the center of the aggregate.
Synonyms: cAMP relay
molecular function activator activity (GO:0140677)
Namespace: molecular_function
Definition: A molecular function regulator that activates or increases the activity of its target via non-covalent binding that does not result in covalent modification to the target.
Comment: This term should only be used in cases when the regulator directly interacts with the enzyme, but does not result in a covalent modification.
molecular function inhibitor activity (GO:0140678)
Namespace: molecular_function
Definition: A molecular function regulator that inhibits or decreases the activity of its target via non-covalent binding that does not result in covalent modification to the target.
Comment: This term should only be used in cases when the regulator directly interacts with the enzyme, but does not result in a covalent modification.
ABC-type sodium transporter activity (GO:0140679)
Namespace: molecular_function
Definition: Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Na(in) = ADP + phosphate + Na(out).
histone H3K36me/H3K36me2 demethylase activity (GO:0140680)
Namespace: molecular_function
Definition: Catalysis of the removal of a methyl group from a di- or a monomethyl-lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate.
Synonyms: histone H3-di/monomethyl-lysine-36 demethylase activity; histone H3K36me demethylase activity; histone H3K36me2 demethylase activity
Comment: Comment: Note that the residue position corresponds to the canonical human H3 histone (UniProtKB:P84243); this residue is conserved across all eukaryotes. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
histone H3K36me2/H3K36me3 demethylase activity (GO:0140681)
Namespace: molecular_function
Definition: Catalysis of the removal of a methyl group from a tri- or a dimethyl-lysine residue at position 36 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate.
Synonyms: histone H3-tri/dimethyl-lysine-36 demethylase activity; histone H3K36me2 demethylase activity; histone H3K36me3 demethylase activity
Comment: Comment: Note that the residue position corresponds to the canonical human H3 histone (UniProtKB:P84243); this residue is conserved across all eukaryotes. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
FAD-dependent H3K4me/H3K4me3 demethylase activity (GO:0140682)
Namespace: molecular_function
Definition: Catalysis of the removal of a methyl group from a di- or a monomethyl-lysine residue at position 4 of the histone H3 protein. This is a flavin adenine dinucleotide (FAD)-dependent amine oxidation reaction.
Synonyms: histone H3-di/monomethyl-lysine-4 FAD-dependent demethylase activity; histone H3K4me demethylase activity; histone H3K4me2 demethylase activity
Comment: Comment: Note that the residue position corresponds to the canonical human H3 histone (UniProtKB:P84243); this residue is conserved across all eukaryotes. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
histone H3K9me/H3K9me2 demethylase activity (GO:0140683)
Namespace: molecular_function
Definition: Catalysis of the removal of a methyl group from a di or a monomethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate.
Synonyms: histone H3-di/monomethyl-lysine-9 demethylase activity; histone H3K9me demethylase activity; histone H3K9me2 demethylase activity
Comment: Comment: Note that the residue position corresponds to the canonical human H3 histone (UniProtKB:P84243); this residue is conserved across all eukaryotes. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
histone H3K9me2/H3K9me3 demethylase activity (GO:0140684)
Namespace: molecular_function
Definition: Catalysis of the removal of a methyl group from a tri or a dimethyl-lysine residue at position 9 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate.
Synonyms: histone H3-tri/dimethyl-lysine-9 demethylase activity; histone H3K9me2 demethylase activity; histone H3K9me3 demethylase activity
Comment: Comment: Note that the residue position corresponds to the canonical human H3 histone (UniProtKB:P84243); this residue is conserved across all eukaryotes. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
FAD-dependent histone H3K9me/H3K9me2 demethylase activity (GO:0140685)
Namespace: molecular_function
Definition: Catalysis of the removal of a methyl group from a di- or a monomethyl-lysine residue at position 9 of the histone H3 protein. This is a flavin adenine dinucleotide (FAD)-dependent amine oxidation reaction.
Synonyms: histone H3-di/monomethyl-lysine-9 FAD-dependent demethylase activity; histone H3K9me demethylase activity; histone H3K9me2 demethylase activity
Comment: Comment: Note that the residue position corresponds to the canonical human H3 histone (UniProtKB:P84243); this residue is conserved across all eukaryotes. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
dihydropyrimidine dehydrogenase (NAD+) complex (GO:0140690)
Namespace: cellular_component
Definition: A heteromultimeric complex capable of dihydropyrimidine dehydrogenase (NAD+); in E. coli, composed of PreA and PreT.
