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

Last Reviewed on: 2011-11-14    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
chromatin binding	IDA: Inferred from Direct Assay Assigned on 2011-11-14	Zhang F, et al.  (2008) Disrupting vesicular trafficking at the endosome attenuates transcriptional activation by Gcn4. Mol Cell Biol 28(22):6796-818	SGD
RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription	IPI: Inferred from Physical Interaction with SGD:RAP1 Assigned on 2011-11-14	Joo YJ, et al.  (2011) Gcn4p-mediated transcriptional repression of ribosomal protein genes under amino-acid starvation. EMBO J 30(5):859-72	SGD
RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription	IMP: Inferred from Mutant Phenotype Assigned on 2011-11-14 IDA: Inferred from Direct Assay Assigned on 2011-11-14 IPI: Inferred from Physical Interaction with SGD:GAL11 Assigned on 2011-11-14	Jedidi I, et al.  (2010) Activator Gcn4 employs multiple segments of Med15/Gal11, including the KIX domain, to recruit mediator to target genes in vivo. J Biol Chem 285(4):2438-55	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2011-11-14	Qiu H, et al.  (2006) The Spt4p subunit of yeast DSIF stimulates association of the Paf1 complex with elongating RNA polymerase II. Mol Cell Biol 26(8):3135-48	SGD
RNA polymerase II transcription factor recruiting transcription factor activity	IMP: Inferred from Mutant Phenotype Assigned on 2011-11-14 IDA: Inferred from Direct Assay Assigned on 2011-11-14 IPI: Inferred from Physical Interaction with SGD:GAL11 Assigned on 2011-11-14	Jedidi I, et al.  (2010) Activator Gcn4 employs multiple segments of Med15/Gal11, including the KIX domain, to recruit mediator to target genes in vivo. J Biol Chem 285(4):2438-55	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2011-11-14	Qiu H, et al.  (2006) The Spt4p subunit of yeast DSIF stimulates association of the Paf1 complex with elongating RNA polymerase II. Mol Cell Biol 26(8):3135-48	SGD
sequence-specific DNA binding	IDA: Inferred from Direct Assay Assigned on 2010-02-26	Arndt K and Fink GR  (1986) GCN4 protein, a positive transcription factor in yeast, binds general control promoters at all 5' TGACTC 3' sequences. Proc Natl Acad Sci U S A 83(22):8516-20	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-02-26	Roussou I, et al.  (1988) Transcriptional-translational regulatory circuit in Saccharomyces cerevisiae which involves the GCN4 transcriptional activator and the GCN2 protein kinase. Mol Cell Biol 8(5):2132-9	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-02-26	Sellers JW, et al.  (1990) Mutations that define the optimal half-site for binding yeast GCN4 activator protein and identify an ATF/CREB-like repressor that recognizes similar DNA sites. Mol Cell Biol 10(10):5077-86	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-02-26	Hope IA and Struhl K  (1986) Functional dissection of a eukaryotic transcriptional activator protein, GCN4 of yeast. Cell 46(6):885-94	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-02-26	Hope IA and Struhl K  (1985) GCN4 protein, synthesized in vitro, binds HIS3 regulatory sequences: implications for general control of amino acid biosynthetic genes in yeast. Cell 43(1):177-88	SGD
sequence-specific DNA binding transcription factor activity	IMP: Inferred from Mutant Phenotype Assigned on 2011-11-14 IDA: Inferred from Direct Assay Assigned on 2011-11-14	Qiu H, et al.  (2006) The Spt4p subunit of yeast DSIF stimulates association of the Paf1 complex with elongating RNA polymerase II. Mol Cell Biol 26(8):3135-48	SGD
TFIID-class binding transcription factor activity	IPI: Inferred from Physical Interaction with SGD:TAF12 Assigned on 2011-11-14	Herbig E, et al.  (2010) Mechanism of Mediator recruitment by tandem Gcn4 activation domains and three Gal11 activator-binding domains. Mol Cell Biol 30(10):2376-90	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
negative regulation of ribosomal protein gene transcription from RNA polymerase II promoter in response to nutrient levels	IMP: Inferred from Mutant Phenotype Assigned on 2011-11-14	Joo YJ, et al.  (2011) Gcn4p-mediated transcriptional repression of ribosomal protein genes under amino-acid starvation. EMBO J 30(5):859-72	SGD
negative regulation of transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2010-03-26	Velasco I, et al.  (2004) Saccharomyces cerevisiae Aqr1 is an internal-membrane transporter involved in excretion of amino acids. Eukaryot Cell 3(6):1492-503	SGD
nitrogen catabolite activation of transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2011-11-14	Teixeira MC, et al.  (2011) Yeast response and tolerance to polyamine toxicity involving the drug : H+ antiporter Qdr3 and the transcription factors Yap1 and Gcn4. Microbiology 157(Pt 4):945-56	SGD
positive regulation of RNA polymerase II transcriptional preinitiation complex assembly	IGI: Inferred from Genetic Interaction with SGD:POP2, SGD:ROX3, SGD:SPT7, SGD:SPT20, SGD:HFI1 Assigned on 2010-03-26 IMP: Inferred from Mutant Phenotype Assigned on 2010-03-26	Qiu H, et al.  (2004) An array of coactivators is required for optimal recruitment of TATA binding protein and RNA polymerase II by promoter-bound Gcn4p. Mol Cell Biol 24(10):4104-17	SGD
	IDA: Inferred from Direct Assay Assigned on 2011-11-14	Zhang F, et al.  (2008) Disrupting vesicular trafficking at the endosome attenuates transcriptional activation by Gcn4. Mol Cell Biol 28(22):6796-818	SGD
positive regulation of transcription initiation from RNA polymerase II promoter	IGI: Inferred from Genetic Interaction with SGD:GCD2 Assigned on 2010-02-26 IMP: Inferred from Mutant Phenotype Assigned on 2010-02-26	Mosch HU, et al.  (1992) Sequence-specific initiator elements focus initiation of transcription to distinct sites in the yeast TRP4 promoter. EMBO J 11(12):4583-90	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
nucleus	IDA: Inferred from Direct Assay Assigned on 2010-03-26	Pries R, et al.  (2004) Nuclear import of yeast Gcn4p requires karyopherins Srp1p and Kap95p. Mol Genet Genomics 271(3):257-66	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-02-26	Pries R, et al.  (2002) Amino acid-dependent Gcn4p stability regulation occurs exclusively in the yeast nucleus. Eukaryot Cell 1(5):663-72	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.

Molecular Function

High-throughput Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
sequence-specific DNA binding	IDA: Inferred from Direct Assay Assigned on 2009-02-05	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	SGD

** 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
DNA binding	IEA: Inferred from Electronic Annotation with EBI:KW-0238 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
sequence-specific DNA binding	IEA: Inferred from Electronic Annotation with EBI:IPR004827 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
sequence-specific DNA binding transcription factor activity	IEA: Inferred from Electronic Annotation with EBI:IPR004827 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 amino acid biosynthetic process	IEA: Inferred from Electronic Annotation with EBI:KW-0028 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
regulation of transcription, DNA-dependent	IEA: Inferred from Electronic Annotation with EBI:IPR004827 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-0805 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:KW-0804 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 Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
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)).