LiteFold/GO huggingface dataset:
obsolete soluble fraction (GO:0005625)
Namespace: cellular_component
Definition: OBSOLETE. That fraction of cells, prepared by disruptive biochemical methods, that is soluble in water.
Synonyms: soluble; soluble fraction
Comment: This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component.
obsolete insoluble fraction (GO:0005626)
Namespace: cellular_component
Definition: OBSOLETE. That fraction of cells, prepared by disruptive biochemical methods, that is not soluble in water.
Synonyms: insoluble fraction; particle-bound
Comment: This term was made obsolete because it refers to a cell fractionation experimental result and not a bona fide cellular component.
obsolete ascus (GO:0005627)
Namespace: cellular_component
Definition: OBSOLETE. A sac-like fruiting body (ascomycete Fungi); contains ascospores (typically eight in number).
Synonyms: ascus
Comment: This term was made obsolete because it is a structure that contains cell (ascospores) rather than a cellular component. To update annotations, consider the external ontology term 'ascus ; FAO:0000014'.
dityrosine layer of spore wall (GO:0005630)
Namespace: cellular_component
Definition: The outermost layer of the spore wall, as described in Saccharomyces.
chitosan layer of spore wall (GO:0005631)
Namespace: cellular_component
Definition: The second outermost layer of the spore wall, as described in Saccharomyces.
inner layer of spore wall (GO:0005632)
Namespace: cellular_component
Definition: Either of the two innermost layers of the spore wall, as described in Saccharomyces.
ascus lipid droplet (GO:0005633)
Namespace: cellular_component
Definition: Any particle of coalesced lipids in an ascus or ascospore. May include associated proteins.
Synonyms: ascus lipid particle
nucleus (GO:0005634)
Namespace: cellular_component
Definition: A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
Synonyms: cell nucleus; horsetail nucleus
nuclear envelope (GO:0005635)
Namespace: cellular_component
Definition: The double lipid bilayer that encloses the nucleus, separating its contents from the cytoplasm. It consists of an inner and outer nuclear membrane, with an intermembrane space (20-40 nm wide, also called the perinuclear space) between them. The envelope is supported by the nuclear lamina and contains nuclear pore complexes, which regulate molecular transport.
nuclear inner membrane (GO:0005637)
Namespace: cellular_component
Definition: The inner, i.e. lumen-facing, lipid bilayer of the nuclear envelope.
Synonyms: inner envelope; inner nuclear membrane; nucleus inner membrane
lamin filament (GO:0005638)
Namespace: cellular_component
Definition: Any of a group of intermediate-filament proteins that form the fibrous matrix on the inner surface of the nuclear envelope. They are classified as lamins A, B and C.
Synonyms: type V intermediate filament
obsolete integral component of nuclear inner membrane (GO:0005639)
Namespace: cellular_component
Definition: OBSOLETE. The component of the nuclear inner membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
Synonyms: integral to nuclear inner membrane
Comment: This term was obsoleted because it represents protein topology, not a cellular component.
nuclear outer membrane (GO:0005640)
Namespace: cellular_component
Definition: The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes.
Synonyms: nucleus outer envelope; perinuclear membrane
nuclear envelope lumen (GO:0005641)
Namespace: cellular_component
Definition: The region between the two lipid bilayers of the nuclear envelope; 20-40 nm wide.
Synonyms: nuclear intermembrane space; nuclear membrane lumen; perinuclear space
Comment: Note that this term should not be confused with the cellular component term 'perinuclear region ; GO:0048471'.
annulate lamellae (GO:0005642)
Namespace: cellular_component
Definition: Stacks of endoplasmic reticulum (ER) membranes containing a high density of nuclear pores, thought to form from excess nuclear membrane components, that have been described in a number of different cells. Annulate lamellar membranes are continuous with and embedded within the ER.
nuclear pore (GO:0005643)
Namespace: cellular_component
Definition: A protein complex providing a discrete opening in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
Synonyms: NPC; nuclear pore complex; nuclear pore membrane protein; nucleopore
obsolete importin (GO:0005646)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: importin; karyopherin
Comment: This term was made obsolete because it represents a single gene product and not a complex.
