LiteFold/GO huggingface dataset:
obsolete hercynylselenocysteine lyase activity (selenoneine-forming) (GO:1990412)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: hercynylselenocysteine + 2H+ = selenoneine + pyruvate + ammonium.
Comment: This term was obsoleted based on PMID:36071162 that has demonstrated that this reaction does not take place.
eyespot apparatus (GO:1990413)
Namespace: cellular_component
Definition: A small pigmented organelle used in single-celled organisms to detect light.
Synonyms: eyespot; stigma
replication-born double-strand break repair via sister chromatid exchange (GO:1990414)
Namespace: biological_process
Definition: The repair of a replication-born double-strand DNA break in which the DNA molecule is repaired using the homologous sequence of the sister chromatid which serves as a template to repair the breaks.
Synonyms: replication-born DSB repair by SCE
snoRNA release from pre-rRNA (GO:1990417)
Namespace: biological_process
Definition: The release of snoRNA from pre-rRNA.
Comment: An example of this process is yeast HAS1 from PMID:16908538, inferred from mutant phenotype assay.
response to insulin-like growth factor stimulus (GO:1990418)
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 an insulin-like growth factor stimulus.
obsolete response to elemental metal (GO:1990419)
Namespace: biological_process
Definition: OBSOLETE. 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 elemental metal stimulus.
Synonyms: response to elemental metal
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
obsolete establishment of septation initiation network asymmetry (GO:1990420)
Namespace: biological_process
Definition: OBSOLETE. The septation initiation signaling process by which the activity of the septation initiation network (SIN) is activated asymmetrically on the spindle pole bodies.
Synonyms: establishment of SIN asymmetry
Comment: The reason for obsoletion is that this term is pre-composed and should be represented as a GO-CAM model.
RZZ complex (GO:1990423)
Namespace: cellular_component
Definition: A kinetochore component required for both meiotic and mitotic spindle assembly checkpoints.
Synonyms: Rod-Zwilch-Zw10 complex
Comment: Example annotations for this term would be D. melanogaster mit(1)15 (Q9W4X9), rod and zwilch (Q9VA00).
protein arginine kinase activity (GO:1990424)
Namespace: molecular_function
Definition: Catalysis of the reaction: ATP + a protein arginine = ADP + protein arginine phosphate.
Synonyms: protein-arginine kinase activity
Comment: This reaction occurs in bacterial species e.g. Bacillus subtilis.
ryanodine receptor complex (GO:1990425)
Namespace: cellular_component
Definition: A voltage-gated calcium-release channel complex of the sarcoplasmic or endoplasmic reticulum. It plays an important role in the excitation-contraction (E-C) coupling of muscle cells. RyR comprises a family of ryanodine receptors, widely expressed throughout the animal kingdom.
Synonyms: RyR
Comment: An example of this is RyR1 in rabbit (P11716) in PMID:2550460 (inferred from electron microscopy).
mitotic recombination-dependent replication fork processing (GO:1990426)
Namespace: biological_process
Definition: Replication fork processing that includes recombination between DNA near the arrested fork and homologous sequences. Proteins involved in homologous recombination are required for replication restart.
Synonyms: homologous recombination dependent replication fork recovery; homologous recombination-dependent replication fork processing; mitotic recombination involved in collapsed replication fork processing; mitotic recombination involved in recovery from replication fork arrest; mitotic recombination involved in recovery from replication fork stalling; mitotic recombination involved in replication fork processing; mitotic recombination involved in replication fork restart; mitotic recombination involved in replication restart
stereocilia tip-link density (GO:1990427)
Namespace: cellular_component
Definition: An electron-dense plaque at either end of a stereocilia tip link that provides the anchor in the stereocilia membrane.
miRNA transport (GO:1990428)
Namespace: biological_process
Definition: The directed movement of microRNA (miRNA) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore.
Synonyms: microRNA transport
peroxisomal importomer complex (GO:1990429)
Namespace: cellular_component
Definition: A protein complex responsible for transporting proteins into the peroxisomal matrix. An example of this complex is Pex14 found in S. cerevisae which has 9 core components and 12 transient interaction partners.
