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

Last Reviewed on: 2012-01-13    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
RNA polymerase II transcription factor binding	IPI: Inferred from Physical Interaction with SGD:CYC8 Assigned on 2011-12-13	Conlan RS, et al.  (1999) The Tup1-Cyc8 protein complex can shift from a transcriptional co-repressor to a transcriptional co-activator. J Biol Chem 274(1):205-10	SGD
sequence-specific DNA binding RNA polymerase II transcription factor activity	IMP: Inferred from Mutant Phenotype Assigned on 2011-12-13 IDA: Inferred from Direct Assay Assigned on 2011-12-13	Jia Y, et al.  (1997) A basic helix-loop-helix-leucine zipper transcription complex in yeast functions in a signaling pathway from mitochondria to the nucleus. Mol Cell Biol 17(3):1110-7	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
cellular response to oleic acid	IMP: Inferred from Mutant Phenotype Assigned on 2012-01-03	Hagerman RA and Willis RA  (2002) The yeast gene COQ5 is differentially regulated by Mig1p, Rtg3p and Hap2p. Biochim Biophys Acta 1578(1-3):51-8	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2011-12-15	Hagerman RA, et al.  (2002) The regulation of COQ5 gene expression by energy source. Free Radic Res 36(4):485-90	SGD
mitochondria-nucleus signaling pathway	IDA: Inferred from Direct Assay Assigned on 2005-11-30	Jia Y, et al.  (1997) A basic helix-loop-helix-leucine zipper transcription complex in yeast functions in a signaling pathway from mitochondria to the nucleus. Mol Cell Biol 17(3):1110-7	SGD
mitochondrion degradation	IMP: Inferred from Mutant Phenotype Assigned on 2012-01-13	Journo D, et al.  (2009) Aup1-mediated Regulation of Rtg3 during Mitophagy. J Biol Chem 284(51):35885-95	SGD
positive regulation of transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2011-12-13 IDA: Inferred from Direct Assay Assigned on 2011-12-13	Rothermel BA, et al.  (1997) Rtg3p, a basic helix-loop-helix/leucine zipper protein that functions in mitochondrial-induced changes in gene expression, contains independent activation domains. J Biol Chem 272(32):19801-7	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2012-01-03	Hagerman RA and Willis RA  (2002) The yeast gene COQ5 is differentially regulated by Mig1p, Rtg3p and Hap2p. Biochim Biophys Acta 1578(1-3):51-8	SGD
transcription factor import into nucleus	IMP: Inferred from Mutant Phenotype Assigned on 2011-12-15	Komeili A, et al.  (2000) Mechanism of metabolic control. Target of rapamycin signaling links nitrogen quality to the activity of the Rtg1 and Rtg3 transcription factors. J Cell Biol 151(4):863-78	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
cytoplasm	IDA: Inferred from Direct Assay Assigned on 2002-08-01	Sekito T, et al.  (2000) Mitochondria-to-nuclear signaling is regulated by the subcellular localization of the transcription factors Rtg1p and Rtg3p. Mol Biol Cell 11(6):2103-15	SGD
nucleus	IDA: Inferred from Direct Assay Assigned on 2002-08-01	Sekito T, et al.  (2000) Mitochondria-to-nuclear signaling is regulated by the subcellular localization of the transcription factors Rtg1p and Rtg3p. Mol Biol Cell 11(6):2103-15	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
protein dimerization activity	IEA: Inferred from Electronic Annotation with EBI:IPR011598 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
mitochondria-nucleus signaling pathway	IEA: Inferred from Electronic Annotation with EBI:IPR024099 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
regulation of transcription, DNA-dependent	IEA: Inferred from Electronic Annotation with EBI:IPR024097, EBI:IPR024099 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)).