Ontology: Molecular Function (GO:0043565)

Definition: Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.

Synonyms: sequence specific DNA binding

View Ontology: (graph) | (text)

This table lists the methods used to annotate genes either directly to the term sequence-specific DNA binding (167 genes) or to its variants containing one or more qualifiers (0 genes). Note that some genes may have been annotated by more than one method so the numbers in the table below may not add up to the totals given here.

Annotation Method	GO Term	# Yeast Genes Annotated
Manually curated (download data)	sequence-specific DNA binding	35
High-throughput (download data)	sequence-specific DNA binding	134
Computational (download data)	sequence-specific DNA binding	52

Links to Additional Annotations:

• View annotations in multiple organisms using
• Search for S. cerevisiae genes annotated, by the Manually curated or High-throughput methods, to this term or to any terms that are descended from this term, i.e., child terms representing more specific biology than this term.

Annotation details for genes that have been directly annotated to the term sequence-specific DNA binding or its variants containing one or more qualifiers (NOT, contributes to, or colocalizes with).

sequence-specific DNA binding      167 genes directly annotated to this term
Locus	Evidence	Annotation Method	Reference	Assigned By
ABF1/YKL112W	IDA: Inferred from Direct Assay Assigned on 2012-02-15	manually curated	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
	IDA: Inferred from Direct Assay Assigned on 2012-02-15	manually curated	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 2009-02-05	high-throughput	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
ACA1/YER045C	IDA: Inferred from Direct Assay Assigned on 2011-08-04	manually curated	Garcia-Gimeno MA and Struhl K  (2000) Aca1 and Aca2, ATF/CREB activators in Saccharomyces cerevisiae, are important for carbon source utilization but not the response to stress. Mol Cell Biol 20(12):4340-9	SGD
	IEA: Inferred from Electronic Annotation with EBI:IPR004827 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
ACE2/YLR131C	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
ADR1/YDR216W	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
AFT1/YGL071W	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	SGD
AFT2/YPL202C	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
ARO80/YDR421W	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	SGD
ARR1/YPR199C	IEA: Inferred from Electronic Annotation with EBI:IPR004827 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
ASG1/YIL130W	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
	IDA: Inferred from Direct Assay Assigned on 2009-03-09	high-throughput	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	SGD
ASH1/YKL185W	IEA: Inferred from Electronic Annotation with EBI:IPR000679 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
AZF1/YOR113W	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
BAS1/YKR099W	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	SGD
BUR6/YER159C	IEA: Inferred from Electronic Annotation with EBI:IPR003958 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
CAD1/YDR423C	IDA: Inferred from Direct Assay Assigned on 2012-01-09	manually curated	Fernandes L, et al.  (1997) Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions. Mol Cell Biol 17(12):6982-93	SGD
	IEA: Inferred from Electronic Annotation with EBI:IPR004827 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
CAT8/YMR280C	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
CBF1/YJR060W	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
	IDA: Inferred from Direct Assay Assigned on 2009-03-09	high-throughput	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	SGD
CEP3/YMR168C	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
	IDA: Inferred from Direct Assay Assigned on 2009-03-09	high-throughput	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	SGD
CHA4/YLR098C	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
	IDA: Inferred from Direct Assay Assigned on 2009-03-09	high-throughput	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	SGD
CIN5/YOR028C	IDA: Inferred from Direct Assay Assigned on 2011-08-16	manually curated	Fordyce PM, et al.  (2010) De novo identification and biophysical characterization of transcription-factor binding sites with microfluidic affinity analysis. Nat Biotechnol 28(9):970-5	SGD
	IDA: Inferred from Direct Assay Assigned on 2011-08-16	manually curated	Fernandes L, et al.  (1997) Yap, a novel family of eight bZIP proteins in Saccharomyces cerevisiae with distinct biological functions. Mol Cell Biol 17(12):6982-93	SGD
	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
	IEA: Inferred from Electronic Annotation with EBI:IPR004827 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
CMR3/YPR013C	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
	IDA: Inferred from Direct Assay Assigned on 2009-03-09	high-throughput	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	SGD
CRZ1/YNL027W	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
CSE4/YKL049C	IDA: Inferred from Direct Assay Assigned on 2006-10-26	manually curated	Hajra S, et al.  (2006) The centromere-specific histone variant Cse4p (CENP-A) is essential for functional chromatin architecture at the yeast 2-microm circle partitioning locus and promotes equal plasmid segregation. J Cell Biol 174(6):779-90	SGD
CST6/YIL036W	IDA: Inferred from Direct Assay Assigned on 2011-10-17	manually curated	Garcia-Gimeno MA and Struhl K  (2000) Aca1 and Aca2, ATF/CREB activators in Saccharomyces cerevisiae, are important for carbon source utilization but not the response to stress. Mol Cell Biol 20(12):4340-9	SGD
	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
	IEA: Inferred from Electronic Annotation with EBI:IPR004827 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
CUP9/YPL177C	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
	IDA: Inferred from Direct Assay Assigned on 2009-03-09	high-throughput	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	SGD
	IEA: Inferred from Electronic Annotation with EBI:IPR001356 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
DAL80/YKR034W	IDA: Inferred from Direct Assay Assigned on 2009-12-01	manually curated	Cunningham TS and Cooper TG  (1993) The Saccharomyces cerevisiae DAL80 repressor protein binds to multiple copies of GATAA-containing sequences (URSGATA). J Bacteriol 175(18):5851-61	SGD
	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
	IEA: Inferred from Electronic Annotation with EBI:IPR000679 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
DAL82/YNL314W	IDA: Inferred from Direct Assay Assigned on 2011-12-19	manually curated	Dorrington RA and Cooper TG  (1993) The DAL82 protein of Saccharomyces cerevisiae binds to the DAL upstream induction sequence (UIS). Nucleic Acids Res 21(16):3777-84	SGD
	IMP: Inferred from Mutant Phenotype Assigned on 2011-12-21	manually curated	Scott S, et al.  (2000) Functional domain mapping and subcellular distribution of Dal82p in Saccharomyces cerevisiae. J Biol Chem 275(10):7198-204	SGD
	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
DLS1/YJL065C	IEA: Inferred from Electronic Annotation with EBI:IPR003958 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
DOT6/YER088C	IDA: Inferred from Direct Assay Assigned on 2009-02-04	manually curated, high-throughput	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	SGD
	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
ECM22/YLR228C	IDA: Inferred from Direct Assay Assigned on 2009-02-05	high-throughput	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
	IDA: Inferred from Direct Assay Assigned on 2009-03-09	high-throughput	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	SGD
ECM23/YPL021W	IDA: Inferred from Direct Assay Assigned on 2009-03-19	manually curated, high-throughput	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
	IEA: Inferred from Electronic Annotation with EBI:IPR000679 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro

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