Synonyms: peroxisomal import pore; peroxisomal protein import machinery; Pex14 complex; Pex17p-Pex14p docking complex
extracellular matrix protein binding (GO:1990430)
Namespace: molecular_function
Definition: Binding to a protein that is part of an extracellular matrix.
priRNA 3'-end processing (GO:1990431)
Namespace: biological_process
Definition: The process of forming the mature 3' end of a priRNA molecule.
Synonyms: primal small RNA 3'-end processing; priRNA 3' end processing
siRNA 3'-end processing (GO:1990432)
Namespace: biological_process
Definition: The process of forming the mature 3' end of a siRNA molecule.
Synonyms: siRNA 3' end processing; small interfering RNA 3'-end processing
lower tip-link density (GO:1990434)
Namespace: cellular_component
Definition: An electron-dense plaque at the lower end of a stereocilia tip link that provides the anchor in the stereocilia membrane at the tip of the stereocilium from which the tip link rises.
Synonyms: LTLD
upper tip-link density (GO:1990435)
Namespace: cellular_component
Definition: An electron-dense plaque at the upper end of a stereocilia tip link that provides the anchor in the stereocilia membrane on the side of the stereocilium where the tip link ends.
Synonyms: UTLD
obsolete MAPK cascade involved in oxidative stress signaling pathway (GO:1990436)
Namespace: biological_process
Definition: OBSOLETE. The series of molecular signals in which a MAP kinase cascade activated by oxidative stress relays one or more of the signals, MAP kinase cascades involve at least three protein kinase activities and culminate in the phosphorylation and activation of a MAP kinase. Just FYI in pombe the osmotic stress and oxidative stress MAPK cascade involve many of the same proteins, but the pathways are slightly different, therefore Im req this term.
Synonyms: MAPK cascade involved in oxidative stress signaling pathway
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
snRNA 2'-O-methylation (GO:1990437)
Namespace: biological_process
Definition: The posttranscriptional addition of a methyl group to the 2' oxygen atom of a nucleotide residue in an snRNA molecule.
U6 2'-O-snRNA methylation (GO:1990438)
Namespace: biological_process
Definition: The posttranscriptional addition a methyl group to the 2'-oxygen atom of a nucleotide residue in an U6 snRNA molecule.
MAP kinase serine/threonine phosphatase activity (GO:1990439)
Namespace: molecular_function
Definition: Catalysis of the reaction: MAP kinase threonine phosphate + H2O = MAP kinase threonine + phosphate and MAP kinase serine phosphate + H2O = MAP kinase serine + phosphate.
obsolete positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)
Namespace: biological_process
Definition: OBSOLETE. Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter as a result of an endoplasmic reticulum stress.
Synonyms: activation of transcription from RNA polymerase II promoter in response to ER stress; ER stress-induced upregulation of transcription; stimulation of transcription from RNA polymerase II promoter in response to ER stress; up-regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress; up-regulation of transcription induced by ER stress; upregulation of Pol II transcription induced by ER stress; upregulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress
Comment: This term was obsoleted because it represents a GO-CAM model.
obsolete negative regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990441)
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 as a result of an endoplasmic reticulum stress.
Synonyms: down regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress; down-regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress; ER stress-induced negative regulation of transcription from RNA polymerase II promoter; inhibition of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress; negative regulation of transcription from RNA polymerase II promoter in response to ER stress; reduction of transcription from RNA polymerase II promoter under ER stress; repression of transcription from RNA polymerase II promoter under ER stress; suppression of transcription from RNA polymerase II promoter under ER stress
Comment: This term was obsoleted because it represents a GO-CAM model.
intrinsic apoptotic signaling pathway in response to nitrosative stress (GO:1990442)
Namespace: biological_process
Definition: The series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to nitrosative stress; a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions.
Synonyms: nitrosative stress-induced apoptosis; nitrosative stress-induced intrinsic apoptotic signaling pathway
peptidyl-threonine autophosphorylation (GO:1990443)
Namespace: biological_process
Definition: The phosphorylation by a protein of one or more of its own threonine amino acid residues, or a threonine residue on an identical protein.
F-box domain binding (GO:1990444)
Namespace: molecular_function
Definition: Binding to an F-box domain of a protein.
obsolete Multiciliate cell differentiation (GO:1990445)
Namespace: biological_process
Definition: OBSOLETE. The process in which a relatively unspecialized cell acquires features of a multiciliated cell, a specialized epithelial cell type that extends anywhere from 150 to 200 motile cilia per cell in order to produce a vigorous fluid flow critical to human health in several organ systems.
