LiteFold/GO huggingface dataset:
mRNA regulatory element binding translation repressor activity (GO:0000900)
Namespace: molecular_function
Definition: Antagonizes the ribosome-mediated translation of mRNA into a polypeptide via direct binding (through a selective and non-covalent interaction) to nucleic acid.
Synonyms: translation repressor activity, mRNA regulatory element binding; translation repressor activity, nucleic acid binding
cytokinesis (GO:0000910)
Namespace: biological_process
Definition: The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
Synonyms: cell cycle cytokinesis; cytokinesis involved in cell cycle
Comment: Note that this term should not be used for direct annotation. When annotating eukaryotic species, mitotic or meiotic cytokinesis should always be specified for manual annotation and for prokaryotic species use 'FtsZ-dependent cytokinesis ; GO:0043093' or Cdv-dependent cytokinesis ; GO:0061639. Also, note that cytokinesis does not necessarily result in physical separation and detachment of the two daughter cells from each other.
cytokinesis by cell plate formation (GO:0000911)
Namespace: biological_process
Definition: The process of dividing the cytoplasm of a parent cell where a structure forms in the cytoplasm and grows until reaching the plasma membrane, thereby completely separating the cytoplasms of adjacent progeny cells. An example of this is found in Arabidopsis thaliana.
cell plate assembly (GO:0000919)
Namespace: biological_process
Definition: The process of assembly, maturation, and growth of the cell plate to the cell periphery in cells that divide by cell plate formation; often involves deposition of cell wall material in and around the phragmoplast.
Synonyms: cell plate formation
equatorial microtubule organizing center (GO:0000923)
Namespace: cellular_component
Definition: A microtubule organizing center formed by a band of gamma-tubulin that is recruited to a circumferential band of F-actin at the midpoint of a cell and which nucleates microtubules from the cell division site at the end of mitosis.
Synonyms: EMTOC; equatorial microtubule organising centre
GARP complex (GO:0000938)
Namespace: cellular_component
Definition: A quatrefoil tethering complex required for retrograde traffic from the early endosome back to the late Golgi and biogenesis of cytoplasmic vesicles.
Synonyms: Golgi associated retrograde protein complex; VFT tethering complex; Vps fifty three tethering complex
inner kinetochore (GO:0000939)
Namespace: cellular_component
Definition: The region of a kinetochore closest to centromeric DNA which contains many CENP proteins organized in various subcomplexes including CENP-C, CENP-LN, CENP-HIKM, CENP-OPQUR and CENP-TWSX, but excluding the CENP-A containing heterochromatin.
Synonyms: condensed chromosome inner kinetochore; condensed nuclear chromosome inner kinetochore; inner centromere core complex; inner kinetochore of condensed chromosome; inner kinetochore of condensed nuclear chromosome; inner kinetochore plate
amino acid catabolic process to alcohol via Ehrlich pathway (GO:0000947)
Namespace: biological_process
Definition: The chemical reactions and pathways involving the catabolism of amino acids to produce alcohols with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of alcohols, often collectively referred to as fusel alcohols. Depending on the redox state of the cells, carboxylic acid derivatives may be produced instead of alcohols.
obsolete L-methionine catabolic process to 3-methylthiopropanoate (GO:0000954)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving the catabolism of amino acids to produce carboxylic acids with one carbon less than the starting amino acid. In S. cerevisiae, this is known to occur for leucine, isoleucine, valine, methionine, phenylalanine, tyrosine, or tryptophan. When L-methionine is used as the substrate, 3-methylthiopropanoate is produced. Often referred to as the Ehrlich pathway, these reactions generally occur during fermentation to produce a variety of carboxylic acids, sometimes collectively referred to as fusel acids. Depending on the redox state of the cells, alcohol derivatives may be produced instead of carboxylic acids.
Comment: This term was obsoleted because it represents a specific instance of a pathway that should be captured as a GO-CAM model.
regulation of mitochondrial RNA catabolic process (GO:0000960)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catabolism in the mitochondrion of RNA transcribed from the mitochondrial genome.
RNA 5'-end processing (GO:0000966)
Namespace: biological_process
Definition: Any process involved in forming the mature 5' end of an RNA molecule.
Synonyms: RNA 5' end processing
obsolete tRNA exon ligation utilizing ATP as source of linkage phosphate (GO:0000969)
Namespace: biological_process
Definition: OBSOLETE. A tRNA exon ligation process in which the splice junction phosphate is derived from exogenous ATP. This type of ligation to rejoin the 5' and 3' exons of a tRNA is observed in vertebrate species.
