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

Last Reviewed on: 2011-10-28    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
core RNA polymerase II binding transcription factor activity	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-14 IPI: Inferred from Physical Interaction with SGD:RPO21 Assigned on 2011-10-14	Sun M, et al.  (2010) A tandem SH2 domain in transcription elongation factor Spt6 binds the phosphorylated RNA polymerase II C-terminal repeat domain (CTD). J Biol Chem 285(53):41597-603	SGD
DNA binding transcription antitermination factor activity	IGI: Inferred from Genetic Interaction with SGD:DST1 Assigned on 2011-10-14 IMP: Inferred from Mutant Phenotype Assigned on 2011-10-14 IDA: Inferred from Direct Assay Assigned on 2011-10-14	Kaplan CD, et al.  (2005) Interaction between transcription elongation factors and mRNA 3'-end formation at the Saccharomyces cerevisiae GAL10-GAL7 locus. J Biol Chem 280(2):913-22	SGD
histone binding	IDA: Inferred from Direct Assay Assigned on 2011-10-13	Bortvin A and Winston F  (1996) Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science 272(5267):1473-6	SGD
nucleosome binding	IMP: Inferred from Mutant Phenotype Assigned on 2011-08-26 IDA: Inferred from Direct Assay Assigned on 2011-08-26	McDonald SM, et al.  (2010) Structure and biological importance of the Spn1-Spt6 interaction, and its regulatory role in nucleosome binding. Mol Cell 40(5):725-35	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
chromatin maintenance	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-13	Malagon F and Aguilera A  (2001) Yeast spt6-140 mutation, affecting chromatin and transcription, preferentially increases recombination in which Rad51p-mediated strand exchange is dispensable. Genetics 158(2):597-611	SGD
chromatin remodeling	IGI: Inferred from Genetic Interaction with SGD:SNF5 Assigned on 2011-10-13 IMP: Inferred from Mutant Phenotype Assigned on 2011-10-13	Bortvin A and Winston F  (1996) Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science 272(5267):1473-6	SGD
negative regulation of transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2009-05-12	Adkins MW and Tyler JK  (2006) Transcriptional activators are dispensable for transcription in the absence of Spt6-mediated chromatin reassembly of promoter regions. Mol Cell 21(3):405-16	SGD
negative regulation of transcription from RNA polymerase II promoter by glucose	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-13	Denis CL  (1984) Identification of new genes involved in the regulation of yeast alcohol dehydrogenase II. Genetics 108(4):833-44	SGD
nucleosome assembly	IDA: Inferred from Direct Assay Assigned on 2001-12-05	Bortvin A and Winston F  (1996) Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science 272(5267):1473-6	SGD
nucleosome organization	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-15	Ivanovska I, et al.  (2011) Control of chromatin structure by spt6: different consequences in coding and regulatory regions. Mol Cell Biol 31(3):531-41	SGD
poly(A)+ mRNA export from nucleus	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-14	Estruch F, et al.  (2009) A genetic screen in Saccharomyces cerevisiae identifies new genes that interact with mex67-5, a temperature-sensitive allele of the gene encoding the mRNA export receptor. Mol Genet Genomics 281(1):125-34	SGD
positive regulation of transcription elongation from RNA polymerase II promoter	IDA: Inferred from Direct Assay Assigned on 2013-03-07	Kuryan BG, et al.  (2012) Histone density is maintained during transcription mediated by the chromatin remodeler RSC and histone chaperone NAP1 in vitro. Proc Natl Acad Sci U S A 109(6):1931-6	SGD
positive regulation of transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-14	Zhang L, et al.  (2008) Spn1 regulates the recruitment of Spt6 and the Swi/Snf complex during transcriptional activation by RNA polymerase II. Mol Cell Biol 28(4):1393-403	SGD
positive regulation of transcription involved in G1/S phase of mitotic cell cycle	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-15	Morillo-Huesca M, et al.  (2010) FACT prevents the accumulation of free histones evicted from transcribed chromatin and a subsequent cell cycle delay in G1. PLoS Genet 6(5):e1000964	SGD
