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Prdm9 PR domain containing 9 [ Mus musculus (house mouse) ]

Gene ID: 213389, updated on 8-Feb-2024

Summary

Official Symbol
Prdm9provided by MGI
Official Full Name
PR domain containing 9provided by MGI
Primary source
MGI:MGI:2384854
See related
Ensembl:ENSMUSG00000051977 AllianceGenome:MGI:2384854
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Rcr1; Dsbc1; repro7; Meisetz; PRDM9-B; G1-419-29
Summary
Enables DNA binding activity; histone-lysine N-methyltransferase activity; and protein homodimerization activity. Involved in several processes, including gamete generation; histone lysine methylation; and meiosis I. Acts upstream of or within several processes, including histone methylation; positive regulation of meiotic nuclear division; and positive regulation of transcription by RNA polymerase II. Located in chromatin and nucleus. Is expressed in embryo and head. Orthologous to human PRDM9 (PR/SET domain 9). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in stomach adult (RPKM 2.6), spleen adult (RPKM 1.6) and 28 other tissues See more
Orthologs
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Genomic context

See Prdm9 in Genome Data Viewer
Location:
17 A2; 17 8.95 cM
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 17 NC_000083.7 (15763334..15784636, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 17 NC_000083.6 (15543072..15564374, complement)

Chromosome 17 - NC_000083.7Genomic Context describing neighboring genes Neighboring gene programmed cell death 2 Neighboring gene STARR-positive B cell enhancer ABC_E5574 Neighboring gene zinc finger protein 91 pseudogene Neighboring gene BRCA1 associated RING domain 1 pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E3182 Neighboring gene predicted pseudogene 6686 Neighboring gene ornithine decarboxylase, structural 1 pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

General gene information

Clone Names

  • MGC21428

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables histone H3K36 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
enables histone H3K36 methyltransferase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone H3K36 methyltransferase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone H3K36 trimethyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H3K4 methyltransferase activity EXP
Inferred from Experiment
more info
PubMed 
enables histone H3K4 methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
 
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 H3K4 methyltransferase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone H3K4 trimethyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
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 methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
enables recombination hotspot binding IBA
Inferred from Biological aspect of Ancestor
more info
 
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 recombination hotspot binding ISO
Inferred from Sequence Orthology
more info
 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
 
enables transferase activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
 
involved_in double-strand break repair involved in meiotic recombination IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in female gamete generation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in homologous chromosome pairing at meiosis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in male gamete generation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of meiosis I IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within meiotic gene conversion ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within methylation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of apoptotic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of fertilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of meiosis I IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in positive regulation of reciprocal meiotic recombination IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within positive regulation of reciprocal meiotic recombination IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within positive regulation of reciprocal meiotic recombination ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within spermatogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
part_of chromatin IDA
Inferred from Direct Assay
more info
PubMed 
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm IC
Inferred by Curator
more info
PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
histone-lysine N-methyltransferase PRDM9
Names
PR domain zinc finger protein 9
PR domain-containing protein 9
VPR domain containing 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 H3 lysine-4 methyltransferase
hybrid sterility protein 1
meiosis-induced factor containing a PR/SET domain and zinc-finger motif
protein-lysine N-methyltransferase PRDM9
NP_001348365.1
NP_659058.3
XP_006524051.1
XP_017172869.1
XP_036016343.1
XP_036016344.1
XP_036016345.1
XP_036016346.1
XP_036016347.1
XP_036016348.1
XP_036016349.1
XP_036016350.1

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001361436.1NP_001348365.1  histone-lysine N-methyltransferase PRDM9 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) includes a 3' terminal exon that extends past a splice site that is used in variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. It encodes isoform 2 which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    BC012016, CT033750
    Consensus CDS
    CCDS88997.1
    Related
    ENSMUSP00000118454.2, ENSMUST00000147532.8
    Conserved Domains (2) summary
    smart00317
    Location:125243
    SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain
    pfam09514
    Location:5080
    SSXRD; SSXRD motif
  2. NM_144809.3NP_659058.3  histone-lysine N-methyltransferase PRDM9 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC154378, BX518160, CT033750, HQ704391
    Consensus CDS
    CCDS49963.2
    UniProtKB/Swiss-Prot
    B8JJZ8, Q0D2N4, Q96EQ9
    Related
    ENSMUSP00000156841.2, ENSMUST00000233295.2
    Conserved Domains (5) summary
    COG5048
    Location:535840
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:539559
    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:2885
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000083.7 Reference GRCm39 C57BL/6J

