The Human Transcription Factors

Conclusion

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

Description

Description:

Kruppel like factor 4 [Source:HGNC Symbol;Acc:HGNC:6348]

Entrez Summary

This gene encodes a protein that belongs to the Kruppel family of transcription factors. The encoded zinc finger protein is required for normal development of the barrier function of skin. The encoded protein is thought to control the G1-to-S transition of the cell cycle following DNA damage by mediating the tumor suppressor gene p53. Mice lacking this gene have a normal appearance but lose weight rapidly, and die shortly after birth due to fluid evaporation resulting from compromised epidermal barrier function. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2015]

Ensembl ID:

ENSG00000136826

External Link:

CisBP

Interpro

IPR007087; IPR015880;

Protein Domain:

ENSP00000363804

Protein Domain:

ENSP00000399921

Protein Domain:

ENSP00000404922

Protein Domain:

ENSP00000483629

Domain:

Protein: ENSP00000363804	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000399921	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000404922	DBD: C2H2 ZF Containing Proteins	Other:
Protein: ENSP00000483629	DBD: C2H2 ZF Containing Proteins	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	No PMIDS:
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:0001010 sequence-specific DNA binding transcription factor recruiting transcription factor activity ISS - GO_REF:0000024 GO:0001077 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a IMP - PMID:21539536 GO:0003700 sequence-specific DNA binding transcription factor activity NAS - PMID:9422764 GO:0032088 negative regulation of NF-kappaB transcription factor activity IDA - PMID:20551324
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
ChIP-seq	Najafabadi2015		Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Transfac	Transfac	License required	Direct
Misc	HocoMoco		Direct
ChIP-seq	hmCHIP		Inferred - Klf4 (100% AA Identity, Mus musculus)
ChIP-seq	JASPAR		Inferred - Klf4 (100% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - KLF2 (94% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - KLF2 (94% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - KLF2 (94% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - KLF1 (84% AA Identity, Homo sapiens)
ChIP-seq	Schmitges2016		Inferred - KLF1 (84% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - KLF1 (84% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - KLF1 (84% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - KLF1 (84% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - KLF1 (83% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - KLF1 (83% AA Identity, Homo sapiens)
PBM	Barrera2016		Inferred - KLF1 (83% AA Identity, Homo sapiens)
ChIP-seq	JASPAR		Inferred - Klf1 (83% AA Identity, Mus musculus)
Misc	HOMER		Inferred - Klf1 (83% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - KLF5 (82% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - KLF5 (82% AA Identity, Homo sapiens)
ChIP-seq	JASPAR		Inferred - KLF5 (82% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - KLF5 (82% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - KLF5 (82% AA Identity, Homo sapiens)
Misc	HOMER		Inferred - KLF5 (82% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - KLF3 (80% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - KLF3 (80% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - KLF3 (80% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - KLF3 (80% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - KLF3 (80% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - KLF3 (80% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - KLF12 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - KLF12 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - KLF12 (78% AA Identity, Homo sapiens)
PBM	DREAM_contest		Inferred - Klf12 (78% AA Identity, Mus musculus)
PBM	Badis09		Inferred - Klf7 (78% AA Identity, Mus musculus)
HT-SELEX	Nitta2015		Inferred - luna (78% AA Identity, Drosophila melanogaster)
ChIP-seq	Schmitges2016		Inferred - KLF12 (78% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - KLF12 (78% AA Identity, Homo sapiens)
ChIP-seq	Schmitges2016		Inferred - KLF7 (78% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - KLF6 (76% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - KLF6 (76% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - KLF6 (76% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - KLF6 (76% AA Identity, Homo sapiens)
PBM	DREAM_contest		Inferred - Klf8 (75% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - KLF8 (75% AA Identity, Homo sapiens)
Misc	HocoMoco		Inferred - KLF8 (75% AA Identity, Homo sapiens)
PBM	CEPD		Inferred - klf-3 (72% AA Identity, Caenorhabditis elegans)

Structure

Structure	PDB	2WBS

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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{"regions": [{"startStyle": "curved", "end": 86, "endStyle": "curved", "aliStart": 62, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 86, "start": 62, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 86, "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": 62, "scoreName": "E-value", "accession": "PF00096.24", "start": 62, "score": 3.2e-18, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 86}}, {"startStyle": "curved", "end": 116, "endStyle": "curved", "aliStart": 92, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 116, "start": 92, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 116, "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": 92, "scoreName": "E-value", "accession": "PF00096.24", "start": 92, "score": 3.2e-18, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 116}}, {"startStyle": "curved", "end": 144, "endStyle": "curved", "aliStart": 122, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 144, "start": 122, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 144, "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": 122, "scoreName": "E-value", "accession": "PF00096.24", "start": 122, "score": 3.2e-18, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 144}}], "length": 146}

TF Info Page for KLF4 (C2H2 ZF(non-KRAB))

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution