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, ... See more...

Aliases for PRDM9 Gene

Aliases for PRDM9 Gene

  • PR/SET Domain 9 2 3 5
  • PFM6 2 3 4
  • [Histone H4]-N-Methyl-L-Lysine20 N-Methyltransferase PRDM9 3 4
  • [Histone H3]-Lysine36 N-Trimethyltransferase PRDM9 3 4
  • [Histone H3]-Lysine4 N-Trimethyltransferase PRDM9 3 4
  • [Histone H3]-Lysine9 N-Trimethyltransferase PRDM9 3 4
  • [Histone H4]-Lysine20 N-Methyltransferase PRDM9 3 4
  • Histone-Lysine N-Methyltransferase PRDM9 3 4
  • Protein-Lysine N-Methyltransferase PRDM9 3 4
  • Minisatellite Binding Protein 3 (115kD) 2 3
  • PR Domain Zinc Finger Protein 9 3 4
  • PR Domain Containing 9 2 3
  • PR Domain 9 2 3
  • ZNF899 2 3
  • KMT8B 2 3
  • Minisatellite Binding Protein 3, 115kDa 2
  • PR-Domain Containing Protein 9 2
  • PR Domain-Containing Protein 9 4
  • Histone Methyl Transferase 3
  • EC 2.1.1.359 4
  • EC 2.1.1.354 4
  • EC 2.1.1.355 4
  • EC 2.1.1.362 4
  • EC 2.1.1.361 4
  • EC 2.1.1.43 50
  • EC 2.1.1.- 4
  • MEISETZ 3
  • MSBP3 3
  • PRDM9 5

External Ids for PRDM9 Gene

Previous HGNC Symbols for PRDM9 Gene

  • MSBP3

Previous GeneCards Identifiers for PRDM9 Gene

  • GC05P023203
  • GC05P023959
  • GC05P023522
  • GC05P023568
  • GC05P023558

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/SET Domain 9) is a Protein Coding gene. Diseases associated with PRDM9 include Haverhill Fever and Velocardiofacial Syndrome. Among its related pathways are Cell Cycle, Mitotic and Chromatin organization. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and histone methyltransferase activity (H3-K4 specific). An important paralog of this gene is ZNF343.

UniProtKB/Swiss-Prot Summary for PRDM9 Gene

  • Histone methyltransferase that sequentially mono-, di-, and tri-methylates both 'Lys-4' (H3K4) and 'Lys-36' (H3K36) of histone H3 to produce respectively trimethylated 'Lys-4' (H3K4me3) and trimethylated 'Lys-36' (H3K36me3) histone H3 and plays a key role in meiotic prophase by determining hotspot localization thereby promoting meiotic recombination (PubMed:24634223, PubMed:24095733, PubMed:26833727). Also can methylate all four core histones with H3 being the best substrate and the most highly modified (PubMed:24095733, PubMed:24634223, PubMed:26833727). Is also able, on one hand, to mono and di-methylate H4K20 and on other hand to trimethylate H3K9 with the di-methylated H3K9 as the best substrate (By similarity). During meiotic prophase, binds specific DNA sequences through its zinc finger domains thereby determining hotspot localization where it promotes local H3K4me3 and H3K36me3 enrichment on the same nucleosomes through its histone methyltransferase activity (PubMed:26833727). Thereby promotes double-stranded breaks (DSB) formation, at this subset of PRDM9-binding sites, that initiates meiotic recombination for the proper meiotic progression (By similarity). During meiotic progression hotspot-bound PRDM9 interacts with several complexes; in early leptonema binds CDYL and EHMT2 followed by EWSR1 and CXXC1 by the end of leptonema. EWSR1 joins PRDM9 with the chromosomal axis through REC8 (By similarity). In this way, controls the DSB repair pathway, pairing of homologous chromosomes and sex body formation (By similarity). Moreover plays a central role in the transcriptional activation of genes during early meiotic prophase thanks to H3K4me3 and H3K36me3 enrichment that represents a specific tag for epigenetic transcriptional activation (By similarity). In addition performs automethylation (By similarity). Acetylation and phosphorylation of histone H3 attenuate or prevent histone H3 methylation (By similarity).

Gene Wiki entry for PRDM9 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PRDM9 Gene

Genomics for PRDM9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PRDM9 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH05J023443 Promoter 0.3 EPDnew 250.7 -0.1 -76 0.1 PRDM9 HSALNG0040597 piR-49400-068 CDH12
GH05J024208 Enhancer 0.6 Ensembl ENCODE 4 +765.3 765315 1.8 NANOG POLR2A EZH2 PRDM9 HSALNG0040624 piR-48749-034 ENSG00000286134 CDH10
GH05J023465 Enhancer 0.9 Ensembl ENCODE 0.4 +23.0 22970 1.6 CEBPA ATF3 YY1 CEBPB MAX EP300 FOXA2 RXRA RFX5 STAT3 piR-60246-124 HSALNG0040597 PRDM9
GH05J023419 Enhancer 0.7 Ensembl ENCODE 0.4 -24.3 -24285 0.6 CTCF PRDM1 TCF7L2 FOXA1 RAD21 DPF2 TRIM28 PKNOX1 FOS piR-49400-068 PRDM9 HSALNG0040597 CDH12
GH05J023507 Promoter/Enhancer 1 Ensembl ENCODE 0.2 +63.6 63615 1.6 YY1 CTCF SP2 GABPB1 E4F1 PKNOX1 POLR2A NRF1 RAD21 NFYC HSALNG0040600 piR-35002-006 PRDM9
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRDM9 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PRDM9

Top Transcription factor binding sites by QIAGEN in the PRDM9 gene promoter:
  • HSF1 (long)
  • HSF1short
  • LCR-F1
  • Pax-4a
  • POU2F1
  • POU2F1a
  • POU2F1b
  • POU2F1c
  • PPAR-gamma1
  • PPAR-gamma2

Genomic Locations for PRDM9 Gene

Latest Assembly
chr5:23,443,586-23,528,093
(GRCh38/hg38)
Size:
84,508 bases
Orientation:
Plus strand

Previous Assembly
chr5:23,507,264-23,528,202
(GRCh37/hg19 by Entrez Gene)
Size:
20,939 bases
Orientation:
Plus strand

chr5:23,507,264-23,528,706
(GRCh37/hg19 by Ensembl)
Size:
21,443 bases
Orientation:
Plus strand

Genomic View for PRDM9 Gene

Genes around PRDM9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRDM9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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:
    • Homodimer (PubMed:26833727, PubMed:24095733, Ref.9). Interacts with EHMT2 and CDYL; interaction only takes place when PRDM9 is bound to hotspot DNA. Interacts with CXXC1; this interaction does not link PRDM9-activated recombination hotspot sites with DSB machinery and is not required for the hotspot recognition pathway. Forms a complex with EWSR1, REC8, SYCP3 and SYCP1; complex formation is dependent of phosphorylated form of REC8 and requires PRDM9 bound to hotspot DNA; EWSR1 joins PRDM9 with the chromosomal axis through REC8 (By similarity).
    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

Selected DME Specific Peptides for PRDM9 Gene

Q9NQV7:
  • EQNLVAFQ
  • QSVLLTHQR
  • HQRTHTGEKPY
  • CRECGRGF
  • GDEYGQELGI

Post-translational modifications for PRDM9 Gene

  • Mono-methylated; automethylated. Tri-methylated; automethylated. Mono-methylation is predominant; automethylation is lower and slower than H3 peptide methylation and is in a highest S-adenosyl-L-methionine concentration-dependent. There are two major sites for automethylation at Lys-368 and Lys-374. Lysines can be simultaneously methylated, such as Lys-368(me3)/Lys-372(me1), Lys-368(me1)/Lys-374(me1) and Lys-368(me1)/Lys-372(me1)/Lys-374(me1). Automethylation is an intramolecular (cis) process.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PRDM9 Gene

Domains & Families for PRDM9 Gene

Gene Families for PRDM9 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for PRDM9 Gene

GenScript: Design optimal peptide antigens:
  • PRDM9 (D2E450_HUMAN)
  • PRDM9 (D2E453_HUMAN)
  • PRDM9 (D2E456_HUMAN)
  • PRDM9 (D2E459_HUMAN)
  • PRDM9 (D2E482_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NQV7

UniProtKB/Swiss-Prot:

PRDM9_HUMAN :
  • The C2H2-type zinc fingers determine the hotspot localization through its binding to specific DNA sequences. Variations in their sequence affect affinity towards DNA-binding motif.
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
Domain:
  • The C2H2-type zinc fingers determine the hotspot localization through its binding to specific DNA sequences. Variations in their sequence affect affinity towards DNA-binding motif.
Family:
  • Belongs to the class V-like SAM-binding methyltransferase superfamily.
genes like me logo Genes that share domains with PRDM9: view

