About   Help   FAQ
Hoxd9 Gene Detail
Summary
  • Symbol
    Hoxd9
  • Name
    homeobox D9
  • Synonyms
    Hox-4.4, Hox-5.2
  • Feature Type
    protein coding gene
  • IDs
    MGI:96210
    NCBI Gene: 15438
  • Member of
    Hoxd cluster
  • Alliance
    gene page
  • Transcription Start Sites
    6 TSS
Location &
Maps
more
  • Sequence Map
    Chr2:74528107-74530552 bp, + strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 2, 44.13 cM
  • Mapping Data
    13 experiments
Strain
Comparison
more
  • SNPs within 2kb
    59 from dbSNP Build 142
  • Strain Annotations
    18
  • PCR
    2
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_96210
 protein coding gene Chr2:74528071-74530552 (+)
129S1/SvImJ MGP_129S1SvImJ_G0025849
 protein coding gene Chr2:75011903-75014384 (+)
A/J MGP_AJ_G0025827
 protein coding gene Chr2:72079029-72081509 (+)
AKR/J MGP_AKRJ_G0025795
 protein coding gene Chr2:74032245-74034726 (+)
BALB/cJ MGP_BALBcJ_G0025821
 protein coding gene Chr2:72265654-72268135 (+)
C3H/HeJ MGP_C3HHeJ_G0025581
 protein coding gene Chr2:74220083-74222564 (+)
C57BL/6NJ MGP_C57BL6NJ_G0026268
 protein coding gene Chr2:77247668-77250149 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0023671
 protein coding gene Chr2:69502265-69504729 (+)
CAST/EiJ MGP_CASTEiJ_G0025045
 protein coding gene Chr2:74537069-74539546 (+)
CBA/J MGP_CBAJ_G0025562
 protein coding gene Chr2:80067191-80069672 (+)
DBA/2J MGP_DBA2J_G0025693
 protein coding gene Chr2:71685574-71688055 (+)
FVB/NJ MGP_FVBNJ_G0025655
 protein coding gene Chr2:71075735-71078216 (+)
LP/J MGP_LPJ_G0025781
 protein coding gene Chr2:74876034-74878515 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0025686
 protein coding gene Chr2:81980813-81983294 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0026325
 protein coding gene Chr2:74147780-74150261 (+)
PWK/PhJ MGP_PWKPhJ_G0024786
 protein coding gene Chr2:71616499-71618975 (+)
SPRET/EiJ MGP_SPRETEiJ_G0024594
 protein coding gene Chr2:74381596-74384070 (+)
WSB/EiJ MGP_WSBEiJ_G0025113
 protein coding gene Chr2:74583715-74586196 (+)



Homology
more
  • Human Ortholog
    HOXD9, homeobox D9
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    HOXD9, homeobox D9
  • Synonyms
    HOX4, Hox-4.3, HOX4C, Hox-5.2
  • Links
    NCBI Gene ID: 3235
    neXtProt AC: NX_P28356
    UniProt: P28356

  • Chr Location
    2q31.1; chr2:176122719-176124937 (+)  GRCh38
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    7 phenotypes from 1 allele in 1 genetic background
    48 phenotypes from multigenic genotypes
    55 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 targeted mutation exhibit anterior transformation of lumbar, sacral, and caudal vertebrae with abnormal humerus morphology.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    48
  • GO References
    11
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
    1246
  • Tissues
    225
  • cDNA Data
    20
  • Literature Summary
    81
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 15438 NCBI Gene Model | MGI Sequence Detail 2446 C57BL/6J ±  kb
    transcript NM_013555 RefSeq | MGI Sequence Detail 2100 ZRU/MplStud  
    polypeptide P28357 UniProt | EBI | MGI Sequence Detail 339 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 65
      Genomic 14
      cDNA 24
      Primer pair 13
      Other 14

      Microarray probesets 2
    Other
    Accession IDs
    less
    MGD-MRK-10851, MGD-MRK-10859, MGD-MRK-10911
    References
    more
    • Summaries
      All 155
      Developmental Gene Expression 81
      Gene Ontology 11
      Phenotypes 55
    • Earliest
      J:9875 Oliver G, et al., Complementary homeo protein gradients in developing limb buds. Genes Dev. 1989 May;3(5):641-50
    • Latest
      J:354194 Oikonomakos I, et al., In vitro differentiation of mouse pluripotent stem cells into corticosteroid-producing adrenocortical cells. Stem Cell Reports. 2024 Sep 10;19(9):1289-1303
    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
    Warranty Disclaimer, Privacy Notice, Licensing, & Copyright
    Send questions and comments to User Support.     		last database update
    12/10/2024
    MGI 6.24     		The Jackson Laboratory