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Hoxd1 Gene Detail
Summary
  • Symbol
    Hoxd1
  • Name
    homeobox D1
  • Synonyms
    Hox-4.9
  • Feature Type
    protein coding gene
  • IDs
    MGI:96201
    NCBI Gene: 15429
  • Member of
    Hoxd cluster
  • Alliance
    gene page
Location &
Maps
more
  • Sequence Map
    Chr2:74593324-74595486 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
    4 experiments
Strain
Comparison
more
  • SNPs within 2kb
    117 from dbSNP Build 142
  • Strain Annotations
    18
  • RFLP
    1
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_96201
 protein coding gene Chr2:74593324-74595486 (+)
129S1/SvImJ MGP_129S1SvImJ_G0025854
 protein coding gene Chr2:75080439-75082593 (+)
A/J MGP_AJ_G0025832
 protein coding gene Chr2:72143760-72145921 (+)
AKR/J MGP_AKRJ_G0025800
 protein coding gene Chr2:74099672-74101834 (+)
BALB/cJ MGP_BALBcJ_G0025826
 protein coding gene Chr2:72331643-72333804 (+)
C3H/HeJ MGP_C3HHeJ_G0025586
 protein coding gene Chr2:74288563-74290718 (+)
C57BL/6NJ MGP_C57BL6NJ_G0026273
 protein coding gene Chr2:77318433-77320646 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0023676
 protein coding gene Chr2:69567477-69569636 (+)
CAST/EiJ MGP_CASTEiJ_G0025050
 protein coding gene Chr2:74609911-74612053 (+)
CBA/J MGP_CBAJ_G0025567
 protein coding gene Chr2:80146858-80149018 (+)
DBA/2J MGP_DBA2J_G0025698
 protein coding gene Chr2:71752304-71754464 (+)
FVB/NJ MGP_FVBNJ_G0025660
 protein coding gene Chr2:71140503-71142664 (+)
LP/J MGP_LPJ_G0025786
 protein coding gene Chr2:74941316-74943477 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0025691
 protein coding gene Chr2:82047552-82049753 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0026330
 protein coding gene Chr2:74216465-74218619 (+)
PWK/PhJ MGP_PWKPhJ_G0024791
 protein coding gene Chr2:71682562-71684803 (+)
SPRET/EiJ MGP_SPRETEiJ_G0024599
 protein coding gene Chr2:74460701-74462862 (+)
WSB/EiJ MGP_WSBEiJ_G0025118
 protein coding gene Chr2:74655832-74657987 (+)



Homology
more
  • Human Ortholog
    HOXD1, homeobox D1
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    HOXD1, homeobox D1
  • Synonyms
    HOX4, Hox-4.7, HOX4G
  • Links
    NCBI Gene ID: 3231
    neXtProt AC: NX_Q9GZZ0
    UniProt: Q9GZZ0

  • Chr Location
    2q31.1; chr2:176188668-176190907 (+)  GRCh38
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    10 phenotypes from 2 alleles in 2 genetic backgrounds
    37 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 reporter allele display abnormal cervical vertebrae. Mice homozygous for a knock-out allele exhibit abnormal nociceptor innervation of the skin, aberrant nociceptor axonal projections in the spinal cord, and deficits in pain sensitivity.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    13
  • GO References
    7
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
    946
  • Tissues
    144
  • cDNA Data
    14
  • Literature Summary
    34
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 15429 NCBI Gene Model | MGI Sequence Detail 2163 C57BL/6J ±  kb
    transcript NM_010467 RefSeq | MGI Sequence Detail 1878 ZRU/MplStud  
    polypeptide Q01822 UniProt | EBI | MGI Sequence Detail 328 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 39
      Genomic 9
      cDNA 15
      Primer pair 9
      Other 6

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGD-MRK-10856, MGD-MRK-10902
    References
    more
    • Summaries
      All 93
      Developmental Gene Expression 34
      Gene Ontology 7
      Phenotypes 37
    • Earliest
      J:9607 Ferguson-Smith AC, et al., The genomics of human homeobox-containing loci. Pathol Immunopathol Res. 1988;7(1-2):119-26
    • Latest
      J:326160 Hintermann A, et al., Developmental and evolutionary comparative analysis of a regulatory landscape in mouse and chicken. Development. 2022 Jun 15;149(12):dev200594
    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
    11/19/2024
    MGI 6.24     		The Jackson Laboratory