Function for PRDM9 Gene

Molecular function for PRDM9 Gene

UniProtKB/Swiss-Prot Function:
Histone methyltransferase that sequentially mono-, di-, and tri-methylates both 'Lys-4' (H3K4) and 'Lys-36' (H3K36) of histone H3 to produce respectively trimethylated 'Lys-4' (H3K4me3) and trimethylated 'Lys-36' (H3K36me3) histone H3 and plays a key role in meiotic prophase by determining hotspot localization thereby promoting meiotic recombination (PubMed:24634223, PubMed:24095733, PubMed:26833727). Also can methylate all four core histones with H3 being the best substrate and the most highly modified (PubMed:24095733, PubMed:24634223, PubMed:26833727). Is also able, on one hand, to mono and di-methylate H4K20 and on other hand to trimethylate H3K9 with the di-methylated H3K9 as the best substrate (By similarity). During meiotic prophase, binds specific DNA sequences through its zinc finger domains thereby determining hotspot localization where it promotes local H3K4me3 and H3K36me3 enrichment on the same nucleosomes through its histone methyltransferase activity (PubMed:26833727). Thereby promotes double-stranded breaks (DSB) formation, at this subset of PRDM9-binding sites, that initiates meiotic recombination for the proper meiotic progression (By similarity). During meiotic progression hotspot-bound PRDM9 interacts with several complexes; in early leptonema binds CDYL and EHMT2 followed by EWSR1 and CXXC1 by the end of leptonema. EWSR1 joins PRDM9 with the chromosomal axis through REC8 (By similarity). In this way, controls the DSB repair pathway, pairing of homologous chromosomes and sex body formation (By similarity). Moreover plays a central role in the transcriptional activation of genes during early meiotic prophase thanks to H3K4me3 and H3K36me3 enrichment that represents a specific tag for epigenetic transcriptional activation (By similarity). In addition performs automethylation (By similarity). Acetylation and phosphorylation of histone H3 attenuate or prevent histone H3 methylation (By similarity).
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl-[protein] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl-[protein] + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:51736, Rhea:RHEA-COMP:9752, Rhea:RHEA-COMP:13053, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; Evidence={ECO:0000250|UniProtKB:Q96EQ9};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=N(6)-methyl-L-lysyl-[protein] + S-adenosyl-L-methionine = H(+) + N(6),N(6)-dimethyl-L-lysyl-[protein] + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:54196, Rhea:RHEA-COMP:13053, Rhea:RHEA-COMP:13827, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61929, ChEBI:CHEBI:61976; Evidence={ECO:0000250|UniProtKB:Q96EQ9};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-[histone H3] + 3 S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:60260, Rhea:RHEA-COMP:15537, Rhea:RHEA-COMP:15547, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.354; Evidence={ECO:0000269|PubMed:24095733, ECO:0000269|PubMed:24634223, ECO:0000269|PubMed:26833727};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl(36)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(36)-[histone H3] + 3 S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:60324, Rhea:RHEA-COMP:9785, Rhea:RHEA-COMP:15536, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.359; Evidence={ECO:0000269|PubMed:24634223};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl(9)-[histone H3] + 3 S-adenosyl-L-methionine = 3 H(+) + N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3] + 3 S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:60276, Rhea:RHEA-COMP:15538, Rhea:RHEA-COMP:15546, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61961; EC=2.1.1.355; Evidence={ECO:0000250|UniProtKB:Q96EQ9};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=L-lysyl(20)-[histone H4] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:60344, Rhea:RHEA-COMP:15554, Rhea:RHEA-COMP:15555, ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; EC=2.1.1.361; Evidence={ECO:0000250|UniProtKB:Q96EQ9};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=N(6)-methyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-methionine = H(+) + N(6),N(6)-dimethyl-L-lysyl(20)-[histone H4] + S-adenosyl-L-homocysteine; Xref=Rhea:RHEA:60348, Rhea:RHEA-COMP:15555, Rhea:RHEA-COMP:15556, ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789, ChEBI:CHEBI:61929, ChEBI:CHEBI:61976; EC=2.1.1.362; Evidence={ECO:0000250|UniProtKB:Q96EQ9};.
UniProtKB/Swiss-Prot BiophysicochemicalProperties:
Kinetic parameters: KM=1 uM for H3K4me0 {ECO:0000269|PubMed:24634223}; KM=1 uM for H3K4me1 {ECO:0000269|PubMed:24634223}; KM=3 uM for H3K4me2 {ECO:0000269|PubMed:24634223}; KM=1.5 uM for H3K36me0 {ECO:0000269|PubMed:24634223}; KM=2.4 uM for H3K36me1 {ECO:0000269|PubMed:24634223}; KM=2.5 uM for H3K36me2 {ECO:0000269|PubMed:24634223}; KM=0.7 uM for native H3-H4 tetramer {ECO:0000269|PubMed:24634223}; KM=120 uM for S-adenosyl-L-methionine (with H3K4me0 as substrate) {ECO:0000269|PubMed:24634223}; KM=170 uM for S-adenosyl-L-methionine (with H3K4me1 as substrate) {ECO:0000269|PubMed:24634223}; KM=140 uM for S-adenosyl-L-methionine (with H3K4me2 as substrate) {ECO:0000269|PubMed:24634223}; KM=87 uM for S-adenosyl-L-methionine (with H3K36me0 as substrate) {ECO:0000269|PubMed:24634223}; KM=130 uM for S-adenosyl-L-methionine (with H3K36me1 as substrate) {ECO:0000269|PubMed:24634223}; KM=62 uM for S-adenosyl-L-methionine (with H3K36me2 as substrate) {ECO:0000269|PubMed:24634223}; KM=240 uM for S-adenosyl-L-methionine (with native H3-H4 tetramer as substrate) {ECO:0000269|PubMed:24634223}; Note=All kinetic experiments are done with 10 mm Tris-HCl, 0.01% Triton X-100, and 10 mm DTT and at pH 8.5. {ECO:0000269|PubMed:24634223}; pH dependence: Optimum pH is 8.5. {ECO:0000269|PubMed:24634223};
UniProtKB/Swiss-Prot EnzymeRegulation:
Inhibited by suramin with an IC(50) of 4.1 uM.