obsolete importin, alpha-subunit (GO:0005647)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: importin, alpha-subunit; karyopherin-alpha
Comment: This term was made obsolete because it represents a single gene product and not a complex.
obsolete importin, beta-subunit (GO:0005648)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: importin, beta-subunit; karyopherin-beta1
Comment: This term was made obsolete because it represents a single gene product and not a complex.
obsolete transportin (GO:0005649)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: karyopherin-beta2; transportin
Comment: This term was made obsolete because it represents a single gene product and not a complex.
obsolete importin, alpha-subunit transport factor (GO:0005650)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: CAS; importin, alpha-subunit transport factor
Comment: This term was made obsolete because it represents a single gene product and not a complex.
obsolete exportin (GO:0005651)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: exportin
Comment: This term was made obsolete because it represents a single gene product and not a complex.
nuclear lamina (GO:0005652)
Namespace: cellular_component
Definition: The fibrous, electron-dense layer lying on the nucleoplasmic side of the inner membrane of a cell nucleus, composed of lamin filaments. The polypeptides of the lamina are thought to be concerned in the dissolution of the nuclear envelope and its re-formation during mitosis. The lamina is composed of lamin A and lamin C filaments cross-linked into an orthogonal lattice, which is attached via lamin B to the inner nuclear membrane through interactions with a lamin B receptor, an IFAP, in the membrane.
nucleoplasm (GO:0005654)
Namespace: cellular_component
Definition: That part of the nuclear content other than the chromosomes or the nucleolus.
nucleolar ribonuclease P complex (GO:0005655)
Namespace: cellular_component
Definition: A ribonuclease P complex located in the nucleolus of a eukaryotic cell, where it catalyzes the 5' endonucleolytic cleavage of precursor tRNAs to yield mature tRNAs. Eukaryotic nucleolar ribonuclease P complexes generally contain a single RNA molecule that is necessary but not sufficient for catalysis, and several protein molecules.
Synonyms: nucleolar RNase P complex
nuclear pre-replicative complex (GO:0005656)
Namespace: cellular_component
Definition: A protein-DNA complex assembled at eukaryotic DNA replication origins during late mitosis and G1, allowing the origin to become competent, or 'licensed', for replication. The complex normally includes the origin recognition complex (ORC), Cdc6, Cdt1 and the MiniChromosome Maintenance (Mcm2-7) proteins.
Synonyms: eukaryotic pre-replicative complex; pre-RC; pre-replicative complex
replication fork (GO:0005657)
Namespace: cellular_component
Definition: The Y-shaped region of a replicating DNA molecule, resulting from the separation of the DNA strands and in which the synthesis of new strands takes place. Also includes associated protein complexes.
Synonyms: replication focus
alpha DNA polymerase:primase complex (GO:0005658)
Namespace: cellular_component
Definition: A complex of four polypeptides, comprising large and small DNA polymerase alpha subunits and two primase subunits, which are capable of catalyzing the synthesis of an RNA primer on the lagging strand of replicating DNA and the subsequent synthesis of a small stretch of DNA. The smaller of the two primase subunits alone can catalyze oligoribonucleotide synthesis.
Synonyms: DNA polymerase alpha:primase complex; heterotetrameric polymerase alpha holoenzyme; pol-prim; primosome
obsolete delta-DNA polymerase cofactor complex (GO:0005660)
Namespace: cellular_component
Definition: OBSOLETE. A complex of proteins that interacts with delta-DNA polymerase, promoting elongation. In humans it is a heteropentamer of subunits of 140/145, 40, 38, 37 and 36.5 kDa, which form a complex with the proliferating cell nuclear antigen (PCNA) in the presence of ATP.
Synonyms: delta DNA polymerase cofactor complex; delta-DNA polymerase cofactor complex
Comment: This term was made obsolete because it refers to two distinct complexes, PCNA and Replication factor C (RFC), the latter of which is already represented as a separate, unrelated GO term (DNA replication factor C complex ; GO:0005663). In addition, the phrase 'delta-DNA polymerase cofactor' to represent both PCNA and RFC is not used in current literature.
