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
EDS1/YBR033W	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
ERT1/YBR239C	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
FHL1/YPR104C	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 2009-02-05	high-throughput	Zhu C, et al.  (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66	SGD
	IEA: Inferred from Electronic Annotation with EBI:IPR001766, EBI:IPR018122 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
FKH1/YIL131C	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
	IEA: Inferred from Electronic Annotation with EBI:IPR018122, EBI:IPR001766 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
FKH2/YNL068C	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:IPR018122, EBI:IPR001766 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
FZF1/YGL254W	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
GAL4/YPL248C	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
GAT1/YFL021W	IGI: Inferred from Genetic Interaction with SGD:GLN3 Assigned on 2010-03-04	manually curated	Stanbrough M, et al.  (1995) Role of the GATA factors Gln3p and Nil1p of Saccharomyces cerevisiae in the expression of nitrogen-regulated genes. Proc Natl Acad Sci U S A 92(21):9450-4	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
	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:IPR000679 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
GAT2/YMR136W	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
GAT3/YLR013W	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
	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:IPR000679 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
GAT4/YIR013C	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:IPR000679 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
GCN4/YEL009C	IDA: Inferred from Direct Assay Assigned on 2010-02-26	manually curated	Hope IA and Struhl K  (1985) GCN4 protein, synthesized in vitro, binds HIS3 regulatory sequences: implications for general control of amino acid biosynthetic genes in yeast. Cell 43(1):177-88	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-02-26	manually curated	Sellers JW, et al.  (1990) Mutations that define the optimal half-site for binding yeast GCN4 activator protein and identify an ATF/CREB-like repressor that recognizes similar DNA sites. Mol Cell Biol 10(10):5077-86	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-02-26	manually curated	Arndt K and Fink GR  (1986) GCN4 protein, a positive transcription factor in yeast, binds general control promoters at all 5' TGACTC 3' sequences. Proc Natl Acad Sci U S A 83(22):8516-20	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-02-26	manually curated	Hope IA and Struhl K  (1986) Functional dissection of a eukaryotic transcriptional activator protein, GCN4 of yeast. Cell 46(6):885-94	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-02-26	manually curated	Roussou I, et al.  (1988) Transcriptional-translational regulatory circuit in Saccharomyces cerevisiae which involves the GCN4 transcriptional activator and the GCN2 protein kinase. Mol Cell Biol 8(5):2132-9	SGD
	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
	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
GIS1/YDR096W	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
GLN3/YER040W	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:IPR000679 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
GSM1/YJL103C	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
GZF3/YJL110C	IDA: Inferred from Direct Assay Assigned on 2010-03-26	manually curated	Coffman JA, et al.  (1997) Cross regulation of four GATA factors that control nitrogen catabolic gene expression in Saccharomyces cerevisiae. J Bacteriol 179(11):3416-29	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
	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:IPR000679 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
HAC1/YFL031W	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
HAL9/YOL089C	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
HAP1/YLR256W	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
HAP3/YBL021C	IEA: Inferred from Electronic Annotation with EBI:IPR003958, EBI:IPR003956 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
HCM1/YCR065W	IDA: Inferred from Direct Assay, IMP: Inferred from Mutant Phenotype Assigned on 2007-08-28	manually curated	Zhu G and Davis TN  (1998) The fork head transcription factor Hcm1p participates in the regulation of SPC110, which encodes the calmodulin-binding protein in the yeast spindle pole body. Biochim Biophys Acta 1448(2):236-44	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:IPR018122, EBI:IPR001766 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
HMLALPHA1/YCL066W	IEA: Inferred from Electronic Annotation with EBI:IPR016325 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
HMLALPHA2/YCL067C	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
HMRA1/YCR097W	IEA: Inferred from Electronic Annotation with EBI:IPR001356, EBI:IPR017970 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
HMRA2/YCR096C	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:IPR001356 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
HMS2/YJR147W	IEA: Inferred from Electronic Annotation with EBI:IPR000232 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
HSF1/YGL073W	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:IPR000232 Last Updated 2013-03-02	computational	DDB, et al.  (2001) Gene Ontology annotation through association of InterPro records with GO terms.	InterPro
IXR1/YKL032C	IDA: Inferred from Direct Assay Assigned on 2010-02-24	manually curated	Bourdineaud JP, et al.  (2000) A Rox1-independent hypoxic pathway in yeast. Antagonistic action of the repressor Ord1 and activator Yap1 for hypoxic expression of the SRP1/TIR1 gene. Mol Microbiol 38(4):879-90	SGD
	IDA: Inferred from Direct Assay Assigned on 2010-02-24	manually curated	Castro-Prego R, et al.  (2010) Regulatory factors controlling transcription of Saccharomyces cerevisiae IXR1 by oxygen levels: a model of transcriptional adaptation from aerobiosis to hypoxia implicating ROX1 and IXR1 cross-regulation. Biochem J 425(1):235-43	SGD
LEU3/YLR451W	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
LYS14/YDR034C	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

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