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

Last Reviewed on: 2003-10-28    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
H3 histone acetyltransferase activity	IGI: Inferred from Genetic Interaction with SGD:GCN5 Assigned on 2008-08-27 IMP: Inferred from Mutant Phenotype Assigned on 2008-08-27	Fillingham J, et al.  (2008) Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109. Mol Cell Biol 28(13):4342-53	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2008-08-27	Schneider J, et al.  (2006) Rtt109 is required for proper H3K56 acetylation: a chromatin mark associated with the elongating RNA polymerase II. J Biol Chem 281(49):37270-4	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2008-08-27 IDA: Inferred from Direct Assay Assigned on 2008-08-27	Driscoll R, et al.  (2007) Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56. Science 315(5812):649-52	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2008-08-27 IDA: Inferred from Direct Assay Assigned on 2008-08-27	Han J, et al.  (2007) Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. Science 315(5812):653-5	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
double-strand break repair via nonhomologous end joining	IMP: Inferred from Mutant Phenotype Assigned on 2008-06-26	Jessulat M, et al.  (2008) Interacting proteins Rtt109 and Vps75 affect the efficiency of non-homologous end-joining in Saccharomyces cerevisiae. Arch Biochem Biophys 469(2):157-64	SGD
histone acetylation	IGI: Inferred from Genetic Interaction with SGD:GCN5 Assigned on 2008-08-27 IMP: Inferred from Mutant Phenotype Assigned on 2008-08-27	Fillingham J, et al.  (2008) Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109. Mol Cell Biol 28(13):4342-53	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2007-02-07	Schneider J, et al.  (2006) Rtt109 is required for proper H3K56 acetylation: a chromatin mark associated with the elongating RNA polymerase II. J Biol Chem 281(49):37270-4	SGD
	IGI: Inferred from Genetic Interaction with SGD:HST4, SGD:HST3 Assigned on 2007-02-07 IMP: Inferred from Mutant Phenotype Assigned on 2007-02-07	Driscoll R, et al.  (2007) Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56. Science 315(5812):649-52	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2007-02-07 IDA: Inferred from Direct Assay Assigned on 2007-02-07	Han J, et al.  (2007) Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. Science 315(5812):653-5	SGD
negative regulation of transposition, RNA-mediated	IMP: Inferred from Mutant Phenotype Assigned on 2008-02-10	Scholes DT, et al.  (2001) Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance. Genetics 159(4):1449-65	SGD
regulation of transcription from RNA polymerase II promoter in response to stress	IMP: Inferred from Mutant Phenotype Assigned on 2009-07-27	Klopf E, et al.  (2009) Cooperation between the INO80 complex and histone chaperones determines adaptation of stress gene transcription in the yeast Saccharomyces cerevisiae. Mol Cell Biol 29(18):4994-5007	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
nucleus	IDA: Inferred from Direct Assay Assigned on 2004-10-08	Sundin BA, et al.  (2004) Localization of proteins that are coordinately expressed with Cln2 during the cell cycle. Yeast 21(9):793-800	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.

Biological Process | Cellular Component

High-throughput Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
response to DNA damage stimulus	IMP: Inferred from Mutant Phenotype Assigned on 2006-04-06	Chang M, et al.  (2002) A genome-wide screen for methyl methanesulfonate-sensitive mutants reveals genes required for S phase progression in the presence of DNA damage. Proc Natl Acad Sci U S A 99(26):16934-9	SGD

High-throughput Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
nucleus	IDA: Inferred from Direct Assay Assigned on 2003-10-28	Huh WK, et al.  (2003) Global analysis of protein localization in budding yeast. Nature 425(6959):686-91	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
histone acetyltransferase activity	IEA: Inferred from Electronic Annotation with IUBMB:2.3.1.48 Last updated 2013-03-02	GOA curators and MGI curators  (2001) Gene Ontology annotation based on Enzyme Commission mapping.	UniProtKB
transferase activity	IEA: Inferred from Electronic Annotation with EBI:KW-0808 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 Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
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
regulation of transcription, DNA-dependent	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
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: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)).