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H3f3a Gene Detail
Summary
  • Symbol
    H3f3a
  • Name
    H3.3 histone A
  • Synonyms
    H3-3a, H3.3A
  • Feature Type
    protein coding gene
  • IDs
    MGI:1097686
    NCBI Gene: 15078
  • Alliance
    genome feature page
  • Transcription Start Sites
    6 TSS
Location &
Maps
more
  • Sequence Map
    Chr1:180630125-180641127 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 1, 84.46 cM, cytoband D2.3
  • Mapping Data
    2 experiments
Strain
Comparison
more
  • SNPs within 2kb
    349 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1097686
 protein coding gene Chr1:180628397-180641508 (-)
129S1/SvImJ MGP_129S1SvImJ_G0016874
 protein coding gene Chr1:187260176-187275877 (-)
A/J MGP_AJ_G0016853
 protein coding gene Chr1:179683855-179702144 (-)
AKR/J MGP_AKRJ_G0016819
 protein coding gene Chr1:185024579-185040759 (-)
BALB/cJ MGP_BALBcJ_G0016811
 protein coding gene Chr1:180309955-180324292 (-)
C3H/HeJ MGP_C3HHeJ_G0016636
 protein coding gene Chr1:185795739-185810240 (-)
C57BL/6NJ MGP_C57BL6NJ_G0017274
 protein coding gene Chr1:193292963-193298088 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0014982
 protein coding gene Chr1:170667960-170680805 (-)
CAST/EiJ MGP_CASTEiJ_G0016217
 protein coding gene Chr1:185143702-185159821 (-)
CBA/J MGP_CBAJ_G0016610
 protein coding gene Chr1:200468560-200483951 (-)
DBA/2J MGP_DBA2J_G0016716
 protein coding gene Chr1:178519654-178532444 (-)
FVB/NJ MGP_FVBNJ_G0016712
 protein coding gene Chr1:176616991-176629725 (-)
LP/J MGP_LPJ_G0016790
 protein coding gene Chr1:188518849-188536264 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0016743
 protein coding gene Chr1:207648358-207661034 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0017311
 protein coding gene Chr1:184808925-184823154 (-)
PWK/PhJ MGP_PWKPhJ_G0016005
 protein coding gene Chr1:177634167-177647075 (-)
SPRET/EiJ MGP_SPRETEiJ_G0015781
 protein coding gene Chr1:183744359-183756903 (-)
WSB/EiJ MGP_WSBEiJ_G0016280
 protein coding gene Chr1:184999545-185012240 (-)



Homology
more
  • Human Ortholog
    H3-3A, H3.3 histone A
  • Vertebrate Orthologs
    9
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    H3-3A, H3.3 histone A
  • Synonyms
    BRYLIB1, H3.3A, H3F3, H3F3A
  • Links
    NCBI Gene ID: 3020
    UniProt: P84243

  • Chr Location
    1q42.12; chr1:226061571-226073206 (+)  GRCh38
  • Human Ortholog
    H3-5, H3.5 histone
  • Synonyms
    H3.3C, H3.5, H3F3C
  • Links
    NCBI Gene ID: 440093
    UniProt: Q6NXT2

  • Chr Location
    12p11.21; chr12:31791185-31792298 (-)  GRCh38
Human Diseases
more
  • Diseases
    2 with human H3-3A,H3-3B associations

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

Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    7 phenotypes from 3 alleles in 3 genetic backgrounds
    28 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.
Homozygous mutants for a hypomorphic gene trap allele display partial neonatal lethality, reduced fertility, growth abnormalities and neuromuscular defects. Mice homozygous for a reporter allele exhibit reduced body size and male fertility.
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
    860
  • Tissues
    75
  • cDNA Data
    28
  • Literature Summary
    19
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 15078 NCBI Gene Model | MGI Sequence Detail 11003 C57BL/6J ±  kb
    transcript NM_008210 RefSeq | MGI Sequence Detail 1043 C57BL/6  
    polypeptide NP_032236 RefSeq | MGI Sequence Detail 136 C57BL/6  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      4 Sequences
    Molecular
    Reagents
    less
    • All nucleic 37
      cDNA 30
      Primer pair 5
      Other 2

      Microarray probesets 9
    References
    more
    • Summaries
      All 116
      Developmental Gene Expression 19
      Phenotypes 28
    • Earliest
      J:42392 Hraba-Renevey S, et al., Expression of a mouse replacement histone H3.3 gene with a highly conserved 3' noncoding region during SV40- and polyoma-induced Go to S-phase transition. Nucleic Acids Res. 1989 Apr 11;17(7):2449-61
    • Latest
      J:371954 Yagi M, et al., Bivalent chromatin instructs lineage specification during hematopoiesis. Cell. 2025 Aug 7;188(16):4314-4331.e29
    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
    06/09/2026
    MGI 6.24     		The Jackson Laboratory