RNA folding chaperone (GO:0140691)
Namespace: molecular_function
Definition: Binding to an RNA or an RNA-containing complex to assist the folding process.
very long-chain fatty acid omega-hydroxylase activity (GO:0140692)
Namespace: molecular_function
Definition: Catalysis of the reaction: an omega-methyl-very-long-chain fatty acid + O2 + reduced [NADPH-hemoprotein reductase] = an omega-hydroxy-very-long-chain fatty acid + H+ + H2O + oxidized [NADPH-hemoprotein reductase]. A very long-chain fatty acid has an aliphatic tail containing more than 22 carbons.
Comment: While there is not universal consensus on the lengths of short-, medium-, long- and very-long-chain fatty acids, the GO uses the definitions in ChEBI (see CHEBI:26666, CHEBI:59554, CHEBI:15904 and CHEBI:27283).
membraneless organelle assembly (GO:0140694)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of a set of components to form a non-membrane-bounded organelle.
Synonyms: non-membrane-bounded organelle assembly; non-membrane-bounded organelle formation; non-membrane-enclosed organelle assembly; non-membrane-enclosed organelle formation
(S)-2-hydroxyglutarate dehydrogenase (quinone) activity (GO:0140696)
Namespace: molecular_function
Definition: Catalysis of the reaction: (S)-2-hydroxyglutarate + a quinone = 2-oxoglutarate + a quinol.
Synonyms: (S)-2-hydroxyglutarate dehydrogenase activity; L-2-hydroxyglutarate dehydrogenase activity
cyclic GMP-AMP synthase activity (GO:0140699)
Namespace: molecular_function
Definition: Catalysis of the reaction: ATP + GTP = 2 diphosphate + cyclic GMP-AMP.
Synonyms: cyclic-GMP-AMP synthase activity
Comment: Note that this term should not be used for direct annotation. It should be possible to annotate to a more specific child term that describes the position of the phosphate group on the cGAMP molecule.
3',2'-cyclic GMP-AMP synthase activity (GO:0140700)
Namespace: molecular_function
Definition: Catalysis of the reaction: GTP + ATP = 3',2'-cGAMP + 2 diphosphate.
Synonyms: 3',2' cyclic-GMP-AMP synthase activity; 3',2'-cyclic GAMP synthase activity
3',3'-cyclic GMP-AMP synthase activity (GO:0140701)
Namespace: molecular_function
Definition: Catalysis of the reaction: ATP + GTP = 2 diphosphate + cyclic G-P(3'-5')A-P(3'-5') (cyclic 3',3' GAMP).
Synonyms: 3',3' cyclic-GAMP synthase activity; 3',3' cyclic-GMP-AMP synthase activity; 3',3'-cyclic GAMP synthase activity
cyclic GMP-AMP binding (GO:0140702)
Namespace: molecular_function
Definition: Binding to cyclic GMP-AMP (cGAMP) nucleotide.
3',3'-cyclic GMP-AMP binding (GO:0140703)
Namespace: molecular_function
Definition: Binding to 3',3' cyclic GMP-AMP (cGAMP) nucleotide, a cyclic purine dinucleotide that consists of AMP and GMP units cyclized via 3',5' and 3',5' linkages.
Synonyms: 3',3' cyclic-GMP-AMP binding; 3',3'-cGAMP binding; 3',3'-cGMP-AMP binding; 3',3'-cyclic GAMP binding
3',2'-cyclic GMP-AMP binding (GO:0140704)
Namespace: molecular_function
Definition: Binding to 3',2' cyclic GMP-AMP (cGAMP) nucleotide, a cyclic purine dinucleotide that consists of AMP and GMP units cyclized via 3',5' and 2',5' linkages.
Synonyms: 3',2' cyclic-GMP-AMP binding; 3',2'-cGAMP binding; 3',2'-cyclic GAMP binding
protein-containing complex localization to centriolar satellite (GO:0140706)
Namespace: biological_process
Definition: A protein-containing complex localization by which the complex is transported to, or maintained in, the centriolar satellite.