Comment: The reason for obsoletion is that this term is a molecular functions.
obsolete transcription factor activity, RNA polymerase III transcription factor binding (GO:0001007)
Namespace: molecular_function
Definition: OBSOLETE. Binding to an RNA polymerase III transcription factor, which may be a single protein or a complex, in order to modulate transcription. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
Synonyms: RNA polymerase III transcription factor binding transcription factor activity
Comment: This term was obsoleted because it represents two separate functions. The corresponding 'binding' term should be used in combination with a transcription regulator activity child.
nitrogen catabolite regulation of transcription from RNA polymerase II promoter (GO:0001079)
Namespace: biological_process
Definition: A transcription regulation process in which the presence of one nitrogen source leads to the modulation of the frequency, rate, or extent of transcription, from an RNA polymerase II promoter, of specific genes involved in the metabolism of other nitrogen sources.
Synonyms: regulation of transcription from RNA polymerase II promoter by nitrogen catabolites
TFIIE-class transcription factor complex binding (GO:0001095)
Namespace: molecular_function
Definition: Binding to a general RNA polymerase II transcription factor belonging to the TFIIE complex, one of the factors involved in formation of the preinitiation complex (PIC) by RNA polymerase II.
Synonyms: TFIIE-class transcription factor binding
obsolete transcription factor activity, RNA polymerase III type 1 promoter sequence-specific binding, TFIIIC recruiting (GO:0001152)
Namespace: molecular_function
Definition: OBSOLETE. The function of binding to a specific DNA sequence motif in a type 1 RNA polymerase III (Pol III) promoter in order to recruit the transcription factor TFIIIC to the promoter.
Synonyms: RNA polymerase III type 1 promoter sequence-specific DNA binding TFIIIC recruiting transcription factor activity; TFIIIA activity; type 1 RNA polymerase III promoter recognition
Comment: This term was made obsolete in the 2018 Transcription branch revision. This represents the activity of TFIIIA only.
RNA polymerase I core promoter sequence-specific DNA binding (GO:0001164)
Namespace: molecular_function
Definition: Binding to a regulatory region composed of the transcription start site and binding sites for transcription factors of the RNA polymerase I transcription machinery. This site is often referred to as the CORE element. In mammalian cells, the CORE element functions in conjunction with the Upstream Control Element (UCE), while in fungi, protozoa, and plants, the CORE element functions without a UCE.
Synonyms: RNA polymerase I CORE element sequence-specific DNA binding; RNA polymerase I CORE element sequence-specific DNA binding transcription factor recruiting transcription factor activity; transcription factor activity, RNA polymerase I CORE element binding transcription factor recruiting
DNA-templated transcriptional start site selection (GO:0001173)
Namespace: biological_process
Definition: Any process involved in the selection of the specific location within the template strand of a DNA-dependent RNA polymerase promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript.
Synonyms: DNA-dependent transcriptional start site selection; transcriptional start site selection at bacterial-type RNA polymerase promoter
regulation of transcriptional start site selection at RNA polymerase II promoter (GO:0001178)
Namespace: biological_process
Definition: Any process that modulates the rate, frequency or extent of a process involved in the selection of the specific location within the template strand of an RNA polymerase II promoter for hybridization of the cognate ribonucleotides and formation of first phosphodiester bond within the nascent transcript.
Synonyms: regulation of transcription start site selection at RNA polymerase II promoter
obsolete positive regulation of mating-type specific transcription from RNA polymerase II promoter (GO:0001197)
Namespace: biological_process
Definition: OBSOLETE. Any mating-type specific process that activates or increases the rate of transcription from an RNA polymerase II promoter.
Synonyms: activation of transcription from an RNA polymerase II promoter, mating-type specific; stimulation of transcription from an RNA polymerase II promoter, mating-type specific; up regulation of transcription from an RNA polymerase II promoter, mating-type specific; up-regulation of transcription from an RNA polymerase II promoter, mating-type specific; upregulation of transcription from an RNA polymerase II promoter, mating-type specific
Comment: This term was obsoleted because it represents a GO-CAM model.
obsolete progressive alteration of chromatin involved in replicative cell aging (GO:0001304)
Namespace: biological_process
Definition: OBSOLETE. A process that results in changes in chromatin structure contributing to replicative cell aging.
Synonyms: progressive alteration of chromatin during replicative cell ageing; progressive alteration of chromatin during replicative cell aging
Comment: This term was obsoleted because it represents an assay, not a true biological process.
obsolete age-dependent response to oxidative stress (GO:0001306)
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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, where the change varies according to the age of the cell or organism.
