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Aliases for PRDM9 Gene

Aliases for PRDM9 Gene

  • PR Domain Containing 9 2 3
  • Minisatellite Binding Protein 3 (115kD) 2 3
  • PR Domain Zinc Finger Protein 9 3 4
  • EC 2.1.1.43 4 63
  • PFM6 3 4
  • Minisatellite Binding Protein 3, 115kDa 2
  • PR-Domain Containing Protein 9 2
  • PR Domain-Containing Protein 9 4
  • MEISETZ 3
  • ZNF899 3
  • MSBP3 3

External Ids for PRDM9 Gene

Previous HGNC Symbols for PRDM9 Gene

  • MSBP3

Previous GeneCards Identifiers for PRDM9 Gene

  • GC05P023203
  • GC05P023959
  • GC05P023522
  • GC05P023568

Summaries for PRDM9 Gene

Entrez Gene Summary for PRDM9 Gene

  • 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]

GeneCards Summary for PRDM9 Gene

PRDM9 (PR Domain Containing 9) is a Protein Coding gene. Diseases associated with PRDM9 include koolen-de vries syndrome. Among its related pathways are Cell Cycle, Mitotic and Chromatin organization. GO annotations related to this gene include nucleic acid binding and histone methyltransferase activity (H3-K4 specific). An important paralog of this gene is ZNF169.

UniProtKB/Swiss-Prot for PRDM9 Gene

  • Histone methyltransferase that specifically trimethylates Lys-4 of histone H3 during meiotic prophase and is essential for proper meiotic progression. Does not have the ability to mono- and dimethylate Lys-4 of histone H3. H3 Lys-4 methylation represents a specific tag for epigenetic transcriptional activation. Plays a central role in the transcriptional activation of genes during early meiotic prophase (By similarity).

Gene Wiki entry for PRDM9 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRDM9 Gene

Genomics for PRDM9 Gene

Genomic Location for PRDM9 Gene

Chromosome:
5
Start:
23,507,155 bp from pter
End:
23,528,597 bp from pter
Size:
21,443 bases
Orientation:
Plus strand

Genomic View for PRDM9 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PRDM9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRDM9 Gene

Proteins for PRDM9 Gene

  • Protein details for PRDM9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQV7-PRDM9_HUMAN
    Recommended name:
    Histone-lysine N-methyltransferase PRDM9
    Protein Accession:
    Q9NQV7
    Secondary Accessions:
    • B4DX22
    • Q27Q50

    Protein attributes for PRDM9 Gene

    Size:
    894 amino acids
    Molecular mass:
    103376 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAF87242.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PRDM9 Gene

neXtProt entry for PRDM9 Gene

Proteomics data for PRDM9 Gene at MOPED

Selected DME Specific Peptides for PRDM9 Gene

Post-translational modifications for PRDM9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PRDM9 Gene

ENSEMBL proteins:
REFSEQ proteins:

Domains & Families for PRDM9 Gene

Gene Families for PRDM9 Gene

Suggested Antigen Peptide Sequences for PRDM9 Gene

Graphical View of Domain Structure for InterPro Entry

Q9NQV7

UniProtKB/Swiss-Prot:

PRDM9_HUMAN :
  • Contains 1 KRAB-related domain.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
  • Contains 14 C2H2-type zinc fingers.
Domain:
  • Contains 1 KRAB-related domain.
  • Contains 1 SET domain.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Similarity:
  • Contains 14 C2H2-type zinc fingers.
genes like me logo Genes that share domains with PRDM9: view

Function for PRDM9 Gene

Molecular function for PRDM9 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone]
UniProtKB/Swiss-Prot Function:
Histone methyltransferase that specifically trimethylates Lys-4 of histone H3 during meiotic prophase and is essential for proper meiotic progression. Does not have the ability to mono- and dimethylate Lys-4 of histone H3. H3 Lys-4 methylation represents a specific tag for epigenetic transcriptional activation. Plays a central role in the transcriptional activation of genes during early meiotic prophase (By similarity).

Enzyme Numbers (IUBMB) for PRDM9 Gene

Gene Ontology (GO) - Molecular Function for PRDM9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding --
GO:0005515 protein binding --
GO:0010844 recombination hotspot binding IEA --
GO:0018024 histone-lysine N-methyltransferase activity --
GO:0042800 histone methyltransferase activity (H3-K4 specific) IEA --
genes like me logo Genes that share ontologies with PRDM9: view
genes like me logo Genes that share phenotypes with PRDM9: view

Animal Models for PRDM9 Gene

MGI Knock Outs for PRDM9:

Animal Model Products

Targeted motifs for PRDM9 Gene
HOMER Transcription Factor Regulatory Elements motif PRDM9
  • Consensus sequence: ADGGYAGYAGCATCT Submotif: canonical Cell Type: Testis GEO ID: GSE35498

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PRDM9

In Situ Assay Products

Flow Cytometry Products

No data available for Transcription Factor Targets for PRDM9 Gene

Localization for PRDM9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM9 Gene

Nucleus. Chromosome.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PRDM9 Gene COMPARTMENTS Subcellular localization image for PRDM9 gene
Compartment Confidence
nucleus 4

Gene Ontology (GO) - Cellular Components for PRDM9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular --
GO:0005634 nucleus --
GO:0005654 nucleoplasm TAS --
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with PRDM9: view

