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

Last Reviewed on: 2012-02-24    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
core RNA polymerase I binding transcription factor activity	IC: Inferred By Curator from positive regulation of transcription elongation from RNA polymerase I promoter, DSIF complex Assigned on 2012-02-24	Schneider DA, et al.  (2006) RNA polymerase II elongation factors Spt4p and Spt5p play roles in transcription elongation by RNA polymerase I and rRNA processing. Proc Natl Acad Sci U S A 103(34):12707-12	SGD
core RNA polymerase II binding transcription factor activity	IC: Inferred By Curator from positive regulation of transcription elongation from RNA polymerase II promoter, DSIF complex Assigned on 2012-02-24	Hartzog GA, et al.  (1998) Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev 12(3):357-69	SGD
rDNA binding	IDA: Inferred from Direct Assay Assigned on 2012-01-06	Schneider DA, et al.  (2006) RNA polymerase II elongation factors Spt4p and Spt5p play roles in transcription elongation by RNA polymerase I and rRNA processing. Proc Natl Acad Sci U S A 103(34):12707-12	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
7-methylguanosine mRNA capping	IGI: Inferred from Genetic Interaction with SGD:CEG1 Assigned on 2012-02-24	Lindstrom DL, et al.  (2003) Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol Cell Biol 23(4):1368-78	SGD
chromatin organization	IMP: Inferred from Mutant Phenotype Assigned on 2012-02-24	Crotti LB and Basrai MA  (2004) Functional roles for evolutionarily conserved Spt4p at centromeres and heterochromatin in Saccharomyces cerevisiae. EMBO J 23(8):1804-14	SGD
chromatin silencing	IMP: Inferred from Mutant Phenotype Assigned on 2004-07-14	Crotti LB and Basrai MA  (2004) Functional roles for evolutionarily conserved Spt4p at centromeres and heterochromatin in Saccharomyces cerevisiae. EMBO J 23(8):1804-14	SGD
chromosome segregation	IMP: Inferred from Mutant Phenotype Assigned on 2003-07-21	Basrai MA, et al.  (1996) Faithful chromosome transmission requires Spt4p, a putative regulator of chromatin structure in Saccharomyces cerevisiae. Mol Cell Biol 16(6):2838-47	SGD
intracellular mRNA localization	IMP: Inferred from Mutant Phenotype Assigned on 2012-02-24	Shen Z, et al.  (2010) Cotranscriptional recruitment of She2p by RNA pol II elongation factor Spt4-Spt5/DSIF promotes mRNA localization to the yeast bud. Genes Dev 24(17):1914-26	SGD
mRNA splicing, via spliceosome	IMP: Inferred from Mutant Phenotype Assigned on 2012-02-24	Lindstrom DL, et al.  (2003) Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol Cell Biol 23(4):1368-78	SGD
negative regulation of transcription elongation from RNA polymerase I promoter	IGI: Inferred from Genetic Interaction with SGD:RPA49 Assigned on 2012-02-24	Anderson SJ, et al.  (2011) The transcription elongation factor Spt5 influences transcription by RNA polymerase I positively and negatively. J Biol Chem 286(21):18816-24	SGD
positive regulation of transcription elongation from RNA polymerase I promoter	IMP: Inferred from Mutant Phenotype Assigned on 2012-02-24	Schneider DA, et al.  (2006) RNA polymerase II elongation factors Spt4p and Spt5p play roles in transcription elongation by RNA polymerase I and rRNA processing. Proc Natl Acad Sci U S A 103(34):12707-12	SGD
positive regulation of transcription elongation from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2012-02-24	Rondon AG, et al.  (2003) Molecular evidence for a positive role of Spt4 in transcription elongation. EMBO J 22(3):612-20	SGD
regulation of rRNA processing	IMP: Inferred from Mutant Phenotype Assigned on 2012-02-24	Lepore N and Lafontaine DL  (2011) A Functional Interface at the rDNA Connects rRNA Synthesis, Pre-rRNA Processing and Nucleolar Surveillance in Budding Yeast. PLoS One 6(9):e24962	SGD
regulation of transcription, DNA-dependent	IMP: Inferred from Mutant Phenotype Assigned on 2001-12-05	Hartzog GA, et al.  (1998) Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev 12(3):357-69	SGD
regulation of transcription-coupled nucleotide-excision repair	IGI: Inferred from Genetic Interaction with SGD:RAD26 Assigned on 2012-02-24	Ding B, et al.  (2010) The C-terminal repeat domain of Spt5 plays an important role in suppression of Rad26-independent transcription coupled repair. J Biol Chem 285(8):5317-26	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
DSIF complex	IPI: Inferred from Physical Interaction with SGD:SPT5 Assigned on 2006-04-21	Hartzog GA, et al.  (1998) Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev 12(3):357-69	SGD
colocalizes_with kinetochore	IDA: Inferred from Direct Assay Assigned on 2012-02-24	Crotti LB and Basrai MA  (2004) Functional roles for evolutionarily conserved Spt4p at centromeres and heterochromatin in Saccharomyces cerevisiae. EMBO J 23(8):1804-14	SGD
colocalizes_with mating-type region heterochromatin	IDA: Inferred from Direct Assay Assigned on 2012-02-24	Crotti LB and Basrai MA  (2004) Functional roles for evolutionarily conserved Spt4p at centromeres and heterochromatin in Saccharomyces cerevisiae. EMBO J 23(8):1804-14	SGD
colocalizes_with nuclear telomeric heterochromatin	IDA: Inferred from Direct Assay Assigned on 2012-02-24	Crotti LB and Basrai MA  (2004) Functional roles for evolutionarily conserved Spt4p at centromeres and heterochromatin in Saccharomyces cerevisiae. EMBO J 23(8):1804-14	SGD
colocalizes_with rDNA heterochromatin	IDA: Inferred from Direct Assay Assigned on 2009-01-23	Schneider DA, et al.  (2006) RNA polymerase II elongation factors Spt4p and Spt5p play roles in transcription elongation by RNA polymerase I and rRNA processing. Proc Natl Acad Sci U S A 103(34):12707-12	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.

There are no High-throughput annotations for SPT4

** 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
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
zinc ion binding	IEA: Inferred from Electronic Annotation with EBI:IPR009287 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
mRNA processing	IEA: Inferred from Electronic Annotation with EBI:KW-0507 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
positive regulation of DNA-dependent transcription, elongation	IEA: Inferred from Electronic Annotation with EBI:IPR009287 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:IPR009287 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
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
chromosome	IEA: Inferred from Electronic Annotation with EBI:KW-0158 Last updated 2013-03-02	UniProt-GOA  (2011) Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.	UniProtKB
chromosome, centromeric region	IEA: Inferred from Electronic Annotation with EBI:SL-0047 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-0137 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:IPR009287 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-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)).