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Prdm9 Gene Detail
Summary
  • Symbol
    Prdm9
  • Name
    PR domain containing 9
  • Synonyms
    Dsbc1, G1-419-29, Meisetz, MGC:21428, Rcr1, repro7
  • Feature Type
    protein coding gene
  • IDs
    MGI:2384854
    NCBI Gene: 213389
  • Alliance
    gene page
  • Transcription Start Sites
    2 TSS
Location &
Maps
more
  • Sequence Map
    Chr17:15763341-15784616 bp, - strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 17, 8.95 cM
  • Mapping Data
    7 experiments
Strain
Comparison
more
  • SNPs within 2kb
    513 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_2384854
 protein coding gene Chr17:15763334-15784636 (-)
129S1/SvImJ MGP_129S1SvImJ_G0023177
 protein coding gene Chr17:13388069-13411760 (-)
A/J MGP_AJ_G0023143
 protein coding gene Chr17:13132643-13153539 (-)
AKR/J MGP_AKRJ_G0023113
 protein coding gene Chr17:13098431-13120087 (-)
BALB/cJ MGP_BALBcJ_G0023143
 protein coding gene Chr17:13084841-13107059 (-)
C3H/HeJ MGP_C3HHeJ_G0022904
 protein coding gene Chr17:13292190-13312819 (-)
C57BL/6NJ MGP_C57BL6NJ_G0023586
 protein coding gene Chr17:13998555-14020939 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0021098
 protein coding gene Chr17:11152852-11174974 (-)
CAST/EiJ MGP_CASTEiJ_G0022421
 protein coding gene Chr17:13202297-13233964 (-)
CBA/J MGP_CBAJ_G0022880
 protein coding gene Chr17:14459758-14484195 (-)
DBA/2J MGP_DBA2J_G0023013
 protein coding gene Chr17:12854268-12875608 (-)
FVB/NJ MGP_FVBNJ_G0022979
 protein coding gene Chr17:12699717-12722884 (-)
LP/J MGP_LPJ_G0023087
 protein coding gene Chr17:13384518-13409404 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0023002
 protein coding gene Chr17:13988588-14011833 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0023622
 protein coding gene Chr17:13339540-13360682 (-)
PWK/PhJ MGP_PWKPhJ_G0022169
 protein coding gene Chr17:12347032-12368838 (-)
SPRET/EiJ MGP_SPRETEiJ_G0021999
 protein coding gene Chr17:12292533-12310912 (-)
WSB/EiJ MGP_WSBEiJ_G0022480
 protein coding gene Chr17:13663603-13687346 (-)



Homology
more
  • Human Ortholog
    PRDM7, PR/SET domain 7
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    PRDM7, PR/SET domain 7
  • Synonyms
    PFM4, ZNF910
  • Links
    NCBI Gene ID: 11105
    neXtProt AC: NX_Q9NQW5
    UniProt: Q9NQW5

  • Chr Location
    16q24.3; chr16:90056566-90092072 (-)  GRCh38
  • Human Ortholog
    PRDM9, PR/SET domain 9
  • Synonyms
    KMT8B, MEISETZ, MSBP3, PFM6, ZNF899
  • Links
    NCBI Gene ID: 56979
    neXtProt AC: NX_Q9NQV7
    UniProt: Q9NQV7

  • Chr Location
    5p14.2; chr5:23443586-23528093 (+)  GRCh38
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    26 phenotypes from 6 alleles in 11 genetic backgrounds
    9 phenotypes from multigenic genotypes
    1 images
    52 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Mice homozygous for a knock-out allele show decreased oocyte number, azoospermia, and sterility in both sexes due to severe impairment of the double-stranded break repair pathway, deficient pairing of homologous chromosomes, and impaired sex body formation.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    65
  • GO References
    21
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    764
  • Tissues
    38
  • cDNA Data
    11
  • Literature Summary
    5
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000051977 Ensembl Gene Model | MGI Sequence Detail 21276 C57BL/6J ±  kb
    transcript ENSMUST00000233295 Ensembl | MGI Sequence Detail 3460 Not Applicable  
    polypeptide ENSMUSP00000156841 Ensembl | MGI Sequence Detail 847 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 17
      Genomic 3
      cDNA 11
      Primer pair 2
      Other 1

      Microarray probesets 2
    Other
    Accession IDs
    less
    MGI:3512775, MGI:3801504, MGI:3839351
    References
    more
    • Summaries
      All 95
      Developmental Gene Expression 5
      Gene Ontology 21
      Phenotypes 52
    • Earliest
      J:214361 Shiroishi T, et al., A new wild-derived H-2 haplotype enhancing K-IA recombination. Nature. 1982 Nov 25;300(5890):370-2
    • Latest
      J:348407 Biot M, et al., Principles of chromosome organization for meiotic recombination. Mol Cell. 2024 May 16;84(10):1826-1841.e5
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
    Citing These Resources
    Funding Information
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    Send questions and comments to User Support.     		last database update
    11/12/2024
    MGI 6.24     		The Jackson Laboratory