This page displays GO annotations in different sections according to the annotation method used to add that annotation to SGD.

Last Reviewed on: 2010-01-15    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
contributes_to RNA-directed RNA polymerase activity	IDA: Inferred from Direct Assay Assigned on 2011-04-01	Lehmann E, et al.  (2007) Molecular basis of RNA-dependent RNA polymerase II activity. Nature 450(7168):445-9	SGD
contributes_to single-stranded DNA binding	IDA: Inferred from Direct Assay Assigned on 2010-01-15	Orlicky SM, et al.  (2001) Dissociable Rpb4-Rpb7 subassembly of rna polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation. J Biol Chem 276(13):10097-102	SGD
contributes_to single-stranded RNA binding	IDA: Inferred from Direct Assay Assigned on 2010-01-15	Orlicky SM, et al.  (2001) Dissociable Rpb4-Rpb7 subassembly of rna polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation. J Biol Chem 276(13):10097-102	SGD
translation initiation factor binding	IPI: Inferred from Physical Interaction with SGD:NIP1 Assigned on 2011-07-28	Harel-Sharvit L, et al.  (2010) RNA Polymerase II Subunits Link Transcription and mRNA Decay to Translation. Cell 143(4):552-63	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
mRNA export from nucleus in response to heat stress	IMP: Inferred from Mutant Phenotype Assigned on 2010-01-15	Farago M, et al.  (2003) Rpb4p, a subunit of RNA polymerase II, mediates mRNA export during stress. Mol Biol Cell 14(7):2744-55	SGD
nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	IMP: Inferred from Mutant Phenotype Assigned on 2006-11-08	Lotan R, et al.  (2005) The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs. Genes Dev 19(24):3004-16	SGD
positive regulation of translational initiation	IMP: Inferred from Mutant Phenotype Assigned on 2011-07-28	Harel-Sharvit L, et al.  (2010) RNA Polymerase II Subunits Link Transcription and mRNA Decay to Translation. Cell 143(4):552-63	SGD
recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex	IMP: Inferred from Mutant Phenotype Assigned on 2008-04-14	Runner VM, et al.  (2008) The Rpb4 subunit of RNA polymerase II contributes to cotranscriptional recruitment of 3' processing factors. Mol Cell Biol 28(6):1883-91	SGD
transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2010-01-15	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
transcription initiation from RNA polymerase II promoter	IDA: Inferred from Direct Assay Assigned on 2010-01-15	Orlicky SM, et al.  (2001) Dissociable Rpb4-Rpb7 subassembly of rna polymerase II binds to single-strand nucleic acid and mediates a post-recruitment step in transcription initiation. J Biol Chem 276(13):10097-102	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
cytoplasm	IDA: Inferred from Direct Assay Assigned on 2005-02-27	Farago M, et al.  (2003) Rpb4p, a subunit of RNA polymerase II, mediates mRNA export during stress. Mol Biol Cell 14(7):2744-55	SGD
cytoplasmic mRNA processing body	IDA: Inferred from Direct Assay Assigned on 2006-11-08	Lotan R, et al.  (2005) The RNA polymerase II subunit Rpb4p mediates decay of a specific class of mRNAs. Genes Dev 19(24):3004-16	SGD
DNA-directed RNA polymerase II, core complex	IDA: Inferred from Direct Assay Assigned on 2010-01-15	Sayre MH, et al.  (1992) Reconstitution of transcription with five purified initiation factors and RNA polymerase II from Saccharomyces cerevisiae. J Biol Chem 267(32):23376-82	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-01-15	Woychik NA, et al.  (1990) Subunits shared by eukaryotic nuclear RNA polymerases. Genes Dev 4(3):313-23	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-01-15	Kolodziej PA, et al.  (1990) RNA polymerase II subunit composition, stoichiometry, and phosphorylation. Mol Cell Biol 10(5):1915-20	SGD
nucleus	IDA: Inferred from Direct Assay Assigned on 2005-02-27	Farago M, et al.  (2003) Rpb4p, a subunit of RNA polymerase II, mediates mRNA export during stress. Mol Biol Cell 14(7):2744-55	SGD

* Manually curated GO annotations reflect our best understanding of the basic molecular function, biological process, and cellular component for this gene product. Manually curated annotations are assigned by SGD curators based on published papers when available, or by curatorial statements if necessary. Curators periodically review all Manually curated GO annotations for accuracy and completeness. The "Last Reviewed on:" date at the top of this section indicates when these annotations were last reviewed.

There are no High-throughput annotations for RPB4

** GO annotations from High-throughput experiments are made based on a variety of large scale high-throughput experiments, including genome-wide experiments. Many of these annotations are made based on GO annotations (or mappings to GO annotations) assigned by the authors, rather than SGD curators. While SGD curators read these publications and often work closely with authors to incorporate the information, each individual annotation may not necessarily be reviewed by a curator. GO Annotations from high-throughput experiments will be assigned only when this type of data is available, and thus may not be assigned in all three aspects of the Gene Ontologies.

Molecular Function | Biological Process | Cellular Component

Computational Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
catalytic activity	IEA: Inferred from Electronic Annotation with EBI:IPR010997 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
DNA-directed RNA polymerase activity	IEA: Inferred from Electronic Annotation with EBI:IPR005574 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
	IEA: Inferred from Electronic Annotation with EBI:KW-0240 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
nucleotide binding	IEA: Inferred from Electronic Annotation with EBI:IPR010997 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro

Computational Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
cellular metabolic process	IEA: Inferred from Electronic Annotation with EBI:IPR010997 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
DNA repair	IEA: Inferred from Electronic Annotation with EBI:KW-0234 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
mRNA processing	IEA: Inferred from Electronic Annotation with EBI:KW-0507 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
response to DNA damage stimulus	IEA: Inferred from Electronic Annotation with EBI:KW-0227 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
transcription, DNA-dependent	IEA: Inferred from Electronic Annotation with EBI:IPR005574 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro

Computational Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
cytoplasm	IEA: Inferred from Electronic Annotation with EBI:SL-0086 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries.	UniProtKB
	IEA: Inferred from Electronic Annotation with EBI:KW-0963 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
cytoplasmic mRNA processing body	IEA: Inferred from Electronic Annotation with EBI:SL-0230 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries.	UniProtKB
nucleus	IEA: Inferred from Electronic Annotation with EBI:SL-0191 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries.	UniProtKB
	IEA: Inferred from Electronic Annotation with EBI:KW-0539 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB

*** Computational GO Annotations are predictions. These annotations are NOT reviewed by a curator. Currently, all computational GO annotations for S. cerevisiae are assigned by an external source (for example, the Gene Ontology Annotation (GOA) project of the European Bioinformatics Institute (EBI)).