LiteFold/GO huggingface dataset:
Syp1 complex (GO:1990252)
Namespace: cellular_component
Definition: A protein complex that contributes to the endocytic process and bud growth in yeast. It is involved in the precise timing of actin assembly during endocytosis.
Synonyms: Syp1 dimer
cellular response to leucine starvation (GO:1990253)
Namespace: biological_process
Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of leucine.
keratin filament binding (GO:1990254)
Namespace: molecular_function
Definition: Binding to a keratin filament, an intermediate filament composed of acidic and basic keratins (types I and II), typically expressed in epithelial cells.
signal clustering (GO:1990256)
Namespace: biological_process
Definition: Grouping of multiple copies of a signal at a cellular location. May promote receptor clustering and alter the signal transduction response.
Synonyms: ligand clustering
piccolo-bassoon transport vesicle (GO:1990257)
Namespace: cellular_component
Definition: A cytoplasmic dense-core vesicle that transports a range of proteins including piccolo, bassoon, N-cadherin and syntaxin. The transported proteins may be associated with the external side of the vesicle, rather than being contained within the vesicle, therefore forming an aggregate of vesicle and proteins. Piccolo-bassoon transport vesicles (or PTVs) range in size from approximately 80 nm in diameter for dense core vesicles to 130 nm by 220 nm in area for aggregates. They are packaged via the trans-Golgi network before being transported through the axon.
Synonyms: PTV
obsolete histone glutamine methylation (GO:1990258)
Namespace: biological_process
Definition: OBSOLETE. The modification of a histone by addition of a methyl group to an glutamine residue.
Comment: This term was obsoleted because it represents a molecular function.
histone H2AQ104 methyltransferase activity (GO:1990259)
Namespace: molecular_function
Definition: Catalysis of the reaction: L-glutamine(104)-[histone H2A] + S-adenosyl-L-methionine = N(5)-methyl-L-glutamine(104)-[histone H2A] + S-adenosyl-L-homocysteine + H+. Note that this corresponds to Q105 in yeast.
Synonyms: histone glutamine methylase activity; histone glutamine methyltransferase activity; histone glutamine N-methyltransferase activity; histone-glutamine methyltransferase activity; histone-glutamine N-methyltransferase activity
Comment: Note that the residue position corresponds to the canonical human H2A2A histone (UniProtKB:Q6FI13); this residue is conserved across all eukaryotes. Note that this resudue is missing from the H2AZ clade. 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.
obsolete negative regulation of transcription from RNA polymerase II promoter by transcription factor localization involved in response to DNA damage checkpoint signaling (GO:1990260)
Namespace: biological_process
Definition: OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter using a mechanism that involves the localization of a transcription factor and initiated in response to the DNA damage checkpoint signaling.
Comment: This term was obsoleted because it represents a GO-CAM model.
pre-mRNA catabolic process (GO:1990261)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of the unspliced pre-mRNA (pre-messenger RNA).
Synonyms: pre-mRNA decay; unspliced RNA decay
anti-Mullerian hormone receptor signaling pathway (GO:1990262)
Namespace: biological_process
Definition: The series of molecular signals initiated by the binding of anti-Mullerian hormone to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription. Upon ligand binding, the receptor  forms a complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators.
Synonyms: anti-Mullerian hormone signaling pathway
Comment: An example of this is Amhr2 in M. musculus (Q8K592) a receptor for anti-mullerian hormone, described in PMID:23624077.
obsolete spore wall assembly MAPK cascade (GO:1990263)
Namespace: biological_process
Definition: OBSOLETE. A MAPK cascade that occurs as a result of deprivation of nourishment.
Synonyms: MAPK cascade in response to starvation; MAPK cascade involved in nutrient response signaling
Comment: This term was obsoleted because this pathway is poorly defined.
peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (GO:1990264)
Namespace: biological_process
Definition: Any peptidyl-tyrosine dephosphorylation that is involved in inactivation of protein kinase activity.
platelet-derived growth factor complex (GO:1990265)
Namespace: cellular_component
Definition: A protein complex consisting of two chains of platelet-derived growth factor (PDGF) subunits. PDGF dimers bind to PDGF receptors in the plasma membrane and induce receptor dimerization and activation. PDGFs are involved in a wide variety of signaling processes. PDGFs are found in all vertebrates where at least 2 different chains (A and B) exist. In human (and other mammals), four types of PDGF chains (A, B, C, and D) are known which form five different dimers (AA, AB, BB, CC and DD).
