TF Info Page for PRDM9 (C2H2 ZF)


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: PR domain 9 [Source:HGNC Symbol;Acc:HGNC:13994]
Entrez Summary The protein encoded by this gene is a zinc finger protein with histone methyltransferase activity that catalyzes histone H3 lysine 4 trimethylation (H3K4me3) during meiotic prophase. This protein contains multiple domains, including a Kruppel-associated box (KRAB) domain, an SSX repression domain (SSXRD), a PRD1-BF1 and RIZ homologous region, a subclass of SET (PR/SET) domain, and a tandem array of C2H2 zinc fingers. The zinc finger array recognizes a short sequence motif, leading to local H3K4me3, and meiotic recombination hotspot activity. The observed allelic variation alters the DNA-binding sequence specificity of the protein, resulting in distinct meiotic recombination hotspots amongst individuals and populations. Multiple alternate alleles of this gene have been described. [provided by RefSeq, Jul 2015]
Ensembl ID: ENSG00000164256
External Link: CisBP
Interpro IPR001214; IPR001909; IPR003655; IPR007087; IPR015880; IPR019041;
Protein Domain: ENSP00000296682
Protein Domain: ENSP00000425471
Protein Domain: ENSP00000489227
Protein: ENSP00000296682DBD: C2H2 ZF Containing ProteinsOther: KRAB, SET, SSXRD, zf-C2H2_4
Protein: ENSP00000425471DBD: C2H2 ZF Containing ProteinsOther: KRAB, Phage_F
Protein: ENSP00000489227DBD: C2H2 ZF Containing ProteinsOther: SET, SSXRD

Previous Annotations

Source Annotation
TF-CAT classification No
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.
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
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


Published Motif Data

Source Annotation Motif Evidence
RCADEImbeault2017Direct - consistent with recognition code (RCADE)


Structure PDB 5EGB

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