DNA replication factor A complex (GO:0005662)
Namespace: cellular_component
Definition: A conserved heterotrimeric complex that binds nonspecifically to single-stranded DNA and is required for multiple processes in eukaryotic DNA metabolism, including DNA replication, DNA repair, and recombination. In all eukaryotic organisms examined the complex is composed of subunits of approximately 70, 30, and 14 kDa.
Synonyms: replication protein A; RPA
DNA replication factor C complex (GO:0005663)
Namespace: cellular_component
Definition: A complex that loads the DNA polymerase processivity factor proliferating cell nuclear antigen (PCNA) onto DNA, thereby permitting processive DNA synthesis catalyzed by DNA polymerase. In eukaryotes the complex consists of five polypeptides.
Synonyms: activator 1 complex; RFC complex
nuclear origin of replication recognition complex (GO:0005664)
Namespace: cellular_component
Definition: A multisubunit complex that is located at the replication origins of a chromosome in the nucleus.
Synonyms: eukaryotic ORC; nuclear ORC
RNA polymerase II, core complex (GO:0005665)
Namespace: cellular_component
Definition: RNA polymerase II, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces mRNAs, snoRNAs, and some of the snRNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The largest subunit of RNA polymerase II contains an essential carboxyl-terminal domain (CTD) composed of a variable number of heptapeptide repeats (YSPTSPS). The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerases I and III. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.
Synonyms: DNA-directed RNA polymerase II, core complex; RNA polymerase II complex; RNAP II complex
RNA polymerase III complex (GO:0005666)
Namespace: cellular_component
Definition: RNA polymerase III, one of three nuclear DNA-directed RNA polymerases found in all eukaryotes, is a multisubunit complex; typically it produces 5S rRNA, tRNAs and some of the small nuclear RNAs. Two large subunits comprise the most conserved portion including the catalytic site and share similarity with other eukaryotic and bacterial multisubunit RNA polymerases. The remainder of the complex is composed of smaller subunits (generally ten or more), some of which are also found in RNA polymerase I and others of which are also found in RNA polymerases I and II. Although the core is competent to mediate ribonucleic acid synthesis, it requires additional factors to select the appropriate template.
Synonyms: DNA-directed RNA polymerase III activity; DNA-directed RNA polymerase III complex
transcription regulator complex (GO:0005667)
Namespace: cellular_component
Definition: A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
Synonyms: cytoplasmic transcription factor complex; nuclear transcription factor complex; transcription factor complex
obsolete transcription-activating factor, 30kD (GO:0005670)
Namespace: cellular_component
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: transcription-activating factor, 30kD
Comment: This term was made obsolete because it represents a single gene product and not a complex.
obsolete Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)
Namespace: cellular_component
Definition: OBSOLETE. A multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. Contains either GCN5 or PCAF in a mutually exclusive manner. The budding yeast complex includes Gcn5p, two proteins of the Ada family, and two TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins. Both ATAC- or SAGA (see GO:0000124, SAGA complex) are involved in the acetylation of histone H3K9 and K14 residues.
Synonyms: ATAC complex
Comment: This term was obsoleted because it was incorrectly annotated. Consider ADA complex ; GO:0140671 or ATAC complex; GO:0140672.
transcription factor TFIIA complex (GO:0005672)
Namespace: cellular_component
Definition: A component of the transcription machinery of RNA Polymerase II. In humans, TFIIA is a heterotrimer composed of an alpha (P35), beta (P19) and gamma subunits (P12).
transcription factor TFIIE complex (GO:0005673)
Namespace: cellular_component
Definition: A transcription factor which in humans consists of a complex of two alpha and two beta chains. Recruits TFIIH to the initiation complex and helps activate both RNA polymerase II and TFIIH.
transcription factor TFIIF complex (GO:0005674)
Namespace: cellular_component
Definition: A general transcription initiation factor which in humans consists of a heterodimer of an alpha and a beta subunit. Helps recruit RNA polymerase II to the initiation complex and promotes translation elongation.
transcription factor TFIIH holo complex (GO:0005675)
Namespace: cellular_component
Definition: A complex that is capable of kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. It is composed of the core TFIIH complex and the TFIIK complex.