Synonyms: Multiciliate cell differentiation
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
U1 snRNP binding (GO:1990446)
Namespace: molecular_function
Definition: Binding to a U1 small nuclear ribonucleoprotein particle.
exon-exon junction complex binding (GO:1990448)
Namespace: molecular_function
Definition: Binding to an exon-exon junction complex, a protein complex deposited by the spliceosome upstream of messenger RNA exon-exon junctions. The exon-exon junction complex provides a binding platform for factors involved in mRNA export and nonsense-mediated mRNA decay.
Synonyms: EJC binding
obsolete amylin receptor (GO:1990449)
Namespace: cellular_component
Definition: OBSOLETE. A G protein-coupled signalling receptor complex consisting of the calcitonin receptor and a receptor activity-modifying protein (RAMP). Amylin is produced in beta-islet cells of the pancreas. It is implicated in selective inhibition of insulin-stimulated glucose utilization and glycogen deposition in muscle, gastric emptying, gastric acid secretion, postprandial glucagon secretion and food intake and aids weight loss.
Synonyms: AMY1 receptor; AMY2 receptor; AMY3 receptor; amylin receptor; CALCR-RAMP1 receptor; CALCR-RAMP2 receptor; CALCR-RAMP3 receptor
Comment: An example of this is CALCR in human (P30988) in PMID:10871269.
linear polyubiquitin binding (GO:1990450)
Namespace: molecular_function
Definition: Binding to a linear polymer of ubiquitin. Linear ubiquitin polymers are formed by linking the amino-terminal methionine (M1) of one ubiquitin molecule to the carboxy-terminal glycine (G76) of the next.
Synonyms: M1-linked ubiquitin chain binding
cellular stress response to acidic pH (GO:1990451)
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 a disturbance in the homeostasis of organismal or cellular pH (with pH < 7). pH is a measure of the acidity or basicity of an aqueous solution.
Synonyms: cellular stress response to acidity
Comment: An example of this is NOX1 in human (Q9Y5S8) in PMID:10615049.
Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)
Namespace: cellular_component
Definition: A ubiquitin ligase complex containing Parkin (PARK2), the F-box protein FBXW7 (also called SEL-10) and a cullin from the Cul1 subfamily; substrate specificity is conferred by the F-box protein.
Synonyms: Park2-FBXW7-Cul1 complex; Parkin-FBXW7-Cul1 protein complex; Parkin-HSel-10-Cullin-1 complex; Parkin/Cul1/F-box protein complex; PRKN-FBXW7-Cul1 complex
TINTIN complex (GO:1990453)
Namespace: cellular_component
Definition: A protein complex involved in the disassembly and subsequent reassembly of nucleosomes. It associates with the coding region of transcriptionally active genes where it interacts with the RNA polymerase II and affects its processivity during co-transcriptional RNA processing and maturation. It exists as a functionally independent part of the NuA4 complex.
Synonyms: eaf5/7/3 complex; nucleosome disassembly/reassembly complex
L-type voltage-gated calcium channel complex (GO:1990454)
Namespace: cellular_component
Definition: A type of voltage-dependent calcium channel responsible for excitation-contraction coupling of skeletal, smooth, and cardiac muscle. 'L' stands for 'long-lasting' referring to the length of activation.
Synonyms: cardiac muscle L-type voltage-gated calcium channel complex; skeletal muscle L-type voltage-gated calcium channel complex
Comment: Examples of this are CACNA1S, CACNA2D1, CACNB1, CACNG1 in rabbit (UniProt symbol P07293, P13806, P19517 and P19518) in PMID:12946355 (inferred from direct assay).
PTEN phosphatase complex (GO:1990455)
Namespace: cellular_component
Definition: A phospholipid phosphatase complex that catalyses the hydrolysis of the second messenger PtdIns (3,4,5)P3. Will also dephosphorylate PtdIns(3,4)P2, PtdIns3P, and Ins(1,3,4,5)P4. Dimerization is critical for its lipid phosphatase function.
Synonyms: phosphatase and tensin homolog; phosphatase and tensin homolog deleted on chromosome ten homodimer; phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN homodimer
Comment: An example of this is PTEN in human (P60484) in PMID:24766807 (inferred from direct assay).
lipooligosaccharide binding (GO:1990458)
Namespace: molecular_function
Definition: Binding to lipooligosaccharide. Lipooligosaccharides (LOSs) are the major glycolipids expressed on mucosal Gram-negative bacteria.
Synonyms: endotoxin binding; LOS binding
Comment: ChEBI distinguishes an oligosaccharide from a polysaccharide as the latter being anything of length 10 or greater.
transferrin receptor binding (GO:1990459)
Namespace: molecular_function
Definition: Binding to a transferrin receptor.
leptin receptor binding (GO:1990460)
Namespace: molecular_function
Definition: Binding to a leptin receptor.
detoxification of iron ion (GO:1990461)
Namespace: biological_process
Definition: Any process that reduces or removes the toxicity of iron ion. These include transport of iron away from sensitive areas and to compartments or complexes whose purpose is sequestration of iron ion.
omegasome (GO:1990462)
Namespace: cellular_component
Definition: Omega-shaped (as in the Greek capital letter) intracellular membrane-bounded organelle enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. Omegasomes are the first step of the formation of autophagosomes via the phagophore assembly sites.
lateral cortical node (GO:1990463)
Namespace: cellular_component
Definition: A protein complex that is anchored at the cortical face of the plasma membrane, and contains proteins involved in regulating cell cycle progression. In Schizosaccharomyces pombe, lateral cortical nodes are several megadaltons in size, and contain Slf1, which anchors the complex at the membrane, and the methyltransferase Skb1 in stoichiometric quantities, and may contain other proteins.
Synonyms: Skb1-containing cortical node
(2R)-hydroxyacid dehydrogenase (quinone) activity (GO:1990464)
Namespace: molecular_function
Definition: Catalysis of the reaction: a (2R)-2-hydroxycarboxylate + a quinone = a 2-oxocarboxylate + a quinol.
Synonyms: (R)-2-hydroxy acid dehydrogenase activity; (R)-2-hydroxy-acid:(acceptor) 2-oxidoreductase activity; (R)-2-hydroxyacid:quinone oxidoreductase activity; D-2-hydroxyacid dehydrogenase (quinone) activity; D-lactate dehydrogenase (quinone) activity; D-lactate dehydrogenase activity; D-lactate:quinone oxidoreductase activity
Comment: (R)-lactate, (R)-malate and meso-tartrate are good substrates. Ubiquinone-1 and the dye 2,6-dichloroindophenol can act as acceptors; NAD+ and NADP+ are not acceptors.
obsolete aldehyde oxygenase (deformylating) activity (GO:1990465)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction a long-chain aldehyde + O2 + 2 NADPH = an alkane + formate + H2O + 2 NADP+.
Comment: This term was obsoleted because it represents the same reaction as aldehyde decarbonylase activity ; GO:0071771.
protein autosumoylation (GO:1990466)
Namespace: biological_process
Definition: The sumoylation by a protein of one or more of its own amino acid residues, or residues on an identical protein.
Synonyms: protein auto-sumoylation; protein self-sumoylation
NuA3a histone acetyltransferase complex (GO:1990467)
Namespace: cellular_component
Definition: A NuA3 complex that catalyzes the acetylation of Histone H3. In S. cerevisiae, this complex consists of Eaf6p, Nto1p, Sas3p, Taf14p, Yng1p and associates with H3K4me3 using Yng1p.
NuA3b histone acetyltransferase complex (GO:1990468)
Namespace: cellular_component
Definition: A NuA3 complex that catalyzes the acetylation of Histone H3. In S. cerevisiae, this complex consists of Eaf6p, Nto1p, Sas3p, Taf14p, Pdp3 and associates with H3K4me3 via Pdp3p.
Rhino-Deadlock-Cutoff Complex (GO:1990469)
Namespace: cellular_component
Definition: Protein complex found in Drosophila consisting of the gene products of cuff, del and rhi. It regulates the licensing of transcription of dual-strand PIWI interacting RNA (piRNA) source loci by binding to dual-strand-cluster chromatin, probably via the H3K9me3-binding activity of Rhi. Rhi binding brings the putative termination cofactor Cuff in close proximity to the nascent piRNA precursor transcript which it appears to protect from degradation.
