The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	1 Monomer or homomultimer	100 perc ID - in vitro

Description

Description:

Kruppel like factor 9 [Source:HGNC Symbol;Acc:HGNC:1123]

Entrez Summary

The protein encoded by this gene is a transcription factor that binds to GC box elements located in the promoter. Binding of the encoded protein to a single GC box inhibits mRNA expression while binding to tandemly repeated GC box elements activates transcription. [provided by RefSeq, Jul 2008]

Ensembl ID:

ENSG00000119138

External Link:

CisBP

Interpro

IPR007087; IPR015880;

Protein Domain:

ENSP00000366330

Domain:

Protein: ENSP00000366330	DBD: C2H2 ZF Containing Proteins	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding Transactivation_ PMIDS:9858544 11751593
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:1356762, PMID:8051167
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
PBM	DREAM_contest		Inferred - Klf9 (100% AA Identity, Mus musculus)
Transfac	Transfac	License required	Inferred - Klf9 (100% AA Identity, Mus musculus)
HT-SELEX	Yin2017		Inferred - KLF13 (82% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - KLF13 (82% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - KLF13 (82% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - KLF13 (82% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - ENSG00000275746 (82% AA Identity, Homo sapiens)
HT-SELEX	Yin2017		Inferred - KLF14 (73% AA Identity, Homo sapiens)
Methyl-HT-SELEX	Yin2017		Inferred - KLF14 (73% AA Identity, Homo sapiens)
ChIP-seq	Schmitges2016		Inferred - KLF14 (73% AA Identity, Homo sapiens)
Transfac	Transfac	License required	Inferred - Klf16 (73% 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

{"regions": [{"startStyle": "curved", "end": 167, "endStyle": "curved", "aliStart": 143, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 167, "start": 143, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 167, "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": 143, "scoreName": "E-value", "accession": "PF00096.24", "start": 143, "score": 1.7e-15, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 167}}, {"startStyle": "curved", "end": 197, "endStyle": "curved", "aliStart": 173, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 197, "start": 173, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 197, "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": 173, "scoreName": "E-value", "accession": "PF00096.24", "start": 173, "score": 1.7e-15, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 197}}, {"startStyle": "curved", "end": 225, "endStyle": "curved", "aliStart": 203, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 225, "start": 203, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 225, "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": 203, "scoreName": "E-value", "accession": "PF00096.24", "start": 203, "score": 1.7e-15, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 225}}], "length": 245}

TF Info Page for KLF9 (C2H2 ZF(non-KRAB))