Comment: This term was obsoleted because it represents a phenotype.
signal transduction involved in filamentous growth (GO:0001402)
Namespace: biological_process
Definition: Relaying of environmental signals promoting filamentous growth.
Synonyms: MAPKKK cascade (pseudohyphal growth); signal transduction during filamentous growth
guanine nucleotide transmembrane transporter activity (GO:0001409)
Namespace: molecular_function
Definition: Enables the transfer of guanine nucleotides (GMP, GDP, and GTP) from one side of a membrane to the other.
chlamydospore formation (GO:0001410)
Namespace: biological_process
Definition: The process whose specific outcome is the progression of the chlamydospore over time, from its formation to the mature structure. A chlamydospores is a mitotic (asexual) one-celled spore, produced primarily for survival, not dispersal, originating endogenously and singly within part of a pre-existing cell and possessing an inner secondary and often thickened cell wall. An example of this is found in Candida albicans.
Synonyms: chlamydospore development
ossification (GO:0001503)
Namespace: biological_process
Definition: The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance.
Synonyms: bone biosynthesis; bone formation; osteogenesis
Comment: Note that this term does not have a 'developmental process' parent because ossification isn't necessarily developmental, can also occur as part of bone remodeling. Instead use 'ossification involved in bone maturation ; GO:0043931'.
outer dense fiber (GO:0001520)
Namespace: cellular_component
Definition: A supramolecular fiber found in the flagella of mammalian sperm that surrounds the nine microtubule doublets. These dense fibers are stiff and noncontractile. In human, they consist of about 10 major and at least 15 minor proteins, where all major proteins are ODF1, ODF2 or ODF2-related proteins.
Synonyms: outer dense fibre
pseudouridine synthesis (GO:0001522)
Namespace: biological_process
Definition: The intramolecular conversion of uridine to pseudouridine within an RNA molecule.
Synonyms: pseudouridylation
obsolete globin (GO:0001524)
Namespace: molecular_function
Definition: OBSOLETE. The colorless and basic protein moiety of hemoglobin and myoglobins.
Synonyms: globin
Comment: This term was made obsolete because it represents a gene product.
regulation of cell growth (GO:0001558)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate, extent or direction of cell growth.
ganglioside biosynthetic process (GO:0001574)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of gangliosides that begins with the synthesis of a tetrasaccharide core Gal-beta-1,3-GalNAc-beta-1,4-Gal-beta-1,4-Glc-ceramide. This core can be further elongated with the sequential addition of various carbohydrate units including the addition of one or more sialic acid residues.
Synonyms: ganglio-series glycosphingolipid biosynthesis; ganglioside anabolism; ganglioside biosynthesis; ganglioside formation; ganglioside synthesis
angiotensin receptor activity (GO:0001595)
Namespace: molecular_function
Definition: Combining with angiotensin to initiate a change in cell activity.
neuromedin U receptor activity (GO:0001607)
Namespace: molecular_function
Definition: Combining with neuromedin U to initiate a change in cell activity.
Synonyms: NMUR activity
purinergic nucleotide receptor activity (GO:0001614)
Namespace: molecular_function
Definition: Combining with a purine nucleotide and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
Synonyms: P2 receptor; purinergic receptor activity; purinoceptor; purinoreceptor
obsolete thyrotropin releasing hormone and secretagogue-like receptors activity (GO:0001615)
Namespace: molecular_function
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: thyrotropin releasing hormone and secretagogue-like receptors activity
Comment: This term was made obsolete because it represents a gene product, was not defined, and is named based on protein features.
obsolete GP40-like receptor activity (GO:0001630)
Namespace: molecular_function
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: GP40-like receptor activity
Comment: This term was made obsolete because it represents a gene product, was not defined, and is named based on protein features.
obsolete secretin-like receptor activity (GO:0001633)
Namespace: molecular_function
Definition: OBSOLETE. A G protein-coupled receptor that is structurally/functionally related to the secretin receptor.
Synonyms: class B G protein coupled receptor; class B G-protein coupled receptor; class B GPCR; class B orphan receptor activity; secretin-like receptor activity
Comment: This term was made obsolete because it represents a gene product and is named based on protein features.
proteinase-activated receptor activity (GO:0001648)
Namespace: molecular_function
Definition: A G protein-coupled receptor activity that is activated by cleavage by a serine protease, exposing a tethered ligand corresponding to the new N-terminus, which binds to the receptor and activates it.
Synonyms: protease-activated receptor activity; proteinase activated receptor activity
branching involved in ureteric bud morphogenesis (GO:0001658)
Namespace: biological_process
Definition: The process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules.
