The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Known motif	1 Monomer or homomultimer	High-throughput in vitro	ChIP-seq motif is consistent with recognition code (RCADE)

Description

Description:

ZFP90 zinc finger protein [Source:HGNC Symbol;Acc:HGNC:23329]

Entrez Summary

This gene encodes a member of the zinc finger protein family that modulates gene expression. The encoded protein derepresses the transcription of certain fetal cardiac genes and may contribute to the genetic reprogramming that occurs during the development of heart failure. Genome wide association studies have identified this gene among ulcerative colitis risk loci. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Mar 2015]

Ensembl ID:

ENSG00000184939

External Link:

CisBP

Interpro

IPR001909; IPR007087; IPR015880; ;

Protein Domain:

ENSP00000454418

Protein Domain:

ENSP00000460547

Protein Domain:

ENSP00000480309

Protein Domain:

ENSP00000458410

Protein Domain:

ENSP00000459846

Domain:

Protein: ENSP00000454418	DBD: C2H2 ZF Containing Proteins	Other: KRAB
Protein: ENSP00000460547	DBD: C2H2 ZF Containing Proteins	Other: KRAB
Protein: ENSP00000480309	DBD: C2H2 ZF Containing Proteins	Other: KRAB
Protein: ENSP00000458410	DBD: C2H2 ZF Containing Proteins	Other: KRAB
Protein: ENSP00000459846	DBD: C2H2 ZF Containing Proteins	Other:

Previous Annotations

Source	Annotation
TF-CAT classification	TF Gene_DNA-Binding sequence-specific_DNA Binding Transactivation_ PMIDS:7576184 11501753
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.	x
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:0001078 RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a 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
RCADE	Imbeault2017		Direct - consistent with recognition code (RCADE)

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 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": 211, "scoreName": "E-value", "accession": "PF00096.24", "start": 211, "score": 1.1e-64, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 233}}, {"startStyle": "curved", "end": 276, "endStyle": "curved", "aliStart": 254, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 276, "start": 254, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 276, "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. 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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. 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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": 450, "scoreName": "E-value", "accession": "PF00096.24", "start": 450, "score": 1.1e-64, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 472}}, {"startStyle": "curved", "end": 519, "endStyle": "curved", "aliStart": 497, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 519, "start": 497, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 519, "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 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": 525, "scoreName": "E-value", "accession": "PF00096.24", "start": 525, "score": 1.1e-64, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 547}}, {"startStyle": "curved", "end": 575, "endStyle": "curved", "aliStart": 553, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 575, "start": 553, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 575, "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": 553, "scoreName": "E-value", "accession": "PF00096.24", "start": 553, "score": 1.1e-64, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 575}}, {"startStyle": "curved", "end": 603, "endStyle": "curved", "aliStart": 581, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 603, "start": 581, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 603, "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": 581, "scoreName": "E-value", "accession": "PF00096.24", "start": 581, "score": 1.1e-64, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 603}}, {"startStyle": "curved", "end": 631, "endStyle": "curved", "aliStart": 609, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 631, "start": 609, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 631, "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": 609, "scoreName": "E-value", "accession": "PF00096.24", "start": 609, "score": 1.1e-64, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 631}}, {"startStyle": "straight", "end": 54, "endStyle": "straight", "aliStart": 13, "text": "KRAB", "colour": "#9999ff", "aliEnd": 54, "start": 13, "href": "http://pfam.xfam.org/family/PF01352.25", "type": "pfama", "display": "true", "metadata": {"end": 54, "description": "The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers.  The KRAB domain is found to be involved in protein-protein interactions [2,3].  The KRAB domain is generally encoded by two exons.  The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation [4].", "database": "PfamA", "aliStart": 13, "scoreName": "E-value", "accession": "PF01352.25", "start": 13, "score": 1.3e-25, "identifier": "KRAB box", "type": "DBD", "aliEnd": 54}}], "length": 637}

{"regions": [{"startStyle": "straight", "end": 54, "endStyle": "straight", "aliStart": 13, "text": "KRAB", "colour": "#9999ff", "aliEnd": 54, "start": 13, "href": "http://pfam.xfam.org/family/PF01352.25", "type": "pfama", "display": "true", "metadata": {"end": 54, "description": "The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers.  The KRAB domain is found to be involved in protein-protein interactions [2,3].  The KRAB domain is generally encoded by two exons.  The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation [4].", "database": "PfamA", "aliStart": 13, "scoreName": "E-value", "accession": "PF01352.25", "start": 13, "score": 1.3999999999999998e-26, "identifier": "KRAB box", "type": "DBD", "aliEnd": 54}}], "length": 114}

{"regions": [{"startStyle": "straight", "end": 43, "endStyle": "straight", "aliStart": 2, "text": "KRAB", "colour": "#9999ff", "aliEnd": 43, "start": 2, "href": "http://pfam.xfam.org/family/PF01352.25", "type": "pfama", "display": "true", "metadata": {"end": 43, "description": "The KRAB domain (or Kruppel-associated box) is present in about a third of zinc finger proteins containing C2H2 fingers.  The KRAB domain is found to be involved in protein-protein interactions [2,3].  The KRAB domain is generally encoded by two exons.  The regions coded by the two exons are known as KRAB-A and KRAB-B. The A box plays an important role in repression by binding to corepressors, while the B box is thought to enhance this repression brought about by the A box. KRAB-containing proteins are thought to have critical functions in cell proliferation and differentiation, apoptosis and neoplastic transformation [4].", "database": "PfamA", "aliStart": 2, "scoreName": "E-value", "accession": "PF01352.25", "start": 2, "score": 1.1e-26, "identifier": "KRAB box", "type": "DBD", "aliEnd": 43}}], "length": 103}

TF Info Page for ZFP90 (C2H2 ZF(KRAB))

Conclusion

Description

Previous Annotations

DNA-Binding

Published Motif Data

Structure

Experimental History

External Contribution