The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	1 Monomer or homomultimer	In vivo/Misc source

Description

Description:

GLI family zinc finger 1 [Source:HGNC Symbol;Acc:HGNC:4317]

Entrez Summary

Ensembl ID:

ENSG00000111087

External Link:

CisBP

Interpro

IPR007087; IPR015880;

Protein Domain:

ENSP00000228682

Protein Domain:

ENSP00000434408

Protein Domain:

ENSP00000434421

Protein Domain:

ENSP00000436671

Domain:

Protein: ENSP00000228682	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000434408	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000434421	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000436671	DBD: C2H2 ZF Containing Proteins	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding Transactivation_ PMIDS:10559945 11719506 15087129
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"	No
GO-Info	GO:0003705 RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity IEA - GO_REF:0000019
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
SELEX	Hallikas2006		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
PBM	Peterson2012		Inferred - Gli1 (99% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - GLI3 (85% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - GLI3 (85% AA Identity, Homo sapiens)
SELEX	Hallikas2006		Inferred - GLI3 (85% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - GLI3 (85% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - GLI3 (85% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - GLI3 (85% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - GLI3 (85% AA Identity, Homo sapiens)
PBM	Peterson2012		Inferred - Gli3 (84% AA Identity, Mus musculus)
ChIP-seq	hmCHIP		Inferred - Gli3 (84% AA Identity, Mus musculus)
Misc	HOMER		Inferred - Gli3 (84% AA Identity, Mus musculus)
HT-SELEX	Jolma2010		Inferred - GLI2 (83% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - GLI2 (83% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - GLI2 (83% AA Identity, Homo sapiens)
PBM	Peterson2012		Inferred - Gli2 (83% AA Identity, Mus musculus)
SELEX	Hallikas2006		Inferred - GLI2 (83% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - GLI2 (83% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - GLI2 (83% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - GLI2 (83% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - GLI2 (83% AA Identity, Homo sapiens)
HT-SELEX	Nitta2015		Inferred - ci (78% AA Identity, Drosophila melanogaster)
SELEX	Hallikas2006		Inferred - ci (78% AA Identity, Drosophila melanogaster)
Transfac	Transfac	License required	Inferred - ci (78% AA Identity, Drosophila melanogaster)

Structure

Structure	PDB	2GLI

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": 321, "scoreName": "E-value", "accession": "PF00096.24", "start": 321, "score": 2.8e-19, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 346}}], "length": 1065}

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TF Info Page for GLI1 (C2H2 ZF(non-KRAB))

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution