LiteFold/GO huggingface dataset:
DNA-templated transcription initiation (GO:0006352)
Namespace: biological_process
Definition: The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place.
Synonyms: DNA-dependent RNA polymerase complex assembly at promoter; DNA-dependent transcription, initiation; DNA-templated transcription, initiation; initiation of DNA-dependent transcription; initiation of transcription, DNA-dependent; transcription initiation factor activity; transcription initiation from bacterial-type RNA polymerase promoter; transcription initiation, DNA-dependent
Comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation.
DNA-templated transcription termination (GO:0006353)
Namespace: biological_process
Definition: The completion of transcription: the RNA polymerase pauses, the RNA-DNA hybrid dissociates, followed by the release of the RNA polymerase from its DNA template.
Synonyms: DNA-dependent transcription, termination; DNA-templated transcription, termination; termination of DNA-dependent transcription; termination of transcription, DNA-dependent; transcription termination factor activity; transcription termination from bacterial-type RNA polymerase promoter; transcription termination, DNA-dependent; transcriptional complex disassembly
DNA-templated transcription elongation (GO:0006354)
Namespace: biological_process
Definition: The extension of an RNA molecule after transcription initiation and promoter clearance at a DNA-dependent RNA polymerase promoter by the addition of ribonucleotides catalyzed by an RNA polymerase.
Synonyms: DNA-dependent transcription, elongation; DNA-templated transcription, elongation; RNA elongation; RNA elongation from bacterial-type RNA polymerase promoter; transcription elongation from bacterial-type RNA polymerase promoter; transcription elongation, DNA-dependent; transcriptional elongation, DNA-dependent
regulation of transcription by RNA polymerase I (GO:0006356)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase I.
Synonyms: regulation of transcription from Pol I promoter; regulation of transcription from RNA polymerase I promoter
regulation of transcription by RNA polymerase III (GO:0006359)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of transcription mediated by RNA ploymerase III.
Synonyms: regulation of transcription from Pol III promoter; regulation of transcription from RNA polymerase III promoter
transcription by RNA polymerase I (GO:0006360)
Namespace: biological_process
Definition: The synthesis of RNA from a DNA template by RNA polymerase I (RNAP I), originating at an RNAP I promoter.
Synonyms: RNA polymerase I transcription factor activity; transcription from Pol I promoter; transcription from RNA polymerase I promoter
transcription initiation at RNA polymerase I promoter (GO:0006361)
Namespace: biological_process
Definition: A transcription initiation process that takes place at a RNA polymerase I gene promoter. Ribosomal RNAs (rRNA) genes are transcribed by RNA polymerase I.
Synonyms: transcription initiation from Pol I promoter; transcription initiation from RNA polymerase I promoter; transcription initiation from RNA polymerase I promoter for nuclear large rRNA transcript
Comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation.
transcription elongation by RNA polymerase I (GO:0006362)
Namespace: biological_process
Definition: The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase I specific promoter by the addition of ribonucleotides catalyzed by RNA polymerase I.
Synonyms: RNA elongation from Pol I promoter; RNA polymerase I transcription elongation factor activity; transcription elongation from RNA polymerase I promoter; transcription elongation from RNA polymerase I promoter for nuclear large rRNA transcript
termination of RNA polymerase I transcription (GO:0006363)
Namespace: biological_process
Definition: A transcription termination process that completes the production of a ribosomal RNA transcript. RNAP I termination requires binding of a terminator protein to specific sequences downstream of the transcription unit.
Synonyms: RNA polymerase I transcription termination; RNA polymerase I transcription termination factor activity; termination of RNA polymerase I transcription from promoter for nuclear large rRNA transcript; transcription termination from Pol I promoter; transcription termination from RNA polymerase I promoter
rRNA processing (GO:0006364)
Namespace: biological_process
Definition: Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
Synonyms: 35S primary transcript processing
transcription by RNA polymerase II (GO:0006366)
Namespace: biological_process
Definition: The synthesis of RNA from a DNA template by RNA polymerase II (RNAP II), originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
Synonyms: gene-specific transcription from RNA polymerase II promoter; general transcription from RNA polymerase II promoter; RNA polymerase II transcription factor activity; specific transcription from RNA polymerase II promoter; transcription from Pol II promoter; transcription from RNA polymerase II promoter
transcription initiation at RNA polymerase II promoter (GO:0006367)
Namespace: biological_process
Definition: A transcription initiation process that takes place at a RNA polymerase II gene promoter. Messenger RNAs (mRNA) genes, as well as some non-coding RNAs, are transcribed by RNA polymerase II.