regulation of histone H3-K36 methylation	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-14 IDA: Inferred from Direct Assay Assigned on 2011-10-14	Youdell ML, et al.  (2008) Roles for Ctk1 and Spt6 in regulating the different methylation states of histone H3 lysine 36. Mol Cell Biol 28(16):4915-26	SGD
regulation of mRNA 3'-end processing	IGI: Inferred from Genetic Interaction with SGD:DST1 Assigned on 2011-10-28 IMP: Inferred from Mutant Phenotype Assigned on 2011-10-28	Kaplan CD, et al.  (2005) Interaction between transcription elongation factors and mRNA 3'-end formation at the Saccharomyces cerevisiae GAL10-GAL7 locus. J Biol Chem 280(2):913-22	SGD
regulation of nucleosome density	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-15	Ivanovska I, et al.  (2011) Control of chromatin structure by spt6: different consequences in coding and regulatory regions. Mol Cell Biol 31(3):531-41	SGD
regulation of transcription by chromatin organization	IMP: Inferred from Mutant Phenotype Assigned on 2008-05-05	Kaplan CD, et al.  (2003) Transcription elongation factors repress transcription initiation from cryptic sites. Science 301(5636):1096-9	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2011-08-26	Hainer SJ, et al.  (2011) Intergenic transcription causes repression by directing nucleosome assembly. Genes Dev 25(1):29-40	SGD
	IGI: Inferred from Genetic Interaction with SGD:SNF5 Assigned on 2011-10-13 IMP: Inferred from Mutant Phenotype Assigned on 2011-10-13	Bortvin A and Winston F  (1996) Evidence that Spt6p controls chromatin structure by a direct interaction with histones. Science 272(5267):1473-6	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
regulation of transcriptional start site selection at RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2011-10-14	Kaplan CD, et al.  (2003) Transcription elongation factors repress transcription initiation from cryptic sites. Science 301(5636):1096-9	SGD
transcription antitermination	IGI: Inferred from Genetic Interaction with SGD:DST1 Assigned on 2011-10-14 IMP: Inferred from Mutant Phenotype Assigned on 2011-10-14	Kaplan CD, et al.  (2005) Interaction between transcription elongation factors and mRNA 3'-end formation at the Saccharomyces cerevisiae GAL10-GAL7 locus. J Biol Chem 280(2):913-22	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
nucleus	IDA: Inferred from Direct Assay Assigned on 2011-10-13	Swanson MS, et al.  (1990) SPT6, an essential gene that affects transcription in Saccharomyces cerevisiae, encodes a nuclear protein with an extremely acidic amino terminus. Mol Cell Biol 10(9):4935-41	SGD
transcriptionally active chromatin	IDA: Inferred from Direct Assay Assigned on 2011-10-28	Kaplan CD, et al.  (2005) Interaction between transcription elongation factors and mRNA 3'-end formation at the Saccharomyces cerevisiae GAL10-GAL7 locus. J Biol Chem 280(2):913-22	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
mitochondrion	IDA: Inferred from Direct Assay Assigned on 2006-12-12	Reinders J, et al.  (2006) Toward the complete yeast mitochondrial proteome: multidimensional separation techniques for mitochondrial proteomics. J Proteome Res 5(7):1543-54	SGD
	IDA: Inferred from Direct Assay Assigned on 2004-09-28	Sickmann A, et al.  (2003) The proteome of Saccharomyces cerevisiae mitochondria. Proc Natl Acad Sci U S A 100(23):13207-12	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
hydrolase activity, acting on ester bonds	IEA: Inferred from Electronic Annotation with EBI:IPR006641 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
nucleobase-containing compound metabolic process	IEA: Inferred from Electronic Annotation with EBI:IPR006641 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
regulation of DNA-dependent transcription, elongation	IEA: Inferred from Electronic Annotation with EBI:IPR017072 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
regulation of transcription from RNA polymerase II promoter	IEA: Inferred from Electronic Annotation with EBI:IPR017072 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: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)).