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

Gene ID: 56979, updated on 29-Jan-2023

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; AllianceGenome:HGNC:13994
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
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Genomic context

See PRDM9 in Genome Data Viewer
Location:
5p14.2
Exon count:
12
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (23507155..23528093)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (23614868..23635807)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (23507264..23528202)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374688 Neighboring gene uncharacterized LOC124901171 Neighboring gene uncharacterized LOC124901158 Neighboring gene uncharacterized LOC107986377

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

EBI GWAS Catalog

Description
Fine-scale recombination rate differences between sexes, populations and individuals.
EBI GWAS Catalog
The landscape of recombination in African Americans.
EBI GWAS 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
enables histone H3K36 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone H3K36 methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone H3K36 methyltransferase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables histone H3K36 trimethyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H3K4 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone H3K4 methyltransferase activity IDA
Inferred from Direct Assay
more info
PubMed 
enables histone H3K4 methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone H3K9 trimethyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H4K20 monomethyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H4K20me methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone lysine N-methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables recombination hotspot binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables recombination hotspot binding IDA
Inferred from Direct Assay
more info
PubMed 
enables recombination hotspot binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables transcription cis-regulatory region binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in double-strand break repair involved in meiotic recombination ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in female gamete generation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in histone methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in homologous chromosome pairing at meiosis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in male gamete generation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within meiotic gene conversion IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of fertilization ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of reciprocal meiotic recombination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within positive regulation of reciprocal meiotic recombination IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in 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_001297143.1
NP_001363829.1
NP_064612.2

NCBI Reference Sequences (RefSeq)

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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_001310214.3NP_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)
    AK301776, AL704903, DB518225, DB636359
    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 isoform PRDM9 B

    Status: REVIEWED

    Source sequence(s)
    AC025451
    Consensus CDS
    CCDS43307.1
    UniProtKB/Swiss-Prot
    Q27Q50
    Related
    ENSP00000425471.2, ENST00000502755.6
    Conserved Domains (5) summary
    COG5048
    Location:611878
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:750770
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam09514
    Location:171201
    SSXRD; SSXRD motif
    cd19193
    Location:240368
    PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
    cl02581
    Location:2785
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
  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
    Q27Q50, Q9NQV7
    Related
    ENSP00000296682.4, ENST00000296682.4
    Conserved Domains (5) summary
    COG5048
    Location:611878
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:750770
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam09514
    Location:171201
    SSXRD; SSXRD motif
    cd19193
    Location:240368
    PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
    cl02581
    Location:2785
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

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

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_025791779.1 Reference GRCh38.p14 PATCHES

    Range
    137172..158109
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    23614868..23635807
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)