Synonyms: ureteric bud branching
formation of primary germ layer (GO:0001704)
Namespace: biological_process
Definition: The formation of the ectoderm, mesoderm and endoderm during gastrulation.
cell fate determination (GO:0001709)
Namespace: biological_process
Definition: The cellular developmental process involved in cell fate commitment that occurs after cell fate specification, in which a cell is irreversibly committed to a cellular developmental fate which is heritable on cell division.
endodermal cell fate commitment (GO:0001711)
Namespace: biological_process
Definition: The cell differentiation process that results in commitment of a cell to become part of the endoderm.
Synonyms: endoderm cell fate commitment
ruffle (GO:0001726)
Namespace: cellular_component
Definition: Projection at the leading edge of a crawling cell; the protrusions are supported by a microfilament meshwork.
Synonyms: membrane ruffle
lipid kinase activity (GO:0001727)
Namespace: molecular_function
Definition: Catalysis of the phosphorylation of a simple or complex lipid.
immunological synapse (GO:0001772)
Namespace: cellular_component
Definition: An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
Synonyms: c-SMAC; supramolecular activation cluster
myeloid dendritic cell activation (GO:0001773)
Namespace: biological_process
Definition: The change in morphology and behavior of a dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
cell activation (GO:0001775)
Namespace: biological_process
Definition: A multicellular organismal process by which exposure to an activating factor such as a cellular or soluble ligand results in a change in the morphology or behavior of a cell.
plasma membrane repair (GO:0001778)
Namespace: biological_process
Definition: The resealing of a cell plasma membrane after cellular wounding due to, for instance, mechanical stress.
regulation of type IIa hypersensitivity (GO:0001796)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate, or extent of type IIa hypersensitivity, a type of inflammatory response.
negative regulation of type I hypersensitivity (GO:0001811)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the rate of type I hypersensitivity, a type of inflammatory response.
Synonyms: down regulation of type I hypersensitivity; down-regulation of type I hypersensitivity; downregulation of type I hypersensitivity; inhibition of type I hypersensitivity
cytokine production (GO:0001816)
Namespace: biological_process
Definition: The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
Synonyms: cytokine biosynthetic process; cytokine metabolic process; cytokine secretion; interferon production; interferon secretion; interleukin production; interleukin secretion
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.
negative regulation of cytokine production (GO:0001818)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the rate of production of a cytokine.
Synonyms: down regulation of cytokine biosynthetic process; down regulation of cytokine production; down-regulation of cytokine biosynthetic process; down-regulation of cytokine production; downregulation of cytokine biosynthetic process; downregulation of cytokine production; inhibition of cytokine biosynthetic process; inhibition of cytokine production; negative regulation of cytokine anabolism; negative regulation of cytokine biosynthesis; negative regulation of cytokine biosynthetic process; negative regulation of cytokine formation; negative regulation of cytokine secretion; negative regulation of cytokine synthesis
opsonin binding (GO:0001846)
Namespace: molecular_function
Definition: Binding to an opsonin, such as a complement component or antibody, deposited on the surface of a bacteria, virus, immune complex, or other particulate material.
Comment: Note that an opsonin is a blood serum protein or fragment which when deposited on the surface of a bacteria, virus, immune complex, or other particulate material acts a signal for phagocytosis to cells bearing the appropriate receptors. Not all complement components or fragments and not all antibodies have opsonic properties.
complement component C1q complex binding (GO:0001849)
Namespace: molecular_function
Definition: Binding to a C1q complex, a component of the classical complement cascade.
collectin receptor activity (GO:0001863)
Namespace: molecular_function
Definition: Combining with a collectin and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
Comment: Note that collectins include such proteins as mannose-binding lectin (MBL) and surfactant proteins A and D (SP-A and SP-D).
complement activation, lectin pathway (GO:0001867)
Namespace: biological_process
Definition: Any process involved in the activation of any of the steps of the lectin pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes.
Synonyms: complement cascade, lectin pathway
Comment: Note that proteins such as mannose-binding lectin (MBL) and certain serum ficolins can activate the lectin complement pathway.
polysaccharide immune receptor activity (GO:0001873)
Namespace: molecular_function
Definition: Combining with a polysaccharide and transmitting the signal to initiate an innate immune response. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
Synonyms: polysaccharide receptor activity
Mullerian duct regression (GO:0001880)
Namespace: biological_process
Definition: The process in which the Mullerian ducts, primordia of the oviducts, uterus and upper vagina, undergo regression in male embryos.
pyrimidine nucleoside binding (GO:0001884)
Namespace: molecular_function
Definition: Binding to a pyrimidine nucleoside, a compound consisting of a pyrimidine base linked either to ribose or deoxyribose.