    Range
    15763334..15784636 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006523988.4XP_006524051.1  histone-lysine N-methyltransferase PRDM9 isoform X4

    See identical proteins and their annotated locations for XP_006524051.1

    UniProtKB/TrEMBL
    E9Q4V2
    Conserved Domains (5) summary
    COG5048
    Location:539844
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:543563
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam09514
    Location:175205
    SSXRD; SSXRD motif
    cd19193
    Location:244372
    PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
    cl02581
    Location:3289
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
  2. XM_036160452.1XP_036016345.1  histone-lysine N-methyltransferase PRDM9 isoform X3

    Conserved Domains (5) summary
    COG5048
    Location:541846
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:545565
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19193
    Location:246374
    PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
    pfam09514
    Location:181207
    SSXRD; SSXRD motif
    cl02581
    Location:3289
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
  3. XM_036160454.1XP_036016347.1  histone-lysine N-methyltransferase PRDM9 isoform X6

    Conserved Domains (5) summary
    cd07765
    Location:3268
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
    COG5048
    Location:505810
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:509529
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19193
    Location:210338
    PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
    pfam09514
    Location:145171
    SSXRD; SSXRD motif
  4. XM_036160451.1XP_036016344.1  histone-lysine N-methyltransferase PRDM9 isoform X3

    Conserved Domains (5) summary
    COG5048
    Location:541846
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:545565
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19193
    Location:246374
    PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
    pfam09514
    Location:181207
    SSXRD; SSXRD motif
    cl02581
    Location:3289
    KRAB_A-box; KRAB (Kruppel-associated box) domain -A box
  5. XM_036160455.1XP_036016348.1  histone-lysine N-methyltransferase PRDM9 isoform X7

    Conserved Domains (4) summary
    COG5048
    Location:416721
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:420440
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19193
    Location:121249
    PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
    pfam09514
    Location:5682
    SSXRD; SSXRD motif
  6. XM_036160457.1XP_036016350.1  histone-lysine N-methyltransferase PRDM9 isoform X8

    Conserved Domains (4) summary
    COG5048
    Location:414719
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:418438
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19193
    Location:119247
    PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
    pfam09514
    Location:5180
    SSXRD; SSXRD motif
  7. XM_036160456.1XP_036016349.1  histone-lysine N-methyltransferase PRDM9 isoform X7

    Conserved Domains (4) summary
    COG5048
    Location:416721
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:420440
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19193
    Location:121249
    PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
    pfam09514
    Location:5682
    SSXRD; SSXRD motif
  8. XM_036160453.1XP_036016346.1  histone-lysine N-methyltransferase PRDM9 isoform X5

    Conserved Domains (5) summary
    COG5048
    Location:396779
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:550570
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19193
    Location:251379
    PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
    pfam00096
    Location:772794
    zf-C2H2; Zinc finger, C2H2 type
    pfam09514
    Location:186212
    SSXRD; SSXRD motif
  9. XM_017317380.3XP_017172869.1  histone-lysine N-methyltransferase PRDM9 isoform X2

    Conserved Domains (4) summary
    COG5048
    Location:544849
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:548568
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam09514
    Location:180210
    SSXRD; SSXRD motif
    cd19193
    Location:249377
    PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
  10. XM_036160450.1XP_036016343.1  histone-lysine N-methyltransferase PRDM9 isoform X1

    Conserved Domains (4) summary
    COG5048
    Location:546851
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:550570
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd19193
    Location:251379
    PR-SET_PRDM7_9; PR-SET domain found in PR domain zinc finger protein 7 (PRDM7) and 9 (PRDM9) and similar proteins
    pfam09514
    Location:186212
    SSXRD; SSXRD motif