Synonyms: transcription initiation from Pol II promoter; transcription initiation from RNA polymerase II promoter
Comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation.
transcription elongation by RNA polymerase II (GO:0006368)
Namespace: biological_process
Definition: The extension of an RNA molecule after transcription pausing and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
Synonyms: RNA elongation from Pol II promoter; RNA polymerase II transcription elongation factor activity; transcription elongation by RNA polymerase II promoter; transcription elongation from RNA polymerase II promoter
termination of RNA polymerase II transcription (GO:0006369)
Namespace: biological_process
Definition: A transcription termination process that completes the production of a primary RNA polymerase II transcript.
Synonyms: RNA 3'-end formation by RNA polymerase II; RNA polymerase II transcription termination; RNA polymerase II transcription termination factor activity; transcription termination from Pol II promoter; transcription termination from RNA polymerase II promoter
7-methylguanosine mRNA capping (GO:0006370)
Namespace: biological_process
Definition: The sequence of enzymatic reactions by which the mRNA 5' cap structure, an inverted 7-methylguanosine linked via a 5'-5' triphosphate bridge (m7G(5')ppp(5')X) to the first transcribed residue, is added to a nascent transcript. Additional methylation can occur on the ribose sugars of the first and second nucleotides adjacent to the m7G nRNA cap. These methylations are often referred to as N6,2'-O-dimethyladenosine (m6,2A) and N6,2'-O-dimethylguanosine (m6,2G), respectively.
Synonyms: 5' end capping; 5' mRNA capping; 5'-end mRNA processing; 5'-end processing; mRNA capping
obsolete mRNA splicing (GO:0006371)
Namespace: biological_process
Definition: OBSOLETE. The process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, so that mRNA consisting only of the joined exons is produced.
Synonyms: mRNA splicing
Comment: This term was made obsolete because it represents several different processes.
obsolete lariat formation, 5'-splice site cleavage (GO:0006372)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: lariat formation, 5'-splice site cleavage
Comment: This term was made obsolete because it represents a molecular function.
obsolete 3'-splice site cleavage, exon ligation (GO:0006373)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: 3'-splice site cleavage, exon ligation
Comment: This term was made obsolete because it represents a molecular function.
mRNA splice site recognition (GO:0006376)
Namespace: biological_process
Definition: Selection of a splice site by components of the assembling spliceosome.
Synonyms: spliceosomal commitment complex biosynthesis; spliceosomal commitment complex formation; spliceosomal E complex biosynthesis; spliceosomal E complex formation
obsolete MATa1 (A1) pre-mRNA splicing (GO:0006377)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: MATa1 (A1) pre-mRNA splicing
Comment: This term was made obsolete because it does not represent a process unique to splicing of the MATa1 (A1) pre-mRNA, but a recycling defect exacerbated by the presence of two introns within the same gene.
obsolete mRNA polyadenylation (GO:0006378)
Namespace: biological_process
Definition: OBSOLETE. The enzymatic addition of a sequence of 40-200 adenylyl residues at the 3' end of a eukaryotic mRNA primary transcript.
Comment: The reason for obsoletion is that this term represents a molecular function.
obsolete mRNA cleavage (GO:0006379)
Namespace: biological_process
Definition: OBSOLETE. Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
Synonyms: cleavage stimulation factor activity
Comment: This term was obsoleted because it represents a molecular function
obsolete poly-A binding (GO:0006380)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: poly-A binding
Comment: This term was made obsolete because it represents a molecular function and not a biological process.
adenosine to inosine editing (GO:0006382)
Namespace: biological_process
Definition: The conversion of an adenosine residue to inosine in an RNA molecule by deamination.
transcription initiation at RNA polymerase III promoter (GO:0006384)
Namespace: biological_process
Definition: A transcription initiation process that takes place at a RNA polymerase III gene promoter. Transfer RNAs (tRNA) genes, as well as some other non-coding RNAs, are transcribed by RNA polymerase III.
Synonyms: transcription initiation from Pol III promoter; transcription initiation from RNA polymerase III hybrid type promoter; transcription initiation from RNA polymerase III promoter; transcription initiation from RNA polymerase III type 1 promoter; transcription initiation from RNA polymerase III type 2 promoter; transcription initiation from RNA polymerase III type 3 promoter
Comment: Note that promoter clearance is represented as a separate step, not part_of either initiation or elongation.
transcription elongation by RNA polymerase III (GO:0006385)
Namespace: biological_process
Definition: The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase III promoter by the addition of ribonucleotides catalyzed by RNA polymerase III.