Phenotypes From GWAS Catalog for PRDM9 Gene

Gene Ontology (GO) - Molecular Function for PRDM9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000976 transcription regulatory region sequence-specific DNA binding IMP 29072575
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IEA --
GO:0008168 methyltransferase activity 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:
Targeted motifs for PRDM9 Gene
HOMER Transcription Factor Regulatory Elements motif PRDM9
  • Consensus sequence: ADGGYAGYAGCATCT Submotif: canonical Cell Type: Testis GEO ID: GSE35498

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRDM9

No data available for Human Phenotype Ontology and Transcription Factor Targets for PRDM9 Gene

Localization for PRDM9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRDM9 Gene

Nucleus. Chromosome. Note=Localizes in nuclei of pre-leptotene, leptotene, and early to mid-zygotene spermatocytes. {ECO:0000250 UniProtKB:Q96EQ9}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PRDM9 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for PRDM9 Gene

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

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PRDM9 Gene

Pathways & Interactions for PRDM9 Gene

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

Pathways by source 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 IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007129 synapsis ISS --
GO:0007292 female gamete generation ISS --
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

(1) Drugs for PRDM9 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
s-adenosylhomocysteine Experimental Pharma 0

(1) Additional Compounds for PRDM9 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
s-adenosylmethionine
  • (3S)-5'-[(3-Amino-3-carboxypropyl)methylsulfonio]-5'-deoxyadenosine, inner salt
  • [1-(Adenin-9-yl)-1,5-dideoxy-beta-D-ribofuranos-5-yl][(3S)-3-amino-3-carboxypropyl](methyl)sulfonium
  • Acylcarnitine
  • AdoMet
  • S-(5'-Deoxyadenosin-5'-yl)-L-methionine
485-80-3
genes like me logo Genes that share compounds with PRDM9: view

Transcripts for PRDM9 Gene

mRNA/cDNA for PRDM9 Gene

3 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRDM9

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

No ASD Table

Relevant External Links for PRDM9 Gene

GeneLoc Exon Structure for
PRDM9

Expression for PRDM9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE 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 and MOPED for PRDM9 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PRDM9

SOURCE GeneReport for Unigene cluster for PRDM9 Gene:

Hs.283096
genes like me logo Genes that share expression patterns with PRDM9: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
Chimpanzee
(Pan troglodytes)
Mammalia PRDM9 29
  • 95.15 (n)
Cow
(Bos Taurus)
Mammalia PRDM7 29
  • 82.33 (n)
PRDM9 30
  • 65 (a)
OneToMany
-- 30
  • 65 (a)
OneToMany
Mouse
(Mus musculus)
Mammalia Prdm9 29 16 30
  • 81.69 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Prdm9 29
  • 80.51 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG4424 31
  • 45 (a)
Species where no ortholog for PRDM9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for PRDM9: view image
Alliance of Genome Resources:
Additional Orthologs for PRDM9

Paralogs for PRDM9 Gene

(546) SIMAP similar genes for PRDM9 Gene using alignment to 37 proteins:

  • PRDM9_HUMAN
  • D2E450_HUMAN
  • D2E453_HUMAN
  • D2E456_HUMAN
  • D2E459_HUMAN
  • D2E482_HUMAN
  • D2E492_HUMAN
  • D2K7E5_HUMAN
  • D2K7E6_HUMAN
  • D2K7E7_HUMAN
  • D2K7E8_HUMAN
  • D2K7E9_HUMAN
  • D2K7F0_HUMAN
  • D2KI84_HUMAN
  • D2KI85_HUMAN
  • D2KI86_HUMAN
  • D2KI87_HUMAN
  • D2KI88_HUMAN
  • D2KI89_HUMAN
  • D2KI90_HUMAN
  • D2KI91_HUMAN
  • D6RD68_HUMAN
  • I6V2Q9_HUMAN
  • I6ZAW9_HUMAN
  • I6ZLR0_HUMAN
  • I6ZLR5_HUMAN
  • I7A6V7_HUMAN
  • I7A6W4_HUMAN
  • I7AFR5_HUMAN
  • I7AJB3_HUMAN
  • U5YQZ9_HUMAN
  • U5YR71_HUMAN
  • U5YS13_HUMAN
  • U5YS18_HUMAN
  • U5YU24_HUMAN
  • U5YUF0_HUMAN
  • U5YUF5_HUMAN
genes like me logo Genes that share paralogs with PRDM9: view

Variants for PRDM9 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for PRDM9 Gene

PRDM9_HUMAN-Q9NQV7
Several alleles exist depending on both the number of zinc finger C2H2 type domains and their identity (PubMed:26833727). Each allele binds to a specific hotspot set (PubMed:26833727). Variations in the zinc finger C2H2 type domains are associated with significant differences in affinity towards DNA-binding motif (PubMed:26833727). The sequence shown is that of allele B.

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PRDM9 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
rs10042274 Benign: not provided 23,521,103(+) C/T
NM_020227.4(PRDM9):c.432C>T (p.Gly144=)
SYNONYMOUS
rs6875787 Likely Benign: not specified 23,527,130(+) C/Gp.Thr681Ser
NM_020227.3(PRDM9):c.2042C>G (p.Thr681Ser)
MISSENSE
rs7714612 Benign: not provided 23,509,490(+) C/T
NM_020227.4(PRDM9):c.90C>T (p.Asp30=)
SYNONYMOUS
rs772744700 Likely Benign: not specified 23,526,794(+) T/A
NM_020227.3(PRDM9):c.1706T>A (p.Ile569Asn)
MISSENSE
rs77287813 Likely Benign: not specified 23,527,456(+) A/Cp.Asn790His
NM_020227.3(PRDM9):c.2368A>C (p.Asn790His)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PRDM9 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
esv2729936 CNV deletion 23290073
esv2742915 CNV deletion 23290073
esv2762506 CNV gain 21179565
esv3380329 OTHER inversion 20981092
esv3427604 CNV duplication 20981092
nsv1017510 CNV gain 25217958
nsv1028347 CNV loss 25217958
nsv597544 CNV gain 21841781
nsv7369 OTHER inversion 18451855
nsv964821 CNV duplication 23825009
nsv968898 CNV duplication 23825009

Variation tolerance for PRDM9 Gene

Residual Variation Intolerance Score: 95.9% 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)

Additional Variant Information for PRDM9 Gene

Human Gene Mutation Database (HGMD)
PRDM9
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRDM9
Leiden Open Variation Database (LOVD)
PRDM9

SNP Genotyping and Copy Number Assays for research

Disorders for PRDM9 Gene

MalaCards: The human disease database

(6) MalaCards diseases for PRDM9 Gene - From: COP and GCD

- elite association - COSMIC cancer census association via MalaCards
Search PRDM9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PRDM9

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
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 MS … Vedadi M (The Journal of biological chemistry 2014) 2 3 4
  2. Two single nucleotide polymorphisms in PRDM9 (MEISETZ) gene may be a genetic risk factor for Japanese patients with azoospermia by meiotic arrest. (PMID: 18941885) Miyamoto T … Sengoku K (Journal of assisted reproduction and genetics 2008) 3 4 40
  3. The yin-yang of PR-domain family genes in tumorigenesis. (PMID: 10668202) Jiang GL … Huang S (Histology and histopathology 2000) 2 3 4
  4. Structural basis for human PRDM9 action at recombination hot spots. (PMID: 26833727) Patel A … Cheng X (Genes & development 2016) 3 4
  5. Molecular basis for the regulation of the H3K4 methyltransferase activity of PRDM9. (PMID: 24095733) Wu H … Kadlec J (Cell reports 2013) 3 4

Products for PRDM9 Gene

Sources for PRDM9 Gene