Synonyms: CAK complex; CDK-activating kinase; cyclin-dependent protein kinase activating kinase holoenzyme complex; holo TFIIH complex
chromatin silencing complex (GO:0005677)
Namespace: cellular_component
Definition: Any protein complex that mediates changes in chromatin structure that result in transcriptional silencing.
obsolete chromatin assembly complex (GO:0005678)
Namespace: cellular_component
Definition: OBSOLETE. Any protein complex that acts in the formation of nucleosomes or higher order chromatin structure.
Synonyms: chromatin assembly complex; nucleosome assembly complex
Comment: This term was made obsolete because its definition no longer reflects and cannot be modified to be consistent with the current state of knowledge.
anaphase-promoting complex (GO:0005680)
Namespace: cellular_component
Definition: A ubiquitin ligase complex that degrades mitotic cyclins and anaphase inhibitory protein, thereby triggering sister chromatid separation and exit from mitosis. Substrate recognition by APC occurs through degradation signals, the most common of which is termed the Dbox degradation motif, originally discovered in cyclin B.
Synonyms: anaphase promoting complex; APC; cyclosome
Comment: Note that the synonym 'APC' should not be confused with the abbreviation for the adenomatous polyposis coli gene and protein.
spliceosomal complex (GO:0005681)
Namespace: cellular_component
Definition: Any of a series of ribonucleoprotein complexes that contain snRNA(s) and small nuclear ribonucleoproteins (snRNPs), and are formed sequentially during the spliceosomal splicing of one or more substrate RNAs, and which also contain the RNA substrate(s) from the initial target RNAs of splicing, the splicing intermediate RNA(s), to the final RNA products. During cis-splicing, the initial target RNA is a single, contiguous RNA transcript, whether mRNA, snoRNA, etc., and the released products are a spliced RNA and an excised intron, generally as a lariat structure. During trans-splicing, there are two initial substrate RNAs, the spliced leader RNA and a pre-mRNA.
Synonyms: spliceosome; spliceosome complex
U5 snRNP (GO:0005682)
Namespace: cellular_component
Definition: A ribonucleoprotein complex that contains small nuclear RNA U5, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U5 snRNP, most of which remain associated with the U5 snRNA both while the U5 snRNP is free or assembled into a series of spliceosomal complexes.
Synonyms: snRNP U5
U7 snRNP (GO:0005683)
Namespace: cellular_component
Definition: A ribonucleoprotein complex that contains the U7 snRNA and is required for the 3'-end processing of replication-dependent histone pre-mRNAs.
Synonyms: snRNP U7
U2-type spliceosomal complex (GO:0005684)
Namespace: cellular_component
Definition: Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron that has canonical consensus sequences near the 5' and 3' ends.
Synonyms: GT-AG spliceosome; major (U2-type) spliceosomal complex; major spliceosomal complex
Comment: A U2-type complex refers to any of the snRNP-based complexes that form during splicing that uses U2 (as opposed to U12). There are complexes that form during U2-splicing that don't necessarily contain the U2 snRNP.
U1 snRNP (GO:0005685)
Namespace: cellular_component
Definition: A ribonucleoprotein complex that contains small nuclear RNA U1, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U1 snRNP, most of which remain associated with the U1 snRNA both while the U1 snRNP is free or assembled into a series of spliceosomal complexes.
Synonyms: snRNP U1
U2 snRNP (GO:0005686)
Namespace: cellular_component
Definition: A ribonucleoprotein complex that contains small nuclear RNA U2, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U2 snRNP, most of which remain associated with the U2 snRNA both while the U2 snRNP is free or assembled into a series of spliceosomal complexes.
