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Kdm3a Gene Detail
Summary
  • Symbol
    Kdm3a
  • Name
    lysine (K)-specific demethylase 3A
  • Synonyms
    1700105C21Rik, C230043E16Rik, Jmjd1, Jmjd1a, mKIAA0742, Tsga
  • Feature Type
    protein coding gene
  • IDs
    MGI:98847
    NCBI Gene: 104263
  • Alliance
    genome feature page
  • Transcription Start Sites
    8 TSS
Location &
Maps
more
  • Sequence Map
    Chr6:71565954-71609963 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 6, 32.18 cM
  • Mapping Data
    1 experiment
Strain
Comparison
more
  • SNPs within 2kb
    777 from dbSNP Build 142
  • Strain Annotations
    19
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_98847
 protein coding gene Chr6:71565954-71609974 (-)
129S1/SvImJ ENSMUSG00200010561
 protein coding gene Chr6:68469495-68513509 (-)
A/J ENSMUSG00195039639
 protein coding gene Chr6:68231505-68275533 (-)
AKR/J ENSMUSG00220041672
 protein coding gene Chr6:67185127-67229330 (-)
BALB/cJ ENSMUSG00180034750
 protein coding gene Chr6:68586510-68630533 (-)
C3H/HeJ ENSMUSG00175011688
 protein coding gene Chr6:108799107-108843126 (+)
C57BL/6NJ ENSMUSG00215040007
 protein coding gene Chr6:68559190-68603213 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0028489
 protein coding gene Chr6:68489070-68532595 (-)
CAST/EiJ ENSTCUG00005031609
 protein coding gene Chr6:68715249-68759318 (-)
CBA/J ENSMUSG00210033738
 protein coding gene Chr6:68407617-68451620 (-)
DBA/2J ENSMUSG00185042470
 protein coding gene Chr6:68967711-69011732 (-)
FVB/NJ ENSMUSG00205025511
 protein coding gene Chr6:67682042-67726064 (-)
JF1/MsJ ENSUMUG00000019480
 protein coding gene Chr6:68004353-68048577 (-)
LP/J ENSMUSG00230023522
 protein coding gene Chr6:70064495-70108509 (-)
NOD/ShiLtJ ENSMUSG00190032196
 protein coding gene Chr6:67924041-67968247 (-)
NZO/HlLtJ ENSMUSG00225006572
 protein coding gene Chr6:72038377-72082395 (-)
PWK/PhJ ENSLUMG00010020323
 protein coding gene Chr6:67375339-67419543 (-)
SPRET/EiJ ENSMSPG00010022315
 protein coding gene Chr6:69259783-69304327 (-)
WSB/EiJ ENSIUOG00005021489
 protein coding gene Chr6:68962788-69006819 (-)



Homology
more
  • Human Ortholog
    KDM3A, lysine demethylase 3A
  • Vertebrate Orthologs
    2
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    KDM3A, lysine demethylase 3A
  • Synonyms
    JHDM2A, JHMD2A, JMJD1, JMJD1A, TSGA
  • Links
    NCBI Gene ID: 55818
    UniProt: Q9Y4C1

  • Chr Location
    2p11.2; chr2:86437044-86492716 (+)  GRCh38
Human Diseases
more
  • Diseases
    1 with Kdm3a mouse models; 2 with human KDM3A associations

Human Disease Mouse Models
      
IDs
 View 1 model
      
IDs
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    1 with disease annotations
  • References
    1 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    56 phenotypes from 5 alleles in 6 genetic backgrounds
    2 images
    43 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.
Male mice homozygous for a hypomorphic allele display infertility, oligoasthenoteratozoospermia, small testis, and impaired spermiogenesis. Mice homozygous for a null allele exhibit abnormal spermatogenesis and obesity associated with hyperlipidemia.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    52
  • GO References
    16
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
    624
  • Tissues
    19
  • cDNA Data
    276
  • Literature Summary
    16
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 104263 NCBI Gene Model | MGI Sequence Detail 44010 C57BL/6J ±  kb
    transcript NM_173001 RefSeq | MGI Sequence Detail 4857 C57BL/6  
    polypeptide Q6PCM1 UniProt | EBI | MGI Sequence Detail 1323 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 281
      cDNA 277
      Primer pair 3
      Other 1
      Antibodies 3

      Microarray probesets 3
    Other
    Accession IDs
    less
    MGD-MRK-15272, MGI:1920820, MGI:2444882
    References
    more
    • Summaries
      All 105
      Developmental Gene Expression 16
      Diseases 1
      Gene Ontology 16
      Phenotypes 43
    • Earliest
      J:11619 Hoog C, et al., Analysis of a murine male germ cell-specific transcript that encodes a putative zinc finger protein. Mol Reprod Dev. 1991 Nov;30(3):173-81
    • Latest
      J:389738 Maeda R, et al., Dynamic regulation of H3K9 dimethylation drives mouse minor zygotic genome activation. Nat Struct Mol Biol. 2026 Jun;33(6):928-938
    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
    09/01/2026
    MGI 6.24     		The Jackson Laboratory