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

Last Reviewed on: 2002-05-07    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
ATP-dependent RNA helicase activity	TAS: Traceable Author Statement Assigned on 2005-04-16	de la Cruz J, et al.  (1999) Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. Trends Biochem Sci 24(5):192-8	SGD
nucleic acid binding	TAS: Traceable Author Statement Assigned on 2002-01-27	Culbertson MR  (1999) RNA surveillance. Unforeseen consequences for gene expression, inherited genetic disorders and cancer. Trends Genet 15(2):74-80	SGD
RNA-dependent ATPase activity	TAS: Traceable Author Statement Assigned on 2005-04-16	de la Cruz J, et al.  (1999) Unwinding RNA in Saccharomyces cerevisiae: DEAD-box proteins and related families. Trends Biochem Sci 24(5):192-8	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
chromatin silencing at silent mating-type cassette	IGI: Inferred from Genetic Interaction with SGD:POL30 Assigned on 2006-09-14	Huang S, et al.  (2005) Rtt106p is a histone chaperone involved in heterochromatin-mediated silencing. Proc Natl Acad Sci U S A 102(38):13410-5	SGD
intracellular mRNA localization	IMP: Inferred from Mutant Phenotype Assigned on 2009-04-01	Sheth U and Parker R  (2006) Targeting of aberrant mRNAs to cytoplasmic processing bodies. Cell 125(6):1095-109	SGD
nuclear-transcribed mRNA catabolic process	IMP: Inferred from Mutant Phenotype Assigned on 2008-02-15	Gaba A, et al.  (2005) Ribosome occupancy of the yeast CPA1 upstream open reading frame termination codon modulates nonsense-mediated mRNA decay. Mol Cell 20(3):449-60	SGD
nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay	IGI: Inferred from Genetic Interaction with SGD:XRN1 Assigned on 2009-03-06 IMP: Inferred from Mutant Phenotype Assigned on 2009-03-06	Takahashi S, et al.  (2003) Interaction between Ski7p and Upf1p is required for nonsense-mediated 3'-to-5' mRNA decay in yeast. EMBO J 22(15):3951-9	SGD
	IGI: Inferred from Genetic Interaction with SGD:DCP1 Assigned on 2009-03-06	Mitchell P and Tollervey D  (2003) An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3'-->5' degradation. Mol Cell 11(5):1405-13	SGD
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	TAS: Traceable Author Statement Assigned on 2002-01-27	Culbertson MR  (1999) RNA surveillance. Unforeseen consequences for gene expression, inherited genetic disorders and cancer. Trends Genet 15(2):74-80	SGD
protein ubiquitination	IMP: Inferred from Mutant Phenotype Assigned on 2008-08-22 IDA: Inferred from Direct Assay Assigned on 2008-08-22 IPI: Inferred from Physical Interaction with SGD:CDC34 Assigned on 2008-08-22	Takahashi S, et al.  (2008) Upf1 potentially serves as a RING-related E3 ubiquitin ligase via its association with Upf3 in yeast. RNA 14(9):1950-8	SGD
regulation of translational termination	TAS: Traceable Author Statement Assigned on 2002-01-27	Culbertson MR  (1999) RNA surveillance. Unforeseen consequences for gene expression, inherited genetic disorders and cancer. Trends Genet 15(2):74-80	SGD
NOT translational frameshifting	IMP: Inferred from Mutant Phenotype Assigned on 2005-03-01	Harger JW and Dinman JD  (2004) Evidence against a direct role for the Upf proteins in frameshifting or nonsense codon readthrough. RNA 10(11):1721-9	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
NOT mitochondrion	IDA: Inferred from Direct Assay Assigned on 2005-03-01	de Pinto B, et al.  (2004) Overexpression of Upf1p compensates for mitochondrial splicing deficiency independently of its role in mRNA surveillance. Mol Microbiol 51(4):1129-42	SGD
polysome	TAS: Traceable Author Statement Assigned on 2002-01-27	Culbertson MR  (1999) RNA surveillance. Unforeseen consequences for gene expression, inherited genetic disorders and cancer. Trends Genet 15(2):74-80	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.

Cellular Component

High-throughput Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
cytoplasm	IDA: Inferred from Direct Assay Assigned on 2013-01-20	Tkach JM, et al.  (2012) Dissecting DNA damage response pathways by analysing protein localization and abundance changes during DNA replication stress. Nat Cell Biol 14(9):966-76	SGD
	IDA: Inferred from Direct Assay Assigned on 2002-05-07	Kumar A, et al.  (2002) Subcellular localization of the yeast proteome. Genes Dev 16(6):707-19	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
ATP binding	IEA: Inferred from Electronic Annotation with EBI:IPR018999 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-0067 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
DNA binding	IEA: Inferred from Electronic Annotation with EBI:IPR018999 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
helicase activity	IEA: Inferred from Electronic Annotation with EBI:IPR018999 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-0347 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
hydrolase activity	IEA: Inferred from Electronic Annotation with EBI:KW-0378 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
metal ion binding	IEA: Inferred from Electronic Annotation with EBI:KW-0479 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
nucleoside-triphosphatase activity	IEA: Inferred from Electronic Annotation with EBI:IPR003593 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
nucleotide binding	IEA: Inferred from Electronic Annotation with EBI:IPR003593 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-0547 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
zinc ion binding	IEA: Inferred from Electronic Annotation with EBI:IPR018999 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
nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA: Inferred from Electronic Annotation with EBI:IPR018999 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-0866 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
cytoplasm	IEA: Inferred from Electronic Annotation with EBI:IPR018999 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: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
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)).