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
PDR3/YBL005W	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
PDR8/YLR266C	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
PIP2/YOR363C	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
PPR1/YLR014C	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
PUT3/YKL015W	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
RAD2/YGR258C	IGI: Inferred from Genetic Interaction with SGD:DST1, SGD:RAD26 Assigned on 2007-10-19	manually curated	Lee SK, et al.  (2002) Requirement of yeast RAD2, a homolog of human XPG gene, for efficient RNA polymerase II transcription. implications for Cockayne syndrome. Cell 109(7):823-34	SGD
RAD3/YER171W	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
RAD6/YGL058W	IPI: Inferred from Physical Interaction with SGD:RPO21 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
RBA50/YDR527W	IMP: Inferred from Mutant Phenotype Assigned on 2005-02-16	manually curated	Jeronimo C, et al.  (2004) RPAP1, a novel human RNA polymerase II-associated protein affinity purified with recombinant wild-type and mutated polymerase subunits. Mol Cell Biol 24(16):7043-58	SGD
RDR1/YOR380W	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
RDS1/YCR106W	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
RDS2/YPL133C	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
RGT1/YKL038W	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
RPB10/YOR210W	IMP: Inferred from Mutant Phenotype Assigned on 2010-01-19	manually curated	Zaros C, et al.  (2007) Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases. Nucleic Acids Res 35(2):634-47	SGD
RPB11/YOL005C	IMP: Inferred from Mutant Phenotype Assigned on 2010-01-19	manually curated	Zaros C, et al.  (2007) Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases. Nucleic Acids Res 35(2):634-47	SGD
RPB2/YOR151C	IMP: Inferred from Mutant Phenotype Assigned on 2009-05-12	manually curated	Scafe C, et al.  (1990) RNA polymerase II mutants defective in transcription of a subset of genes. Mol Cell Biol 10(3):1010-6	SGD
RPB3/YIL021W	IMP: Inferred from Mutant Phenotype Assigned on 2010-01-19	manually curated	Kolodziej P and Young RA  (1989) RNA polymerase II subunit RPB3 is an essential component of the mRNA transcription apparatus. Mol Cell Biol 9(12):5387-94	SGD
RPB4/YJL140W	IMP: Inferred from Mutant Phenotype Assigned on 2010-01-15	manually curated	Miyao T, et al.  (2001) Deletion of the RNA polymerase subunit RPB4 acts as a global, not stress-specific, shut-off switch for RNA polymerase II transcription at high temperatures. J Biol Chem 276(49):46408-13	SGD
RPB5/YBR154C	IGI: Inferred from Genetic Interaction with SGD:RPO21, IMP: Inferred from Mutant Phenotype Assigned on 2010-01-19	manually curated	Miyao T and Woychik NA  (1998) RNA polymerase subunit RPB5 plays a role in transcriptional activation. Proc Natl Acad Sci U S A 95(26):15281-6	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2010-01-19	manually curated	Zaros C, et al.  (2007) Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases. Nucleic Acids Res 35(2):634-47	SGD
RPB7/YDR404C	IGI: Inferred from Genetic Interaction with SGD:RPB4 Assigned on 2010-01-19	manually curated	Sheffer A, et al.  (1999) Rpb7 can interact with RNA polymerase II and support transcription during some stresses independently of Rpb4. Mol Cell Biol 19(4):2672-80	SGD
RPB8/YOR224C	IPI: Inferred from Physical Interaction with SGD:RPO21 Assigned on 2010-01-20	manually curated	Briand JF, et al.  (2001) Partners of Rpb8p, a small subunit shared by yeast RNA polymerases I, II and III. Mol Cell Biol 21(17):6056-65	SGD
RPB9/YGL070C	IMP: Inferred from Mutant Phenotype Assigned on 2010-01-19	manually curated	Zaros C, et al.  (2007) Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases. Nucleic Acids Res 35(2):634-47	SGD
RPC10/YHR143W-A	IMP: Inferred from Mutant Phenotype Assigned on 2010-01-19	manually curated	Rubbi L, et al.  (1999) Functional characterization of ABC10alpha, an essential polypeptide shared by all three forms of eukaryotic DNA-dependent RNA polymerases. J Biol Chem 274(44):31485-92	SGD
RPO21/YDL140C	IMP: Inferred from Mutant Phenotype Assigned on 2010-01-19	manually curated	Nonet M, et al.  (1987) Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol Cell Biol 7(5):1602-11	SGD
	IEA: Inferred from Electronic Annotation with EBI:IPR000684 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
RPO26/YPR187W	IMP: Inferred from Mutant Phenotype Assigned on 2010-01-19	manually curated	Tan Q, et al.  (2003) Loss of the Rpb4/Rpb7 subcomplex in a mutant form of the Rpb6 subunit shared by RNA polymerases I, II, and III. Mol Cell Biol 23(9):3329-38	SGD
RSF1/YMR030W	IMP: Inferred from Mutant Phenotype Assigned on 2003-10-14	manually curated	Lu L, et al.  (2003) Rsf1p, a protein required for respiratory growth of Saccharomyces cerevisiae. Curr Genet 43(4):263-72	SGD
RTR1/YER139C	IGI: Inferred from Genetic Interaction with SGD:RPB9, SGD:RPB4, SGD:RPB5, SGD:RPB7, IMP: Inferred from Mutant Phenotype, IPI: Inferred from Physical Interaction with SGD:RPO21 Assigned on 2008-05-21	manually curated	Gibney PA, et al.  (2008) Rtr1 is the Saccharomyces cerevisiae homolog of a novel family of RNA polymerase II-binding proteins. Eukaryot Cell 7(6):938-48	SGD
SEF1/YBL066C	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
SIP4/YJL089W	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
SOH1/YGL127C	IGI: Inferred from Genetic Interaction Assigned on 2002-10-09	manually curated	Fan HY, et al.  (1996) Mutations in the RNA polymerase II transcription machinery suppress the hyperrecombination mutant hpr1 delta of Saccharomyces cerevisiae. Genetics 142(3):749-59	SGD
	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

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