CAT tailing (GO:0140708)
Namespace: biological_process
Definition: The C-terminal elongation of 60S-anchored stalled nascent polypeptide chains with untemplated alanine and threonine tails (CAT tails). CAT tails participate in the recognition of stalled nascent chains by the ribosome quality control system.
Frizzled Nuclear Import pathway (GO:0140709)
Namespace: biological_process
Definition: A type of non-canonical Wnt signaling in which Wnt binding to its receptor on the surface a the target cell results in internalization and cleavage of the frizzled receptor to yield a C-terminal fragment that is imported into the nucleus. The frizzled C-terminal fragment is incorporated into large ribonucleoprotein particles and stimulates their egress via nuclear budding.
Synonyms: FNI; Frizzled Nuclear Import Wnt Pathway
regulation of Frizzled Nuclear Import pathway (GO:0140710)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of a Frizzled Nuclear Import pathway.
Synonyms: regulation of FNI; regulation of Frizzled Nuclear Import Wnt Pathway
positive regulation of Frizzled Nuclear Import pathway (GO:0140711)
Namespace: biological_process
Definition: Any process that activates or increases the frequency, rate or extent of a Frizzled Nuclear Import pathway.
Synonyms: positive regulation of FNI; positive regulation of Frizzled Nuclear Import Wnt Pathway
negative regulation of Frizzled Nuclear Import pathway (GO:0140712)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the frequency, rate or extent of a Frizzled Nuclear Import pathway.
Synonyms: negative regulation of FNI; negative regulation of Frizzled Nuclear Import Wnt Pathway
histone chaperone activity (GO:0140713)
Namespace: molecular_function
Definition: Binding to and carrying a histone or a histone complex to unload or deposit it as a nucleosome. The histone can be newly synthesized or result from nucleosome disassembly (either spontaneously, or by a histone chaperone).
Synonyms: histone carrier activity; nucleosome remodeling activity
large ribosomal subunit pre-assembly complex (GO:0140714)
Namespace: cellular_component
Definition: A protein complex that assists early maturation of nascent 60S ribosomal subunits. The complex interacts with the large ribosomal subunit rRNA via one of the components (Urb2 in S. cerevisiae) and requires a RNA helicase (Dbp6 in S. cerevisiae).
serine-tRNA ligase complex (GO:0140715)
Namespace: cellular_component
Definition: A heterodimeric enzyme complex that catalyzes the ligation of serine to tRNA(Ser), forming L-seryl-tRNA(Ser).
entry into host through the stromata (GO:0140717)
Namespace: biological_process
Definition: Entry of a symbiont into host plant tissue via the stromata, microscopic pores in the epidermis of the aerial parts of terrestrial plants. These pores are essential for photosynthesis, as they allow CO2 to diffuse into the plant. The host is defined as the larger of the organisms involved in a symbiotic interaction.
facultative heterochromatin formation (GO:0140718)
Namespace: biological_process
Definition: The compaction of chromatin into a conformation that is refractory to transcription but that can be converted to euchromatin and allow transcription in specific contexts. These can be temporal (e.g., developmental states or specific cell-cycle stages), spatial (e.g., nuclear localization changes from the center to the periphery or vice versa due to exogenous factors/signals), or parental/heritable (e.g., monoallelic gene expression). In metazoa, this involves the methylation of histone H3K27, and in certain cases methylation of H3K9. On the other hand, in unicellular eukaryotes, only methylation of H3K9 is involved and H3K27 is not methylated.
Synonyms: facultative heterochromatin assembly; fHC assembly
Comment: Note that facultative heterochromatin can be reprogrammed, as opposed to constitutive heterochromatin which usually cannot be reprogrammed to a transcriptionally-competent state. Note also that facultative heterochromatin formation does not usually involve DNA methylation, while constitutive heterochromatin formation does.
constitutive heterochromatin formation (GO:0140719)
Namespace: biological_process
Definition: The compaction of chromatin into heterochromatin, a conformation that is refractory to transcription and in that involves the methylation of histone H3K9. Constitutive heterochromatin cannot be converted back to euchromatin, the transcriptionally-active conformation.
