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PRDM9 PR/SET domain 9 [ Homo sapiens (human) ]

Gene ID: 56979, updated on 4-Jun-2020

Summary

Official Symbol
PRDM9provided by HGNC
Official Full Name
PR/SET domain 9provided by HGNC
Primary source
HGNC:HGNC:13994
See related
Ensembl:ENSG00000164256 MIM:609760
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PFM6; KMT8B; MSBP3; ZNF899; MEISETZ
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]
Expression
Restricted expression toward testis (RPKM 2.2) See more
Orthologs

Genomic context

See PRDM9 in Genome Data Viewer
Location:
5p14.2
Exon count:
12
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (23507155..23528093)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (23507724..23528706)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene protein tyrosine phosphatase non-receptor type 11 pseudogene Neighboring gene uncharacterized LOC105374688 Neighboring gene uncharacterized LOC107986377 Neighboring gene chromosome 5 putative open reading frame 17 Neighboring gene ADH5 pseudogene 5

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Fine-scale recombination rate differences between sexes, populations and individuals.
NHGRI GWA Catalog
The landscape of recombination in African Americans.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
histone methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone methyltransferase activity (H3-K36 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone methyltransferase activity (H3-K36 specific) IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone methyltransferase activity (H3-K36 specific) ISS
Inferred from Sequence or Structural Similarity
more info
 
histone methyltransferase activity (H3-K4 specific) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone methyltransferase activity (H3-K4 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone methyltransferase activity (H3-K4 specific) IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone-lysine N-methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
 
recombination hotspot binding IDA
Inferred from Direct Assay
more info
PubMed 
recombination hotspot binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
sequence-specific DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription regulatory region sequence-specific DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
double-strand break repair involved in meiotic recombination ISS
Inferred from Sequence or Structural Similarity
more info
 
female gamete generation ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H3-K36 dimethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K36 trimethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H3-K4 dimethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H3-K4 methylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K4 monomethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K4 monomethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H3-K4 trimethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H3-K4 trimethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
histone H3-K9 methylation ISS
Inferred from Sequence or Structural Similarity
more info
 
male gamete generation ISS
Inferred from Sequence or Structural Similarity
more info
 
meiotic gene conversion IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleosome positioning IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of fertilization ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of histone H3-K36 trimethylation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of histone H3-K4 trimethylation ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of reciprocal meiotic recombination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of reciprocal meiotic recombination IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
synapsis ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
chromosome IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
histone-lysine N-methyltransferase PRDM9
Names
PR domain 9
PR domain containing 9
PR domain zinc finger protein 9
[histone H3]-lysine36 N-trimethyltransferase PRDM9
[histone H3]-lysine4 N-trimethyltransferase PRDM9
[histone H3]-lysine9 N-trimethyltransferase PRDM9
[histone H4]-N-methyl-L-lysine20 N-methyltransferase PRDM9
[histone H4]-lysine20 N-methyltransferase PRDM9
histone methyl transferase
minisatellite binding protein 3 (115kD)
protein-lysine N-methyltransferase PRDM9
NP_001363829.1
NP_064612.2

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001310214.2NP_001297143.1  histone-lysine N-methyltransferase PRDM9 isoform PRDM9 A

    See identical proteins and their annotated locations for NP_001297143.1

    Status: REVIEWED

    Source sequence(s)
    AC025451, AK301776
    UniProtKB/Swiss-Prot
    Q9NQV7
    Conserved Domains (7) summary
    smart00317
    Location:246364
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00349
    Location:2785
    KRAB; krueppel associated box
    COG5048
    Location:611878
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:750770
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:2762
    KRAB; KRAB box
    pfam09514
    Location:171201
    SSXRD; SSXRD motif
    pfam13465
    Location:846870
    zf-H2C2_2; Zinc-finger double domain
  2. NM_001376900.1NP_001363829.1  histone-lysine N-methyltransferase PRDM9 PRDM9 C

    Status: REVIEWED

    Source sequence(s)
    AC025451
  3. NM_020227.4NP_064612.2  histone-lysine N-methyltransferase PRDM9 isoform PRDM9 B

    See identical proteins and their annotated locations for NP_064612.2

    Status: REVIEWED

    Source sequence(s)
    AC025451
    Consensus CDS
    CCDS43307.1
    UniProtKB/Swiss-Prot
    Q9NQV7
    Related
    ENSP00000296682.3, ENST00000296682.3
    Conserved Domains (7) summary
    smart00317
    Location:246364
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    smart00349
    Location:2785
    KRAB; krueppel associated box
    COG5048
    Location:611878
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:750770
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam01352
    Location:2762
    KRAB; KRAB box
    pfam09514
    Location:171201
    SSXRD; SSXRD motif
    pfam13465
    Location:846870
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    23507155..23528093
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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