Pathways & Interactions for PRDM9 Gene

genes like me logo Genes that share pathways with PRDM9: view

Pathways by source for PRDM9 Gene

Interacting Proteins for PRDM9 Gene

Gene Ontology (GO) - Biological Process for PRDM9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006311 meiotic gene conversion IDA 21750151
GO:0006325 chromatin organization TAS --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated --
GO:0007283 spermatogenesis IEA --
genes like me logo Genes that share ontologies with PRDM9: view

No data available for SIGNOR curated interactions for PRDM9 Gene

Drugs & Compounds for PRDM9 Gene

(2) Drugs for PRDM9 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
S-Adenosylmethionine Approved Nutra 0
s-adenosylhomocysteine Experimental Pharma 0
genes like me logo Genes that share compounds with PRDM9: view

Transcripts for PRDM9 Gene

mRNA/cDNA for PRDM9 Gene

(2) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(4) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PRDM9 Gene

PR domain containing 9:
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PRDM9

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PRDM9 Gene

No ASD Table

Relevant External Links for PRDM9 Gene

GeneLoc Exon Structure for
PRDM9
ECgene alternative splicing isoforms for
PRDM9

Expression for PRDM9 Gene

mRNA expression in normal human tissues for PRDM9 Gene

mRNA differential expression in normal tissues according to GTEx for PRDM9 Gene

This gene is overexpressed in Testis (x51.6).

Protein differential expression in normal tissues from HIPED for PRDM9 Gene

This gene is overexpressed in Breast (24.3), Pancreas (16.4), Bone (12.3), and CD8 Tcells (8.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PRDM9 Gene



SOURCE GeneReport for Unigene cluster for PRDM9 Gene Hs.283096

genes like me logo Genes that share expression patterns with PRDM9: view

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Protein tissue co-expression partners for PRDM9 Gene

Orthologs for PRDM9 Gene

This gene was present in the common ancestor of animals.

Orthologs for PRDM9 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia PRDM7 35
  • 82.33 (n)
  • 74.8 (a)
-- 36
  • 65 (a)
OneToMany
PRDM9 36
  • 65 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Prdm9 35
  • 81.69 (n)
  • 73.78 (a)
Prdm9 16
Prdm9 36
  • 69 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PRDM9 35
  • 95.15 (n)
  • 91.94 (a)
rat
(Rattus norvegicus)
Mammalia Prdm9 35
  • 80.51 (n)
  • 70.08 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG4424 37
  • 45 (a)
Species with no ortholog for PRDM9:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for PRDM9 Gene

ENSEMBL:
Gene Tree for PRDM9 (if available)
TreeFam:
Gene Tree for PRDM9 (if available)

Paralogs for PRDM9 Gene

Paralogs for PRDM9 Gene

genes like me logo Genes that share paralogs with PRDM9: view

Variants for PRDM9 Gene

Sequence variations from dbSNP and Humsavar for PRDM9 Gene

SNP ID Clin Chr 05 pos Sequence Context AA Info Type MAF
VAR_054417 -

Structural Variations from Database of Genomic Variants (DGV) for PRDM9 Gene

Variant ID Type Subtype PubMed ID
nsv7369 OTHER Inversion 18451855
nsv880521 CNV Gain 21882294
esv2729936 CNV Deletion 23290073
esv2742915 CNV Deletion 23290073

Variation tolerance for PRDM9 Gene

Residual Variation Intolerance Score: 95.87% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.52; 55.49% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PRDM9 Gene

HapMap Linkage Disequilibrium report
PRDM9
Human Gene Mutation Database (HGMD)
PRDM9

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM9 Gene

Disorders for PRDM9 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PRDM9 Gene - From: DISEASES

Disorder Aliases PubMed IDs
koolen-de vries syndrome
  • koolen de vries syndrome
- elite association
Search PRDM9 in MalaCards View complete list of genes associated with diseases

Relevant External Links for PRDM9

Genetic Association Database (GAD)
PRDM9
Human Genome Epidemiology (HuGE) Navigator
PRDM9
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PRDM9
genes like me logo Genes that share disorders with PRDM9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PRDM9 Gene

Publications for PRDM9 Gene

  1. Trimethylation of histone H3 lysine 36 by human methyltransferase PRDM9 protein. (PMID: 24634223) Eram M.S. … Vedadi M. (J. Biol. Chem. 2014) 2 67
  2. The yin-yang of PR-domain family genes in tumorigenesis. (PMID: 10668202) Jiang G.L. … Huang S. (Histol. Histopathol. 2000) 2 67
  3. Two hypervariable minisatellite DNA binding proteins. (PMID: 2062643) Wahls W.P. … Moore P.D. (Nucleic Acids Res. 1991) 2 67
  4. Allelic variants of PRDM9 associated with high hyperdiploid childhood acute lymphoblastic leukaemia. (PMID: 24754746) Woodward E.L. … Paulsson K. (Br. J. Haematol. 2014) 67
  5. DNA recombination. Recombination initiation maps of individual human genomes. (PMID: 25395542) Pratto F. … Camerini-Otero R.D. (Science 2014) 67

Products for PRDM9 Gene

Sources for PRDM9 Gene

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