Synonyms: constitutive heterochromatin assembly
Comment: Note that constitutive heterochromatin usually cannot be reprogrammed to a transcriptionally-competent state, as opposed to facultative heterochromatin, which can be reprogrammed. Note also that constitutive usually involves DNA methylation, while facultative heterochromatin formation does not.
subtelomeric heterochromatin (GO:0140720)
Namespace: cellular_component
Definition: Heterochromatin that is located adjacent to the telomere, and characterized by methylated H3 histone at lysine 9 (H3K9me2/H3K9me3).
nuclease inhibitor activity (GO:0140721)
Namespace: molecular_function
Definition: Binds to and modulates the activity of a nuclease.
mycophenolic acid biosynthetic process (GO:0140722)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of mycophenolic acid (MPA). MPA is the first isolated antibiotic natural product in the world obtained from a culture of Penicillium brevicompactum in 1893.
Synonyms: MPA anabolism; MPA biosynthesis; MPA formation; MPA synthesis; mycophenolic acid anabolism; mycophenolic acid biosynthesis; mycophenolic acid formation; mycophenolic acid synthesis
patulin biosynthetic process (GO:0140723)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of patulin, an acetate-derived tetraketide mycotoxin produced by several fungal species that shows antimicrobial properties against several bacteria.
Synonyms: patulin anabolism; patulin biosynthesis; patulin formation; patulin synthesis
positive regulation of patulin biosynthetic process (GO:0140724)
Namespace: biological_process
Definition: Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of patulin.
Synonyms: positive regulation of patulin anabolism; positive regulation of patulin formation; positive regulation of patulin synthesis
detoxification of free heme (GO:0140725)
Namespace: biological_process
Definition: Any process that reduces or removes the toxicity of free heme. These include transport of heme away from sensitive areas and to compartments or complexes whose purpose is sequestration of heme.
Synonyms: free heme detoxification
siRNA-mediated pericentric heterochromatin formation (GO:0140727)
Namespace: biological_process
Definition: The formation of pericentric heterochromatin by a process mediated by a small interfering RNA (siRNA).
Synonyms: RNAi-mediated heterochromatin assembly at centromere; siRNA dependent pericentric heterochromatin assembly; siRNA-dependent pericentric heterochromatin assembly; siRNA-dependent pericentric heterochromatin formation
GC-box binding (GO:0140728)
Namespace: molecular_function
Definition: Binding to a GC-box, a DNA motif with the consensus sequence GGGCGG that is located upstream of the start point of eukaryotic transcription units. The GC-box may occur in multiple copies or in either orientation relative to the transcription start site.
Synonyms: GC box binding; GC rich promoter region binding; GC-rich region binding; GC_rich_promoter_region binding
detoxification of endogenously produced metabolite (GO:0140729)
Namespace: biological_process
Definition: A process that reduces or removes the toxicity of an endogenously produced substance. Mechanisms of resistance to endogenously produced compounds include modification the compound, export, sequestration, or mutations in the target enzyme.
Synonyms: prevention of self-toxicity; self-resistance to bioactive secondary metabolite; self-resistance to endogenously produced compound; self-resistance to endogenously produced metabolite; self-resistance to endogenously produced toxin
amphiregulin production (GO:0140730)
Namespace: biological_process
Definition: The appearance of amphiregulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Amphiregulin (AREG) is a ligand of the epidermal growth factor receptor (EGFR), a widely expressed transmembrane tyrosine kinase. AREG is synthesized as a membrane-anchored precursor protein that can engage in juxtacrine signaling on adjacent cells. Alternatively, after proteolytic processing by cell membrane proteases, mainly TACE/ADAM17, AREG is secreted and behaves as an autocrine or paracrine factor.
Synonyms: AREG production
Comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select one of the 'regulation' children terms.
regulation of amphiregulin production (GO:0140731)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate, or extent of production of amphiregulin.
Synonyms: regulation of AREG production
positive regulation of amphiregulin production (GO:0140732)
Namespace: biological_process
Definition: Any process that activates or increases the frequency, rate or extent of production of amphiregulin.
Synonyms: positive regulation of AREG production
tRNA ligase activator activity (GO:0140733)
Namespace: molecular_function
Definition: Binds to and increases the activity of a tRNA ligase.
ammonium excretion (GO:0140734)
Namespace: biological_process
Definition: The elimination of ammonium ions from an excretory cell.
Synonyms: ammonia excretion