Ontology: Biological Process (GO:0006366)

Definition: The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).

Synonyms: transcription from Pol II promoter; specific transcription from RNA polymerase II promoter; gene-specific transcription from RNA polymerase II promoter; general transcription from RNA polymerase II promoter; RNA polymerase II transcription factor activity

View Ontology: (graph) | (text)

This table lists the methods used to annotate genes either directly to the term transcription from RNA polymerase II promoter (106 genes) or to its variants containing one or more qualifiers (0 genes). Note that some genes may have been annotated by more than one method so the numbers in the table below may not add up to the totals given here.

Annotation Method	GO Term	# Yeast Genes Annotated
Manually curated (download data)	transcription from RNA polymerase II promoter	52
High-throughput	none	none
Computational (download data)	transcription from RNA polymerase II promoter	57

Links to Additional Annotations:

• View annotations in multiple organisms using
• Search for S. cerevisiae genes annotated, by the Manually curated or High-throughput methods, to this term or to any terms that are descended from this term, i.e., child terms representing more specific biology than this term.

Annotation details for genes that have been directly annotated to the term transcription from RNA polymerase II promoter or its variants containing one or more qualifiers (NOT, contributes to, or colocalizes with).

transcription from RNA polymerase II promoter      106 genes directly annotated to this term
Locus	Evidence	Annotation Method	Reference	Assigned By
ABD1/YBR236C	IMP: Inferred from Mutant Phenotype Assigned on 2011-04-21	manually curated	Schroeder SC, et al.  (2004) A function of yeast mRNA cap methyltransferase, Abd1, in transcription by RNA polymerase II. Mol Cell 13(3):377-87	SGD
ARG81/YML099C	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
ARO80/YDR421W	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
ASG1/YIL130W	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
BRE1/YDL074C	IGI: Inferred from Genetic Interaction with SGD:RPB9 Assigned on 2009-11-11	manually curated	Xiao T, et al.  (2005) Histone H2B ubiquitylation is associated with elongating RNA polymerase II. Mol Cell Biol 25(2):637-51	SGD
	IPI: Inferred from Physical Interaction with SGD:PAF1 Assigned on 2009-11-11	manually curated	Kim J and Roeder RG  (2009) Direct Bre1-Paf1 Complex Interactions and RING Finger-independent Bre1-Rad6 Interactions Mediate Histone H2B Ubiquitylation in Yeast. J Biol Chem 284(31):20582-92	SGD
CAT8/YMR280C	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
CCL1/YPR025C	IDA: Inferred from Direct Assay Assigned on 2010-05-19	manually curated	Yang C, et al.  (2010) Improved methods for expression and purification of Saccharomyces cerevisiae TFIIF and TFIIH; Identification of a functional Escherichia coli promoter and internal translation initiation within the N-terminal coding region of the TFIIF TFG1 subunit. Protein Expr Purif 70(2):172-178	SGD
CEP3/YMR168C	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
CHA4/YLR098C	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
DAL81/YIR023W	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
ECM22/YLR228C	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
EDS1/YBR033W	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
ERT1/YBR239C	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
GAL4/YPL248C	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
GSM1/YJL103C	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
HAL9/YOL089C	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
HAP1/YLR256W	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
HFI1/YPL254W	IMP: Inferred from Mutant Phenotype Assigned on 2002-11-14	manually curated	Horiuchi J, et al.  (1997) ADA1, a novel component of the ADA/GCN5 complex, has broader effects than GCN5, ADA2, or ADA3. Mol Cell Biol 17(6):3220-8	SGD
INO80/YGL150C	IDA: Inferred from Direct Assay, IMP: Inferred from Mutant Phenotype Assigned on 2002-10-11	manually curated	Shen X, et al.  (2000) A chromatin remodelling complex involved in transcription and DNA processing. Nature 406(6795):541-4	SGD
KIN28/YDL108W	IMP: Inferred from Mutant Phenotype Assigned on 2010-06-01	manually curated	Valay JG, et al.  (1995) The KIN28 gene is required both for RNA polymerase II mediated transcription and phosphorylation of the Rpb1p CTD. J Mol Biol 249(3):535-44	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-05-19	manually curated	Yang C, et al.  (2010) Improved methods for expression and purification of Saccharomyces cerevisiae TFIIF and TFIIH; Identification of a functional Escherichia coli promoter and internal translation initiation within the N-terminal coding region of the TFIIF TFG1 subunit. Protein Expr Purif 70(2):172-178	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-06-01	manually curated	Cismowski MJ, et al.  (1995) KIN28 encodes a C-terminal domain kinase that controls mRNA transcription in Saccharomyces cerevisiae but lacks cyclin-dependent kinase-activating kinase (CAK) activity. Mol Cell Biol 15(6):2983-92	SGD
LEU3/YLR451W	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
LYS14/YDR034C	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
MAL13/YGR288W	IEA: Inferred from Electronic Annotation with EBI:IPR001138, EBI:IPR020448 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
MAL33/YBR297W	IEA: Inferred from Electronic Annotation with EBI:IPR020448, EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
MED4/YOR174W	IDA: Inferred from Direct Assay Assigned on 2001-01-18	manually curated	Myers LC, et al.  (1998) The Med proteins of yeast and their function through the RNA polymerase II carboxy-terminal domain. Genes Dev 12(1):45-54	SGD
NHP6B/YBR089C-A	IGI: Inferred from Genetic Interaction with SGD:NHP6A Assigned on 2010-03-16	manually curated	Paull TT, et al.  (1996) Yeast HMG proteins NHP6A/B potentiate promoter-specific transcriptional activation in vivo and assembly of preinitiation complexes in vitro. Genes Dev 10(21):2769-81	SGD
NUT1/YGL151W	IDA: Inferred from Direct Assay Assigned on 2009-04-20	manually curated	Cai G, et al.  (2009) Mediator structural conservation and implications for the regulation mechanism. Structure 17(4):559-67	SGD
OAF1/YAL051W	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
OAF3/YKR064W	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC
PDR1/YGL013C	IEA: Inferred from Electronic Annotation with EBI:IPR001138 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	GOC

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