Synonyms: RDC complex; rhi-del-cuff complex
Comment: An example of this is cuff in Drosophila melanogaster (Q9V629) in PMID:24906153.
piRNA cluster binding (GO:1990470)
Namespace: molecular_function
Definition: Binding to piRNA clusters, double-stranded DNA regions that give rise to PIWI-interacting RNAs (piRNAs).
Comment: An example of this is rhi in Drosophila melanogaster (Q7JXA8) in PMID:24906153 (inferred from direct assay).
piRNA dual-strand cluster binding (GO:1990472)
Namespace: molecular_function
Definition: Binding to dual-strand piRNA clusters, double-stranded DNA regions that give rise to PIWI-interacting RNAs (piRNAs) where piRNAs originate from both DNA strands via noncanonical transcription.
Comment: An example of this is rhi in Drosophila melanogaster (Q7JXA8) in PMID:24906153 (inferred from direct assay).
ciliary targeting signal binding (GO:1990473)
Namespace: molecular_function
Definition: Binding to a ciliary targeting sequence, a specific peptide sequence that acts as a signal to localize a membrane protein to the ciliary membrane.
Synonyms: CTS binding
synaptic vesicle, readily releasable pool (GO:1990474)
Namespace: cellular_component
Definition: A synaptic vesicle belonging to the pool of vesicles that are the first to be released as a result of chemical or electrical stimulation e.g. by an action potential, have the highest presynaptic membrane fusion probability and correspond to about 1% of the total number of synaptic vesicles at a resting terminal bouton.
Synonyms: readily releasable pool of synaptic vesicles; RRP
synaptic vesicle, resting pool (GO:1990476)
Namespace: cellular_component
Definition: A synaptic vesicle belonging to the pool that remain unreleased even after prolonged stimulation causes a saturating degree of vesicular turnover. 50-80% of the total number of synaptic vesicles at a resting terminal bouton are in this pool.
Synonyms: reserve pool of synaptic vesicles; resting pool of synaptic vesicles
MTREC complex (GO:1990477)
Namespace: cellular_component
Definition: Protein complex formed by an RNA binding protein Red1, an RNA helicase Mtl1, Red5, Rmn1, Iss10/Pir1, and Ars2/Pir2. This complex is required for the recruitment of the nuclear exosome to Mmi1 nuclear focus. It is likely related to the human CBCN complex. This complex is also known as RNA silencing (NURS) complex.
Synonyms: Mtl1-Red1 core complex; NURS complex; PAXT complex
response to ultrasound (GO:1990478)
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 an ultrasonic stimulus.
obsolete geranyl diphosphate synthase (GO:1990480)
Namespace: molecular_function
Definition: OBSOLETE. Catalyzes the condensation of dimethylallyl diphosphate and isopentenyl diphosphate to geranyl diphosphate, the key precursor of monoterpene biosynthesis.
Comment: This term was obsoleted at the TermGenie Gatekeeper stage.
mRNA pseudouridine synthesis (GO:1990481)
Namespace: biological_process
Definition: The intramolecular conversion of uridine to pseudouridine in an mRNA molecule.
Synonyms: mRNA pseudouridylation
sphingolipid alpha-glucuronosyltransferase activity (GO:1990482)
Namespace: molecular_function
Definition: Catalysis of the reaction: UDP-glucuronate + inositol phosphorylceramide (IPC) = UDP + GlcA-IPC.
Synonyms: inositol phosphorylceramide glucuronosyltransferase activity
obsolete Clr6 histone deacetylase complex I'' (GO:1990483)
Namespace: cellular_component
Definition: OBSOLETE. A histone deacetylase complex involved in chromatin organization. In Schizosaccharomyces pombe this complex consists of Clr6, Nts1, Mug165, and Png3.
Comment: The reason for obsoletion is that there is no evidence that this function/process/component exists.
aerobic lactate catabolic process (GO:1990484)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of lactate (2-hydroxypropanoic acid) in the presence of oxygen.
Synonyms: aerobic lactic acid catabolic process
anaerobic lactate catabolic process (GO:1990485)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of lactate (2-hydroxypropanoic acid) in the absence of oxygen.
Synonyms: anaerobic lactic acid catabolic process