Synonyms: PDGF complex; PDGF-AA dimer; PDGF-AB dimer; PDGF-BB dimer; PDGF-CC dimer; PDGF-DD dimer
Comment: An example of this is PDGFA in human (P04085) in PMID:20534510 (inferred from direct assay).
neutrophil migration (GO:1990266)
Namespace: biological_process
Definition: The movement of a neutrophil within or between different tissues and organs of the body.
response to transition metal nanoparticle (GO:1990267)
Namespace: biological_process
Definition: 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 transition metal nanoparticle.
Synonyms: response to colloidal metal; response to neutral metal atoms
response to gold nanoparticle (GO:1990268)
Namespace: biological_process
Definition: 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 gold nanoparticle stimulus.
RNA polymerase II C-terminal domain phosphoserine binding (GO:1990269)
Namespace: molecular_function
Definition: Binding to phosphorylated serine residues in the C-terminal domain of RNA polymerase II.
Synonyms: RNA Pol II C-terminal domain phosphoserine binding; RNAP II C-terminal domain phosphoserine binding
platelet-derived growth factor receptor-ligand complex (GO:1990270)
Namespace: cellular_component
Definition: A tetrameric protein complex consisting of two platelet-derived growth factor (PDGF) receptor subunits and two PDGF ligand subunits. Binding of the PDGF ligand dimer to the PDGF receptor in the plasma membrane induces receptor dimerization and activation. PDGFs are involved in a wide variety of signaling processes and are found in all vertebrates. At least two different receptor chains (A and B) and four types of ligand chains (A, B, C, and D) are known forming a wide variety of combinations of receptor-ligand complexes.
Synonyms: PDGF complex; PDGF receptor-ligand complex; PDGF-AA-receptor alpha complex; PDGF-AB-receptor alpha complex; PDGF-AB-receptor beta complex; PDGF-BB-receptor alpha complex; PDGF-BB-receptor alpha-beta complex; PDGF-BB-receptor beta complex; PDGF-CC-receptor alpha complex; PDGF-CC-receptor alpha-beta complex; PDGF-CC-receptor beta complex; PDGF-DD-receptor alpha-beta complex; PDGF-DD-receptor beta complex; receptor-ligand complex
Comment: An example of this is PDGFA-PGFRA in human (UniProt symbols P04085, P16234) in PMID:7679113 (inferred from direct assay).
obsolete anti-Mullerian hormone (GO:1990271)
Namespace: molecular_function
Definition: OBSOLETE. Combining with anti-Mullerian hormone to initiate a change in cell activity.
Synonyms: anti-Mullerian hormone
Comment: An example of this is Amdh2 in M. musculus, UniprotKB:Q8K592-1 in PMID:23624077.
anti-Mullerian hormone receptor activity (GO:1990272)
Namespace: molecular_function
Definition: Combining with anti-Mullerian hormone to initiate a change in cell activity.
Comment: An example of this is Amdh2 in M. musculus, UniprotKB:Q8K592-1 in PMID:23624077.
snRNA 2,2,7-trimethylguanosine (TMG) capping (GO:1990273)
Namespace: biological_process
Definition: The sequence of enzymatic reactions by which a 2,2,7-trimethylguanosine cap structure is added to the 5' end of an snRNA. The snRNA capping process includes the formation of 7-methyl-G caps found on all RNA polymerase II transcripts, followed by hypermethylation at the 2' position of the guanosine residue to convert a mono-methylated cap to a 2,2,7-trimethylguanosine cap structure. Note that the pol III transcribed U6 snRNA is also TMG capped.
Synonyms: snRNA 2,2,7-trimethylguanosine (TMG) cap formation; snRNA 5'-end processing; snRNA capping
obsolete mitotic actomyosin contractile ring disassembly (GO:1990274)
Namespace: biological_process
Definition: OBSOLETE. Any disaggregation of an actomyosin contractile ring into its constituent components that is involved in a mitotic cell cycle.
Comment: The reason for obsoletion is that the data from the paper for which the term was requested can be accurately described using another term
preribosome binding (GO:1990275)
Namespace: molecular_function
Definition: Binding to a preribosome.
RNA 5'-gamma-phosphate methyltransferase activity (GO:1990276)
Namespace: molecular_function
Definition: Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the 5'-gamma-phosphate in an RNA molecule.
Synonyms: RNA 5'-methyltransferase activity
parasexual reproduction with cellular fusion (GO:1990277)
Namespace: biological_process
Definition: A type of reproduction in which new individuals are produced from two individuals, with the fusion of two somatic cells.
Synonyms: mating; parasexual conjugation with cellular fusion
obsolete positive regulation of MBF transcription factor activity (GO:1990278)
Namespace: biological_process
Definition: OBSOLETE. Any process that activates or increases the frequency, rate or extent of activity of the transcription factor MBF.
Synonyms: positive regulation of MBF transcription factor activity
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
obsolete negative regulation of MBF transcription factor activity (GO:1990279)
Namespace: biological_process
Definition: OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor MBF.
Synonyms: negative regulation of MBF transcription factor activity
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
RNA localization to chromatin (GO:1990280)
Namespace: biological_process
Definition: A process in which RNA is transported to and maintained in a part of a chromosome that is organized into chromatin.
Synonyms: RNA localisation to chromatin
efflux pump complex (GO:1990281)
Namespace: cellular_component
Definition: A protein complex that is capable of efflux transmembrane transporter activity.
Synonyms: efflux pump; efflux transmembrane transporter complex
obsolete peptidyl-threonine trans-autophosphorylation (GO:1990294)
Namespace: biological_process
Definition: OBSOLETE. The phosphorylation of a peptidyl-threonine to form peptidyl-O-phospho-L-threonine on an identical protein. For example, phosphorylation by the other kinase within a homodimer.
Comment: This term was obsoleted because it represents a molecular function.
post-anaphase microtubule array (GO:1990295)
Namespace: cellular_component
Definition: A cytoskeletal part that consists of an array of microtubules and associated molecules that forms at the end of anaphase, and in which microtubules are nucleated from an equatorial microtubule organizing center.
Synonyms: PAA; post-anaphase array
Comment: The best-characterized example is found in the fission yeast Schizosaccharomyces pombe. The eMTOC is cortical, but the post-anaphase array microtubules are not exclusively cortical.
bub1-bub3 complex (GO:1990298)
Namespace: cellular_component
Definition: Protein complex that associates with the kinetochores.
Bub1-Bub3 complex localization to kinetochore (GO:1990299)
Namespace: biological_process
Definition: A cellular protein complex localization that acts on a Bub1-Bub3 complex; as a result, the complex is transported to, or maintained in, a specific location at the kinetochore.
cellulosome binding (GO:1990300)
Namespace: molecular_function
Definition: Binding to a cellulosome, an extracellular multi-enzyme complex containing several enzymes aligned on a non-catalytic scaffolding that functions to hydrolyze plant cell wall polysaccharides.
Synonyms: scaffoldin complex binding
Bre1-Rad6 ubiquitin ligase complex (GO:1990302)
Namespace: cellular_component
Definition: A ubiquitin ligase complex consisting of Bre1 and Rad6 that mediates monoubiquitination of histone H2B to form H2BK123ub1. H2BK123ub1 gives a specific tag for epigenetic transcriptional activation, elongation by RNA polymerase II, telomeric silencing, and is also a prerequisite for H3K4me and H3K79me formation. It thereby plays a central role in histone code and gene regulation. It also modulates the formation of double-strand breaks during meiosis.
Synonyms: Bre1-Rad6 complex
Comment: This complex has been identified in Saccharomyces cerevisiae (P19812) - see PMID:19531475 (inferred from direct assay).
UBR1-RAD6 ubiquitin ligase complex (GO:1990303)
Namespace: cellular_component
Definition: A ubiquitin ligase complex consisting of UBR1 and RAD6 components. It polyubiquitinates proteins containing non-acetylated N-terminal residues causing their subsequent degradation by the proteasome as part of the Ac/N-End Rule pathway. It recognizes non-acetylated N-terminal methionine if it is followed by a hydrophobic residue. Additionally, it acts in an N-end rule independent manner as a component of a novel quality control pathway for proteins synthesized on cytosolic ribosomes.
Synonyms: UBR1-RAD6 complex
Comment: This complex has been identified in Saccharomyces cerevisiae (P19812) - see PMID:19531475 (inferred from direct assay).
MUB1-RAD6-UBR2 ubiquitin ligase complex (GO:1990304)
Namespace: cellular_component
Definition: A ubiquitin ligase complex consisting of MUB1, RAD6 and UBR2 components. It ubiquitinates, and targets for destruction, the RPN4 transcription factor, which upregulates the proteasome genes. The binding of MUB1 may position the RPN4 ubiquitylation site proximal to the Ubiquitin-RAD6 thioester and allow the transfer of Ubiquitin from RAD6 to RPN4. One of its components, MUB1, is a short-lived protein ubiquitinated by the UBR2-RAD6 ubiquitin conjugating enzyme.
Comment: This complex has been identified in Saccharomyces cerevisiae (UniProt symbol P19812) - see PMID:18070918.
RAD6-UBR2 ubiquitin ligase complex (GO:1990305)
Namespace: cellular_component
Definition: A ubiquitin ligase complex consisting of RAD6 and UBR2 components. It may act in a quality control pathway for proteins synthesized on cytosolic ribosomes. The UBR2 component lacks sequence motifs required for N-end rule degradation.
Synonyms: RAD6-UBR2 complex
Comment: This complex has been identified in Saccharomyces cerevisiae (P19812) - see PMID:15504724
RSP5-BUL ubiquitin ligase complex (GO:1990306)
Namespace: cellular_component
Definition: A ubiquitin ligase complex consisting of RSP5 and BUL components. It polyubiquinates plasma membrane transporters and permeases, required for their endocytosis and subsequent degradation in the vacuole. BUL1 or BUL2, respectively, bind to the target protein, enabling ubiquitylation by Rsp5. Phosphorylation of BUL proteins results in binding to 14-3-3 proteins, protecting the permeases from down-regulation.
Synonyms: RSP5-BUL1 complex; RSP5-BUL2 complex
Comment: This complex has been identified in Saccharomyces cerevisiae (P19812) - see PMID:9931424
type-I dockerin domain binding (GO:1990308)
Namespace: molecular_function
Definition: Binding to a type-I dockerin domain of a protein. Type-I dockerin domain is the binding partner of type-1 cohesin domain.
type-II dockerin domain binding (GO:1990309)
Namespace: molecular_function
Definition: Binding to a type-II dockerin domain of a protein. Type-II dockerin domain is the binding partner of type-II cohesin domain.
type-III dockerin domain binding (GO:1990310)
Namespace: molecular_function
Definition: Binding to a type-III dockerin domain of a protein. Type-III dockerin domain is the binding partner of type-III cohesin domain.
type-I cohesin domain binding (GO:1990311)
Namespace: molecular_function
Definition: Binding to a type-I cohesin domain of a protein. Type-I cohesin domain is the binding partner of type-I dockerin domain.
type-II cohesin domain binding (GO:1990312)
Namespace: molecular_function
Definition: Binding to a type-II cohesin domain of a protein. Type-II cohesin domain is the binding partner of type-II dockerin domain.
type-III cohesin domain binding (GO:1990313)
Namespace: molecular_function
Definition: Binding to a type-III cohesin domain of a protein. Type-III cohesin domain is the binding partner of type-III dockerin domain.
cellular response to insulin-like growth factor stimulus (GO:1990314)
Namespace: biological_process
Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin-like growth factor stimulus.
Synonyms: cellular response to insulin-like growth factor
Mcs4 RR-MAPKKK complex (GO:1990315)
Namespace: cellular_component
Definition: A protein complex that consists of a phospho relay component and a MAPK cascade component. The complex is involved in signaling oxidative stress and osmostress.
Comment: In S. pombe it consists of Mpr1, Tdh1, Mcs4, Win1, Wis4 and Wis1.
Atg1/ULK1 kinase complex (GO:1990316)
Namespace: cellular_component
Definition: A protein complex consisting of Atg1 (or Atg1 homologs e.g. ULK1, ULK2 in mammals) and Atg13 along with other proteins that regulate its function (e.g. Atg17 in yeast or RB1CC1(FIP200) in mammals). This complex has serine/threonine protein kinase activity and is involved in autophagosome formation.
Synonyms: ATG1 kinase complex; ATG1-ATG13 complex; ATG1/ULK1 signaling complex; Atg1p signalling complex; autophagy-initiation complex; ULK complex; ULK1 complex; ULK1 signaling complex; ULK1-ATG13-FIP200 complex; ULK1-ATG13-RB1CC1 complex
Gin4 complex (GO:1990317)
Namespace: cellular_component
Definition: A protein complex involved in septin ring formation during mitosis. In Saccharomyces cerevisiae it consists of BNI5, CDC3, CDC10, CDC11, CDC12, GIN4, NAP1 and SHS1. At least 2 GIN4 molecules are involved.
