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Hoxa9 Gene Detail
Summary
  • Symbol
    Hoxa9
  • Name
    homeobox A9
  • Synonyms
    D6a9, Hox-1.7
  • Feature Type
    protein coding gene
  • IDs
    MGI:96180
    NCBI Gene: 15405
  • Member of
    Hoxa cluster
  • Alliance
    gene page
  • Transcription Start Sites
    7 TSS
Location &
Maps
more
  • Sequence Map
    Chr6:52200077-52203169 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 6, 25.40 cM
  • Mapping Data
    9 experiments
Strain
Comparison
more
  • SNPs within 2kb
    174 from dbSNP Build 142
  • Strain Annotations
    18
  • PCR
    1
  • RFLP
    2
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_96180
 protein coding gene Chr6:52200077-52208069 (-)
129S1/SvImJ MGP_129S1SvImJ_G0030747
 protein coding gene Chr6:51464260-51472260 (-)
A/J MGP_AJ_G0030716
 protein coding gene Chr6:49058936-49066921 (-)
AKR/J MGP_AKRJ_G0030643
 protein coding gene Chr6:50765340-50773340 (-)
BALB/cJ MGP_BALBcJ_G0030728
 protein coding gene Chr6:49419585-49427569 (-)
C3H/HeJ MGP_C3HHeJ_G0030441
 protein coding gene Chr6:50774399-50782377 (-)
C57BL/6NJ MGP_C57BL6NJ_G0031183
 protein coding gene Chr6:52600579-52608558 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0028389
 protein coding gene Chr6:46706741-46714764 (-)
CAST/EiJ MGP_CASTEiJ_G0029844
 protein coding gene Chr6:50589354-50597324 (-)
CBA/J MGP_CBAJ_G0030415
 protein coding gene Chr6:54799743-54809576 (-)
DBA/2J MGP_DBA2J_G0030565
 protein coding gene Chr6:48981357-48989342 (-)
FVB/NJ MGP_FVBNJ_G0030517
 protein coding gene Chr6:48592943-48600920 (-)
LP/J MGP_LPJ_G0030650
 protein coding gene Chr6:51442949-51450949 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0030551
 protein coding gene Chr6:57429373-57437375 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0031213
 protein coding gene Chr6:50694012-50702012 (-)
PWK/PhJ MGP_PWKPhJ_G0029557
 protein coding gene Chr6:48605357-48613322 (-)
SPRET/EiJ MGP_SPRETEiJ_G0029391
 protein coding gene Chr6:50029440-50037415 (-)
WSB/EiJ MGP_WSBEiJ_G0029921
 protein coding gene Chr6:50710176-50718175 (-)



Homology
more
  • Human Ortholog
    HOXA9, homeobox A9
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    HOXA9, homeobox A9
  • Synonyms
    ABD-B, HOX1, HOX1.7, HOX1G
  • Links
    NCBI Gene ID: 3205
    UniProt: P31269

  • Chr Location
    7p15.2; chr7:27162438-27175180 (-)  GRCh38
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    8 phenotypes from 2 alleles in 2 genetic backgrounds
    33 phenotypes from multigenic genotypes
    40 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.
Homozygotes for targeted null mutations exhibit homeotic transformations affecting lumbar vertebrae, reduced spleen and thymus weights, and defects in myeloid, erythroid, and lymphoid hematopoiesis.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    66
  • 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
    1243
  • Tissues
    276
  • cDNA Data
    27
  • Literature Summary
    84
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 15405 NCBI Gene Model | MGI Sequence Detail 3093 C57BL/6J ±  kb
    transcript NM_010456 RefSeq | MGI Sequence Detail 2048 ZRU/MplStud  
    polypeptide P09631 UniProt | EBI | MGI Sequence Detail 271 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 78
      Genomic 17
      cDNA 29
      Primer pair 22
      Other 10

      Microarray probesets 5
    Other
    Accession IDs
    less
    MGD-MRK-10823, MGD-MRK-10881
    References
    more
    • Summaries
      All 177
      Developmental Gene Expression 84
      Gene Ontology 22
      Phenotypes 40
    • Earliest
      J:8939 Rubin MR, et al., Murine Hox-1.7 homeo-box gene: cloning, chromosomal location, and expression [published erratum appears in Mol Cell Biol 1988 Dec;8(12):5593]. Mol Cell Biol. 1987 Oct;7(10):3836-41
    • Latest
      J:365966 Koch P, et al., A versatile toolbox for determining IRES activity in cells and embryonic tissues. EMBO J. 2025 May;44(9):2695-2724
    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
    03/25/2025
    MGI 6.24     		The Jackson Laboratory