The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	1 Monomer or homomultimer	High-throughput in vitro

Description

Description:	early growth response 3 [Source:HGNC Symbol;Acc:HGNC:3240]
Entrez Summary	TBA
Ensembl ID:	ENSG00000179388
External Link:	T044597_1.02
Interpro	IPR007087; IPR015880; IPR021849; ;
Protein Domain:
Protein: ENSP00000318057	DBD: C2H2 ZF Containing Proteins	Other: DUF3446
Protein: ENSP00000430310	DBD: C2H2 ZF Containing Proteins	Other: DUF3446
Protein: ENSP00000429370	DBD: C2H2 ZF Containing Proteins	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene Candidate_DNA-Binding sequence-specific_Transactivation_ PMIDS:1906159
Vaquerizas 2009 TF classification "a" Has direct evidence of TF function; "b" Has evidence for an orthologous TF; "c" contains likely DBDs, but has no functional evidence; "x" is an unlikely TF such as predicted gene, genes with likely non-specific DBDs or that have function outside transcription; "other" category contains proteins without clear DBDs they curated from external sources.	a
CisBP considers it as a TF?	Yes
TFclass considers it as a TF?	Yes
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding"	Yes
GO-Info	GO:0003700 sequence-specific DNA binding transcription factor activity TAS - PMID:1906159, PMID:9731539
Initial Assessment 1a1 Protein has a high confidence PWM (HT-SELEX, PBM or B1H model) or there is a crystal structure that supports sequence specific DNA binding; 1a2 There is high confidence data for a close ortholog (as defined in CisBP); 2a1 There is lower confidence direct evidence, such as a Jaspar, Hocomoco or Transfac model; 2a2 There is lower confidence evidence for an close ortholog; 3a There is decent circumstantial evidence for its role as a TF or not; 4a Two or more datasets predict it as a TF; 5a One of the source datasets predicts is as a TF	1a1, Direct HQ evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence
HT-SELEX	Jolma2013		Direct
RCADE	Schmitges2016		Direct
HT-SELEX	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
PBM	DREAM_contest		Inferred - Egr3 (100% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - EGR2 (90% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - EGR2 (90% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - EGR2 (90% AA Identity, Homo sapiens)
PBM	DREAM_contest		Inferred - Egr2 (90% AA Identity, Mus musculus)
SELEX	JASPAR		Inferred - EGR2 (90% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EGR2 (90% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EGR2 (90% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - EGR2 (90% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - Egr2 (90% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - EGR1 (88% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - EGR1 (88% AA Identity, Homo sapiens)
PBM	Berger06		Inferred - Egr1 (88% AA Identity, Mus musculus)
SMiLE-seq	Isakova2017		Inferred - Egr1 (88% AA Identity, Mus musculus)
PBM	Zoo_01		Inferred - Egr1 (88% AA Identity, Mus musculus)
PBM	Barrera2016		Inferred - EGR2 (88% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - EGR2 (88% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - EGR2 (88% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - EGR2 (88% AA Identity, Homo sapiens)
ChIP-seq	ENCODE		Inferred - EGR1 (88% AA Identity, Homo sapiens)
ChIP-seq	ENCODE		Inferred - EGR1 (88% AA Identity, Homo sapiens)
ChIP-seq	ENCODE		Inferred - EGR1 (88% AA Identity, Homo sapiens)
ChIP-seq	JASPAR		Inferred - EGR1 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EGR1 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EGR1 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EGR1 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EGR1 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EGR1 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EGR1 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EGR1 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EGR1 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EGR1 (88% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EGR1 (88% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - EGR1 (88% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - EGR1 (88% AA Identity, Homo sapiens)
PBM	Badis09		Inferred - Egr1 (87% AA Identity, Mus musculus)
PBM	CEPD		Inferred - egrh-1 (81% AA Identity, Caenorhabditis elegans)
HT-SELEX	Yin2017		Inferred - EGR4 (77% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - EGR4 (77% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - EGR4 (77% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - EGR4 (77% AA Identity, Homo sapiens)

Structure

Structure	PDB	Not_Covered

Experimental History

Method	Constructs
Tried in PBM? (Whether the protein was tried in PBM or not)
Tried in HT-SELEX (Whether the protein was tried in HT-SELEX or not, and if so, then what kind of clones were tested)
Other Information? (Tried with another method and failed?)

External Contribution

Name
Email
Comment
Reference

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The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. 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The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 267, "scoreName": "E-value", "accession": "PF00096.24", "start": 267, "score": 5.2e-15, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 289}}, {"startStyle": "curved", "end": 317, "endStyle": "curved", "aliStart": 295, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 317, "start": 295, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 317, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. 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The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity  site for Sp1 binding to the wt1 promoter [2].", "database": "PfamA", "aliStart": 295, "scoreName": "E-value", "accession": "PF00096.24", "start": 295, "score": 5.2e-15, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 317}}, {"startStyle": "jagged", "end": 293, "endStyle": "jagged", "aliStart": 257, "text": "zfBED", "colour": "#2cb42c", "aliEnd": 289, "start": 252, "href": "http://pfam.xfam.org/family/PF02892.13", "type": "pfama", "display": "true", "metadata": {"end": 293, "description": "The BED finger, which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain [PUBMED:10973053].", "database": "PfamA", "aliStart": 257, "scoreName": "E-value", "accession": "PF02892.13", "start": 252, "score": 0.0063, "identifier": "BED zinc finger", "type": "DBD", "aliEnd": 289}}, {"startStyle": "straight", "end": 118, "endStyle": "straight", "aliStart": 49, "text": "DUF3446", "colour": "#9999ff", "aliEnd": 118, "start": 49, "href": "http://pfam.xfam.org/family/PF11928.6", "type": "pfama", "display": "true", "metadata": {"end": 118, "description": "This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 80 to 99 amino acids in length. 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TF Info Page for EGR3 (C2H2 ZF(non-KRAB))