Synonyms: 17S U2 snRNP; snRNP U2
Comment: U2 snRNP refers to the U2 small nuclear RNA and the proteins that associate with it. U2 snRNP is not considered to be a type of spliceosomal complex by itself.
U4 snRNP (GO:0005687)
Namespace: cellular_component
Definition: A ribonucleoprotein complex that contains small nuclear RNA U4, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U4 snRNP, most of which remain associated with the U4 snRNA both while the U4 snRNP is free or assembled into the U4/U6 snRNP or into a series of spliceosomal complexes.
Synonyms: snRNP U4
U6 snRNP (GO:0005688)
Namespace: cellular_component
Definition: A ribonucleoprotein complex that contains small nuclear RNA U6, the Lsm2-8 heptameric ring complex, as well as several proteins that are unique to the U6 snRNP, most of which remain associated with the U6 snRNA both while the U6 snRNP is free or assembled into the U4/U6 snRNP or into a series of spliceosomal complexes.
Synonyms: snRNP U6
U12-type spliceosomal complex (GO:0005689)
Namespace: cellular_component
Definition: Any spliceosomal complex that forms during the splicing of a messenger RNA primary transcript to excise an intron; the series of U12-type spliceosomal complexes is involved in the splicing of the majority of introns that contain atypical AT-AC terminal dinucleotides, as well as other non-canonical introns. The entire splice site signal, not just the terminal dinucleotides, is involved in determining which spliceosome utilizes the site.
Synonyms: AT-AC spliceosomal complex; minor (U12-type) spliceosomal complex; minor spliceosomal complex
U4atac snRNP (GO:0005690)
Namespace: cellular_component
Definition: A ribonucleoprotein complex that contains small nuclear RNA U4atac, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U4atac snRNP, most of which remain associated with the U4atac snRNA both while the U4atac snRNP is free or assembled into the U4atac/U6atac complex or into a series of spliceosomal complexes.
Synonyms: snRNP U4atac
U6atac snRNP (GO:0005691)
Namespace: cellular_component
Definition: A ribonucleoprotein complex that contains small nuclear RNA U6atac, the Lsm2-8 heptameric ring complex, as well as several proteins that are unique to the U6atac snRNP, most of which remain associated with the U6atac snRNA both while the U6atac snRNP is free or assembled into the U4atac/U6atac snRNP or into a series of spliceosomal complexes.
Synonyms: snRNP U6atac
U11 snRNP (GO:0005692)
Namespace: cellular_component
Definition: A ribonucleoprotein complex that contains small nuclear RNA U11, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U11 snRNP, most of which remain associated with the U11 snRNA both while the U11 snRNP is free or assembled into a series of spliceosomal complexes.
Synonyms: 12S U11 snRNP; snRNP U11
U12 snRNP (GO:0005693)
Namespace: cellular_component
Definition: A ribonucleoprotein complex that contains small nuclear RNA U12, a heptameric ring of Sm proteins, as well as several proteins that are unique to the U12 snRNP, most of which remain associated with the U12 snRNA both while the U12 snRNP is free or assembled into a series of spliceosomal complexes.
Synonyms: snRNP U12
chromosome (GO:0005694)
Namespace: cellular_component
Definition: A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
Synonyms: chromatid; interphase chromosome; prophase chromosome
Comment: Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
obsolete chromatid (GO:0005695)
Namespace: cellular_component
Definition: OBSOLETE. One of the two daughter strands of a duplicated chromosome that become apparent between early prophase and metaphase in mitosis and between diplotene and second metaphase in meiosis.
Synonyms: chromatid
Comment: This term was made obsolete because it is not a unique subcellular component, i.e. the difference between this term and 'chromosome' is based on temporal and process distinctions.
telomerase holoenzyme complex (GO:0005697)
Namespace: cellular_component
Definition: Telomerase is a ribonucleoprotein enzyme complex, with a minimal catalytic core composed of a catalytic reverse transcriptase subunit and an RNA subunit that provides the template for telomeric DNA addition. In vivo, the holoenzyme complex often contains additional subunits.