Synonyms: RNA elongation from Pol III promoter; RNA polymerase III transcription elongation factor activity; transcription elongation by RNA polymerase III promoter; transcription elongation from RNA polymerase III promoter
termination of RNA polymerase III transcription (GO:0006386)
Namespace: biological_process
Definition: A transcription termination process that completes the production of a primary RNA polymerase II transcript. RNA polymerase III has an intrinsic ability to terminate transcription upon incorporation of at least 4 contiguous U residues.
Synonyms: RNA polymerase III transcription termination; RNA polymerase III transcription termination factor activity; transcription termination from Pol III promoter; transcription termination from RNA polymerase III promoter
obsolete snRNA capping (GO:0006387)
Namespace: biological_process
Definition: OBSOLETE. The sequence of enzymatic reactions resulting in the addition of a cap to the 5' end of a nascent snRNA transcript.
Synonyms: snRNA capping
Comment: This term was made obsolete because it has been replaced with a more specific term to describe cap hypermethylation. All RNA polymerase II transcripts receive a 7-methyl-G cap. Then for (at least) small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs), the 7-methyl-G cap is hypermethylated to become a 2,2,7-trimethylguanosine (TMG) cap.
tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)
Namespace: biological_process
Definition: Splicing of tRNA substrates via recognition of the folded RNA structure that brings the 5' and 3' splice sites into proximity and cleavage of the RNA at both the 3' and 5' splice sites by an endonucleolytic mechanism, followed by ligation of the exons.
Synonyms: tRNA-Y splicing
Comment: Note that while typically associated with tRNA splicing, splicing via endonucleolytic cleavages and subsequent ligation of the free exon ends is known to be used for some non-tRNA substrates, e.g. HAC1 (YFL031W) in S. cerevisiae and an intron in the 23S rRNA of the Archaeal species Desulfurococcus mobilis.
obsolete tRNA-Y splicing (GO:0006389)
Namespace: biological_process
Definition: OBSOLETE. (Was not defined before being made obsolete).
Synonyms: tRNA-Y splicing
Comment: This term was made obsolete because it does not represent a process unique to splicing of the tyrosyl (Y) tRNA.
mitochondrial transcription (GO:0006390)
Namespace: biological_process
Definition: The synthesis of RNA from a mitochondrial DNA template, usually by a specific mitochondrial RNA polymerase.
Synonyms: transcription from mitochondrial promoter
transcription initiation at mitochondrial promoter (GO:0006391)
Namespace: biological_process
Definition: A transcription initiation process that takes place at a promoter on the mitochondrial chromosome.
Synonyms: transcription initiation from mitochondrial promoter
transcription elongation by mitochondrial RNA polymerase (GO:0006392)
Namespace: biological_process
Definition: The extension of an RNA molecule after transcription initiation and promoter clearance at mitochondrial promoter by the addition of ribonucleotides catalyzed by a mitchondrial RNA polymerase.
Synonyms: RNA elongation from mitochondrial promoter; transcription elongation from mitochondrial promoter
RNA processing (GO:0006396)
Namespace: biological_process
Definition: Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
mRNA processing (GO:0006397)
Namespace: biological_process
Definition: Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
Synonyms: mRNA maturation
tRNA metabolic process (GO:0006399)
Namespace: biological_process
Definition: The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established.
Synonyms: tRNA metabolism
tRNA modification (GO:0006400)
Namespace: biological_process
Definition: The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
Synonyms: tRNA editing
Comment: The term 'RNA editing' (GO:0016547) was merged into 'RNA modification' (GO:0009451) on the basis of statements in the preface of Modification and Editing of RNA (ISBN:1555811337) that there is no clear distinction between modification and editing. Parallel changes were made for substrate (e.g. tRNA, rRNA, etc.) specific child terms of 'RNA editing'.
RNA catabolic process (GO:0006401)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
Synonyms: RNA breakdown; RNA catabolism; RNA degradation
mRNA catabolic process (GO:0006402)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
Synonyms: mRNA breakdown; mRNA catabolism; mRNA decay; mRNA degradation
RNA import into nucleus (GO:0006404)
Namespace: biological_process
Definition: The import of RNA from the cytoplasm to the nucleus.
Synonyms: RNA import into cell nucleus; RNA transport from cytoplasm to nucleus; RNA-nucleus import
RNA export from nucleus (GO:0006405)
Namespace: biological_process
Definition: The directed movement of RNA from the nucleus to the cytoplasm.