Synonyms: Gin4-septin complex
collagen type XIX trimer (GO:1990318)
Namespace: cellular_component
Definition: A collagen homotrimer made of three alpha1(XIX) collagen chains, each presenting interrupted triple helical collagen domains. Localizes to basement membrane ECMs, not known to associate with any fibrillar collagens that are predominantly found in the interstitial extracellular matrix.
Comment: The collagen XIX trimer is often classified as a FACIT collagen trimer (which stands for Fibril Associated Collagens with Interrupted Triple helices) because of the presence of interrupted triple helical collagen domains, similar to other FACIT members. However, evidence show that collagen XIX localizes to basement membrane ECMs, and none of the basement membrane collagens are fibrillar.
collagen type XX trimer (GO:1990319)
Namespace: cellular_component
Definition: A collagen homotrimer of alpha1(XX) chains.
collagen type XXI trimer (GO:1990320)
Namespace: cellular_component
Definition: A collagen homotrimer of alpha1(XXI) chains; type XXI collagen triple helices found in the extracellular matrix component of blood vessel walls and in the cytoplasm of cultured human aortic smooth muscle.
collagen type XXII trimer (GO:1990321)
Namespace: cellular_component
Definition: A collagen homotrimer of alpha1(XXII) chains; type XXII collagen triple helices acts as a cell adhesion ligand for skin epithelial cells and fibroblasts.
collagen type XXIII trimer (GO:1990322)
Namespace: cellular_component
Definition: A collagen homotrimer of alpha1(XXIII) chains; type XXIII collagen triple helices span the plasma membrane.
collagen type XXIV trimer (GO:1990323)
Namespace: cellular_component
Definition: A collagen homotrimer of alpha1(XXIV) chains; type XXIV collagen triple helices may participate in regulating type I collagen fibrillogenesis at specific anatomical locations during fetal development.
collagen type XXVI trimer (GO:1990324)
Namespace: cellular_component
Definition: A collagen homotrimer of alpha1(XXVI) chains.
collagen type XXVII trimer (GO:1990325)
Namespace: cellular_component
Definition: A collagen homotrimer of alpha1(XXVII) chains. These trimers form thin, non-striated fibrils. Type XXVII collagen triple helices play a role during the calcification of cartilage and the transition of cartilage to bone.
collagen type XXVIII trimer (GO:1990326)
Namespace: cellular_component
Definition: A collagen homotrimer of alpha1(XXVIII) chains.
collagen type XXV trimer (GO:1990327)
Namespace: cellular_component
Definition: A collagen homotrimer of alpha1(XXV) chains; type XXV collagen triple helices span the plasma membrane.
RPB4-RPB7 complex (GO:1990328)
Namespace: cellular_component
Definition: A protein complex that cycles between the nucleus where it is part of the RNA polymerase II and the cytoplasmic mRNA processing body where it mediates the two major cytoplasmic mRNA decay pathways.
Synonyms: RNA polymerase II, RPB4-RPB7 subcomplex
IscS-TusA complex (GO:1990329)
Namespace: cellular_component
Definition: A heterotetrameric protein complex involved in the sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm5s2U) at tRNA wobble positions. In E. coli it consists of a central IscS dimer with the two TusA protomers bound to one of the IscS units each via persulfide (-SSH) groups.
IscS-IscU complex (GO:1990330)
Namespace: cellular_component
Definition: A heterotetrameric protein complex involved in the sulfur transfer during iron-sulfur cluster assembly and in the modification of tRNA wobble positions. In E. coli it consists of a central IscS dimer with the IscU protomers attached to one of the IscS units each via a disulfide (-SSH) group.
Hpa2 acetyltransferase complex (GO:1990331)
Namespace: cellular_component
Definition: A tetrameric protein complex capable of acetyltransferase activity. It can catalyze the transfer of an acetyl group from acetyl-CoA to an acceptor residue on histone H-3, histone H-4, or on polyamines. The complex is also capable of acetylating certain small basic proteins. The two Hpa2 dimers that make up the tetramer are held together by interactions between the bound acetyl-CoA molecules.