The Human Transcription Factors

Conclusion

Assessment	Binding Mode	Motif Status	Notes	Comments
Likely to be sequence specific TF	1 Monomer or homomultimer	No motif

Description

Description:	PR domain 13 [Source:HGNC Symbol;Acc:HGNC:13998]
Entrez Summary	TBA
Ensembl ID:	ENSG00000112238
External Link:	T044289_1.02
Interpro	IPR001214; IPR007087; IPR015880; ;
Protein Domain:
Protein: ENSP00000358217	DBD: C2H2 ZF Containing Proteins	Other: SET

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.	b
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
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	4a, two or more datasets predict it as a TF
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source	Annotation	Motif	Evidence

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": 137, "scoreName": "E-value", "accession": "PF00096.24", "start": 137, "score": 2.1e-18, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 159}}, {"startStyle": "jagged", "end": 595, "endStyle": "curved", "aliStart": 575, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 595, "start": 573, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 595, "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": 575, "scoreName": "E-value", "accession": "PF00096.24", "start": 573, "score": 2.1e-18, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 595}}, {"startStyle": "curved", "end": 623, "endStyle": "curved", "aliStart": 602, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 623, "start": 601, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 623, "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": 602, "scoreName": "E-value", "accession": "PF00096.24", "start": 601, "score": 2.1e-18, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 623}}, {"startStyle": "curved", "end": 653, "endStyle": "curved", "aliStart": 630, "text": "zfC2H2", "colour": "#228B22", "aliEnd": 653, "start": 630, "href": "http://pfam.xfam.org/family/PF00096.24", "type": "pfama", "display": "true", "metadata": {"end": 653, "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": 630, "scoreName": "E-value", "accession": "PF00096.24", "start": 630, "score": 2.1e-18, "identifier": "Zinc finger, C2H2 type", "type": "DBD", "aliEnd": 653}}, {"startStyle": "jagged", "end": 161, "endStyle": "curved", "aliStart": 132, "text": "zfBED", "colour": "#2cb42c", "aliEnd": 159, "start": 117, "href": "http://pfam.xfam.org/family/PF02892.13", "type": "pfama", "display": "true", "metadata": {"end": 161, "description": "The BED finger, which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. 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The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain [PUBMED:10973053].", "database": "PfamA", "aliStart": 575, "scoreName": "E-value", "accession": "PF02892.13", "start": 568, "score": 2.7000000000000002e-05, "identifier": "BED zinc finger", "type": "DBD", "aliEnd": 593}}, {"startStyle": "jagged", "end": 654, "endStyle": "curved", "aliStart": 618, "text": "zfBED", "colour": "#2cb42c", "aliEnd": 654, "start": 614, "href": "http://pfam.xfam.org/family/PF02892.13", "type": "pfama", "display": "true", "metadata": {"end": 654, "description": "The BED finger, which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain [PUBMED:10973053].", "database": "PfamA", "aliStart": 618, "scoreName": "E-value", "accession": "PF02892.13", "start": 614, "score": 2.7000000000000002e-05, "identifier": "BED zinc finger", "type": "DBD", "aliEnd": 654}}, {"startStyle": "jagged", "end": 112, "endStyle": "straight", "aliStart": 88, "text": "SET", "colour": "#9999ff", "aliEnd": 111, "start": 11, "href": "http://pfam.xfam.org/family/PF00856.26", "type": "pfama", "display": "true", "metadata": {"end": 112, "description": "SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases) [2].  A subset of SET domains have been called PR domains.  These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction [3].  The SET domain consists of two regions known as SET-N and SET-C.  SET-C forms an unusual and conserved knot-like structure of probably functional importance.  Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure [5].", "database": "PfamA", "aliStart": 88, "scoreName": "E-value", "accession": "PF00856.26", "start": 11, "score": 0.0018, "identifier": "SET domain", "type": "DBD", "aliEnd": 111}}], "length": 708}

TF Info Page for PRDM13 (C2H2 ZF(non-KRAB))