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

Last Reviewed on: 2012-02-15    Molecular Function | Biological Process | Cellular Component

Manually curated Molecular Function
Annotation(s)	Evidence	Reference(s)	Assigned By
DNA replication origin binding	IDA: Inferred from Direct Assay Assigned on 2012-02-15	Diffley JF and Stillman B  (1988) Purification of a yeast protein that binds to origins of DNA replication and a transcriptional silencer. Proc Natl Acad Sci U S A 85(7):2120-4	SGD
	IDA: Inferred from Direct Assay Assigned on 2007-08-24	Kawasaki Y, et al.  (2006) Reconstitution of Saccharomyces cerevisiae prereplicative complex assembly in vitro. Genes Cells 11(7):745-56	SGD
RNA polymerase II core promoter proximal region sequence-specific DNA binding	IDA: Inferred from Direct Assay Assigned on 2012-02-15	Yoo HY, et al.  (1995) Transcriptional control of the Saccharomyces cerevisiae ADH1 gene by autonomously replicating sequence binding factor 1. Curr Microbiol 31(3):163-8	SGD
RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription	IDA: Inferred from Direct Assay Assigned on 2012-02-15	Yoo HY, et al.  (1995) Transcriptional control of the Saccharomyces cerevisiae ADH1 gene by autonomously replicating sequence binding factor 1. Curr Microbiol 31(3):163-8	SGD
sequence-specific DNA binding	IDA: Inferred from Direct Assay Assigned on 2012-02-15	Yoo HY, et al.  (1995) Transcriptional control of the Saccharomyces cerevisiae ADH1 gene by autonomously replicating sequence binding factor 1. Curr Microbiol 31(3):163-8	SGD
	IDA: Inferred from Direct Assay Assigned on 2012-02-15	Buchman AR, et al.  (1988) Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae. Mol Cell Biol 8(1):210-25	SGD
sequence-specific DNA binding, bending	IDA: Inferred from Direct Assay Assigned on 2012-02-15	McBroom LD and Sadowski PD  (1994) DNA bending by Saccharomyces cerevisiae ABF1 and its proteolytic fragments. J Biol Chem 269(23):16461-8	SGD

Manually curated Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
chromatin remodeling	IGI: Inferred from Genetic Interaction with SGD:ARS1 Assigned on 2012-02-15 IDA: Inferred from Direct Assay Assigned on 2012-02-15	Bodmer-Glavas M, et al.  (2001) RNA polymerase II and III transcription factors can stimulate DNA replication by modifying origin chromatin structures. Nucleic Acids Res 29(22):4570-80	SGD
	IGI: Inferred from Genetic Interaction with SGD:RPS28A Assigned on 2012-02-15 IDA: Inferred from Direct Assay Assigned on 2012-02-15	Lascaris RF, et al.  (2000) Different roles for abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene. Nucleic Acids Res 28(6):1390-6	SGD
chromatin silencing at silent mating-type cassette	IMP: Inferred from Mutant Phenotype Assigned on 2012-02-15	Zou Y, et al.  (2006) Asymmetric positioning of nucleosomes and directional establishment of transcriptionally silent chromatin by Saccharomyces cerevisiae silencers. Mol Cell Biol 26(20):7806-19	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2005-10-20	Loo S, et al.  (1995) Roles of ABF1, NPL3, and YCL54 in silencing in Saccharomyces cerevisiae. Genetics 141(3):889-902	SGD
DNA-dependent DNA replication	IDA: Inferred from Direct Assay Assigned on 2012-02-15	Miyake T, et al.  (2002) Identification of a multifunctional domain in autonomously replicating sequence-binding factor 1 required for transcriptional activation, DNA replication, and gene silencing. Mol Cell Biol 22(2):505-16	SGD
global genome nucleotide-excision repair	IMP: Inferred from Mutant Phenotype Assigned on 2012-02-15	Reed SH, et al.  (1999) Yeast autonomously replicating sequence binding factor is involved in nucleotide excision repair. Genes Dev 13(23):3052-8	SGD
	IDA: Inferred from Direct Assay Assigned on 2012-02-15	Yu S, et al.  (2004) The yeast Rad7/Rad16/Abf1 complex generates superhelical torsion in DNA that is required for nucleotide excision repair. DNA Repair (Amst) 3(3):277-87	SGD
negative regulation of transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2005-10-20	Miyake T, et al.  (2004) Genome-wide analysis of ARS (autonomously replicating sequence) binding factor 1 (Abf1p)-mediated transcriptional regulation in Saccharomyces cerevisiae. J Biol Chem 279(33):34865-72	SGD
positive regulation of transcription from RNA polymerase II promoter	IMP: Inferred from Mutant Phenotype Assigned on 2005-10-20	Miyake T, et al.  (2004) Genome-wide analysis of ARS (autonomously replicating sequence) binding factor 1 (Abf1p)-mediated transcriptional regulation in Saccharomyces cerevisiae. J Biol Chem 279(33):34865-72	SGD

Manually curated Cellular Component
Annotation(s)	Evidence	Reference(s)	Assigned By
nucleotide-excision repair factor 4 complex	IDA: Inferred from Direct Assay Assigned on 2012-02-15	Reed SH, et al.  (1999) Yeast autonomously replicating sequence binding factor is involved in nucleotide excision repair. Genes Dev 13(23):3052-8	SGD
nucleus	IMP: Inferred from Mutant Phenotype Assigned on 2005-10-20 IDA: Inferred from Direct Assay Assigned on 2005-10-20	Loch CM, et al.  (2004) Functional and physical interactions between autonomously replicating sequence-binding factor 1 and the nuclear transport machinery. Traffic 5(12):925-35	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	Badis G, et al.  (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32(6):878-87	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:IPR006774 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-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

Computational Biological Process
Annotation(s)	Evidence	Reference(s)	Assigned By
chromatin remodeling	IEA: Inferred from Electronic Annotation with EBI:IPR006774 Last updated 2013-03-02	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
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
DNA replication	IEA: Inferred from Electronic Annotation with EBI:KW-0235 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:IPR006774 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)).