Synonyms: RNA export from cell nucleus; RNA export out of nucleus; RNA transport from nucleus to cytoplasm; RNA-nucleus export
mRNA export from nucleus (GO:0006406)
Namespace: biological_process
Definition: The directed movement of mRNA from the nucleus to the cytoplasm.
Synonyms: mRNA export from cell nucleus; mRNA export out of nucleus; mRNA transport from nucleus to cytoplasm; mRNA-nucleus export
obsolete rRNA export from nucleus (GO:0006407)
Namespace: biological_process
Definition: OBSOLETE. The directed movement of rRNA from the nucleus to the cytoplasm; the rRNA is usually in the form of ribonucleoproteins.
Synonyms: rRNA export from cell nucleus; rRNA export out of nucleus; rRNA transport from nucleus to cytoplasm; rRNA-nucleus export
Comment: The reason for obsoletion is that this term was added in error (rRNA is only exported as part of the pre ribosome).
snRNA export from nucleus (GO:0006408)
Namespace: biological_process
Definition: The directed movement of snRNA from the nucleus to the cytoplasm.
Synonyms: snRNA export from cell nucleus; snRNA export out of nucleus; snRNA transport from nucleus to cytoplasm; snRNA-nucleus export
tRNA export from nucleus (GO:0006409)
Namespace: biological_process
Definition: The directed movement of tRNA from the nucleus to the cytoplasm.
Synonyms: tRNA export from cell nucleus; tRNA export out of nucleus; tRNA transport from nucleus to cytoplasm; tRNA-nucleus export
obsolete transcription, RNA-dependent (GO:0006410)
Namespace: biological_process
Definition: OBSOLETE. The cellular synthesis of DNA on a template of RNA.
Synonyms: transcription, RNA-dependent
Comment: This term was obsoleted because the name and the definition mean two completely different things: 1) "transcription, RNA-dependent", i.e. RNA-dependent production of an RNA transcript and 2) "reverse transcription", i.e. RNA-dependent DNA synthesis.
translation (GO:0006412)
Namespace: biological_process
Definition: The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
Synonyms: protein translation
translational initiation (GO:0006413)
Namespace: biological_process
Definition: The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
Synonyms: biopolymerisation; biopolymerization; protein synthesis initiation; translation initiation
translational elongation (GO:0006414)
Namespace: biological_process
Definition: The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
Synonyms: protein synthesis elongation; translation elongation
translational termination (GO:0006415)
Namespace: biological_process
Definition: The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
Synonyms: protein synthesis termination; translation termination; translational complex disassembly
regulation of translation (GO:0006417)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
Synonyms: regulation of protein anabolism; regulation of protein biosynthesis; regulation of protein formation; regulation of protein synthesis
tRNA aminoacylation for protein translation (GO:0006418)
Namespace: biological_process
Definition: The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA and the alpha carboxylic acid group of an amino acid, to be used in ribosome-mediated polypeptide synthesis.
Synonyms: tRNA charging
alanyl-tRNA aminoacylation (GO:0006419)
Namespace: biological_process
Definition: The process of coupling alanine to alanyl-tRNA, catalyzed by alanyl-tRNA synthetase. The alanyl-tRNA synthetase is a class-II synthetases. The activated amino acid is transferred to the 3'-OH group of an alanine accetping tRNA.
asparaginyl-tRNA aminoacylation (GO:0006421)
Namespace: biological_process
Definition: The process of coupling asparagine to asparaginyl-tRNA, catalyzed by asparaginyl-tRNA synthetase. The asparaginyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of an asparagine-accetping tRNA.
cysteinyl-tRNA aminoacylation (GO:0006423)
Namespace: biological_process
Definition: The process of coupling cysteine to cysteinyl-tRNA, catalyzed by cysteinyl-tRNA synthetase. A cysteinyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a cysteine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
glutamyl-tRNA aminoacylation (GO:0006424)
Namespace: biological_process
Definition: The process of coupling glutamate to glutamyl-tRNA, catalyzed by glutamyl-tRNA synthetase. The glutamyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a glutamic acid-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
glutaminyl-tRNA aminoacylation (GO:0006425)
Namespace: biological_process
Definition: The process of coupling glutamine to glutaminyl-tRNA, catalyzed by glutaminyl-tRNA synthetase. The glutaminyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a glutamine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
glycyl-tRNA aminoacylation (GO:0006426)
Namespace: biological_process
Definition: The process of coupling glycine to glycyl-tRNA, catalyzed by glycyl-tRNA synthetase. The glycyll-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a glycine-accepting tRNA.