The Human Transcription Factors

Conclusion

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

Description

Description:	GLI family zinc finger 3 [Source:HGNC Symbol;Acc:HGNC:4319]
Entrez Summary	TBA
Ensembl ID:	ENSG00000106571
External Link:	T044283_1.02
Interpro	IPR007087; IPR015880;
Protein Domain:
Protein: ENSP00000407963	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000406135	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000379258	DBD: C2H2 ZF Containing Proteins	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding Transactivation_ PMIDS:10433919 12435627 16396903
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:0001077 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a IC - GO_REF:0000036 GO:0003700 sequence-specific DNA binding transcription factor activity IDA - PMID:10077605, PMID:17000779, PMID:17764085
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	Yin2017		Direct
Methyl-HT-SELEX	Yin2017		Direct
SELEX	Hallikas2006		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
PBM	Peterson2012		Inferred - Gli3 (98% AA Identity, Mus musculus)
ChIP-seq	hmCHIP		Inferred - Gli3 (98% AA Identity, Mus musculus)
Misc	HOMER		Inferred - Gli3 (98% AA Identity, Mus musculus)
HT-SELEX	Jolma2010		Inferred - GLI2 (92% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - GLI2 (92% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - GLI2 (92% AA Identity, Homo sapiens)
SELEX	Hallikas2006		Inferred - GLI2 (92% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - GLI2 (92% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - GLI2 (92% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - GLI2 (92% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - GLI2 (92% AA Identity, Homo sapiens)
PBM	Peterson2012		Inferred - Gli2 (91% AA Identity, Mus musculus)
HT-SELEX	Nitta2015		Inferred - ci (85% AA Identity, Drosophila melanogaster)
SELEX	Hallikas2006		Inferred - ci (85% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - ci (85% AA Identity, Drosophila melanogaster)
SELEX	Hallikas2006		Inferred - GLI1 (85% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - GLI1 (85% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - GLI1 (85% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - GLI1 (85% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - GLI1 (85% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - GLI1 (85% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - GLI1 (85% AA Identity, Homo sapiens)
PBM	Peterson2012		Inferred - Gli1 (84% AA Identity, Mus musculus)

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. 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": 576, "scoreName": "E-value", "accession": "PF00096.24", "start": 576, "score": 1.6999999999999999e-19, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 601}}, {"startStyle": "curved", "end": 632, "endStyle": "curved", "aliStart": 607, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 632, "start": 607, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 632, "description": "The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. 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": 607, "scoreName": "E-value", "accession": "PF00096.24", "start": 607, "score": 1.6999999999999999e-19, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 632}}], "length": 1581}

TF Info Page for GLI3 (C2H2 ZF(non-KRAB))