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Hoxa2 Gene Detail
Summary
  • Symbol
    Hoxa2
  • Name
    homeobox A2
  • Synonyms
    Hox-1.11
  • Feature Type
    protein coding gene
  • IDs
    MGI:96174
    NCBI Gene: 15399
  • Member of
    Hoxa cluster
  • Alliance
    genome feature page
  • Transcription Start Sites
    4 TSS
Location &
Maps
more
  • Sequence Map
    Chr6:52139397-52141811 bp, - strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 6, 25.40 cM
  • Mapping Data
    6 experiments
Strain
Comparison
more
  • SNPs within 2kb
    37 from dbSNP Build 142
  • Strain Annotations
    19
  • PCR
    1
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_96174
 protein coding gene Chr6:52139389-52141811 (-)
129S1/SvImJ ENSMUSG00200004110
 protein coding gene Chr6:49116718-49119132 (-)
A/J ENSMUSG00195006139
 protein coding gene Chr6:48840616-48843030 (-)
AKR/J ENSMUSG00220003174
 protein coding gene Chr6:48549707-48552121 (-)
BALB/cJ ENSMUSG00180021871
 protein coding gene Chr6:49142335-49144749 (-)
C3H/HeJ ENSMUSG00175015898
 protein coding gene Chr6:48908894-48911308 (-)
C57BL/6NJ ENSMUSG00215005336
 protein coding gene Chr6:49093166-49095580 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0028382
 protein coding gene Chr6:46646026-46648416 (-)
CAST/EiJ ENSTCUG00005004821
 protein coding gene Chr6:48399218-48401634 (-)
CBA/J ENSMUSG00210017956
 protein coding gene Chr6:48953191-48955605 (-)
DBA/2J ENSMUSG00185012638
 protein coding gene Chr6:49535442-49537856 (-)
FVB/NJ ENSMUSG00205020402
 protein coding gene Chr6:49193569-49195983 (-)
JF1/MsJ ENSUMUG00000010038
 protein coding gene Chr6:48908081-48910495 (-)
LP/J ENSMUSG00230016322
 protein coding gene Chr6:50614023-50616437 (-)
NOD/ShiLtJ ENSMUSG00190027135
 protein coding gene Chr6:48870577-48872991 (-)
NZO/HlLtJ ENSMUSG00225012699
 protein coding gene Chr6:52597983-52600397 (-)
PWK/PhJ ENSLUMG00010020087
 protein coding gene Chr6:48645100-48647515 (-)
SPRET/EiJ ENSMSPG00010008234
 protein coding gene Chr6:49229036-49231450 (-)
WSB/EiJ ENSIUOG00005025259
 protein coding gene Chr6:49216046-49218460 (-)



Homology
more
  • Human Ortholog
    HOXA2, homeobox A2
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    HOXA2, homeobox A2
  • Synonyms
    HOX1K, MCOHI
  • Links
    NCBI Gene ID: 3199
    UniProt: O43364

  • Chr Location
    7p15.2; chr7:27100354-27102686 (-)  GRCh38
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    95 phenotypes from 12 alleles in 16 genetic backgrounds
    19 phenotypes from multigenic genotypes
    67 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.
Mutant homozygotes lack skeletal elements normally derived from the second branchial arch and show duplication of elements derived from the first branchial arch, such as ossification centers of the middle ear. Mutants die perinatally with cleft palate.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    50
  • GO References
    22
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
    1363
  • Tissues
    377
  • cDNA Data
    28
  • Literature Summary
    141
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000014704 Ensembl Gene Model | MGI Sequence Detail 2415 C57BL/6J ±  kb
    transcript ENSMUST00000014848 Ensembl | MGI Sequence Detail 1775 Not Applicable  
    polypeptide ENSMUSP00000014848 Ensembl | MGI Sequence Detail 372 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 77
      Genomic 8
      cDNA 28
      Primer pair 19
      Other 22
      Antibodies 6

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGD-MRK-10817, MGD-MRK-10875, MGI:2141392
    References
    more
    • Summaries
      All 219
      Developmental Gene Expression 141
      Gene Ontology 22
      Phenotypes 67
    • Earliest
      J:621 Hunt P, et al., A distinct Hox code for the branchial region of the vertebrate head. Nature. 1991 Oct 31;353(6347):861-4
    • Latest
      J:389749 Ben Zouari Y, et al., Polycomb chromatin topology enables long-range enhancer recruitment during craniofacial development. Nat Commun. 2026 May 14;17(1)
    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
    09/08/2026
    MGI 6.24     		The Jackson Laboratory