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Hoxa1 Gene Detail
Summary
  • Symbol
    Hoxa1
  • Name
    homeobox A1
  • Synonyms
    early retinoic acid, ERA1, Hox-1.6
  • Feature Type
    protein coding gene
  • IDs
    MGI:96170
    NCBI Gene: 15394
  • Member of
    Hoxa cluster
  • Alliance
    gene page
  • Transcription Start Sites
    1 TSS
Location &
Maps
more
  • Sequence Map
    Chr6:52132573-52135299 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
    5 experiments
Strain
Comparison
more
  • SNPs within 2kb
    74 from dbSNP Build 142
  • Strain Annotations
    18
  • PCR
    1
  • RFLP
    1
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_96170
 protein coding gene Chr6:52132570-52135299 (-)
129S1/SvImJ MGP_129S1SvImJ_G0030738
 protein coding gene Chr6:51388689-51391416 (-)
A/J MGP_AJ_G0030708
 protein coding gene Chr6:48991102-48993832 (-)
AKR/J MGP_AKRJ_G0030634
 protein coding gene Chr6:50694981-50697708 (-)
BALB/cJ MGP_BALBcJ_G0030719
 protein coding gene Chr6:49350434-49353164 (-)
C3H/HeJ MGP_C3HHeJ_G0030433
 protein coding gene Chr6:50705271-50708001 (-)
C57BL/6NJ MGP_C57BL6NJ_G0031174
 protein coding gene Chr6:52528565-52531292 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0028381
 protein coding gene Chr6:46639163-46641882 (-)
CAST/EiJ MGP_CASTEiJ_G0029835
 protein coding gene Chr6:50517311-50520057 (-)
CBA/J MGP_CBAJ_G0030406
 protein coding gene Chr6:54724332-54727062 (-)
DBA/2J MGP_DBA2J_G0030556
 protein coding gene Chr6:48914085-48916815 (-)
FVB/NJ MGP_FVBNJ_G0030508
 protein coding gene Chr6:48523838-48526568 (-)
LP/J MGP_LPJ_G0030641
 protein coding gene Chr6:51369910-51372637 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0030542
 protein coding gene Chr6:57359516-57362243 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0031204
 protein coding gene Chr6:50621090-50623820 (-)
PWK/PhJ MGP_PWKPhJ_G0029548
 protein coding gene Chr6:48535649-48538389 (-)
SPRET/EiJ MGP_SPRETEiJ_G0029383
 protein coding gene Chr6:49958964-49961690 (-)
WSB/EiJ MGP_WSBEiJ_G0029912
 protein coding gene Chr6:50637397-50640124 (-)



Homology
more
  • Human Ortholog
    HOXA1, homeobox A1
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    HOXA1, homeobox A1
  • Synonyms
    BSAS, HOX1, HOX1F
  • Links
    NCBI Gene ID: 3198
    neXtProt AC: NX_P49639
    UniProt: P49639

  • Chr Location
    7p15.2; chr7:27092993-27096000 (-)  GRCh38
Human Diseases
more
  • Diseases
    1 with Hoxa1 mouse models; 2 with human HOXA1 associations

Human Disease Mouse Models
      
IDs
 View 1 model
      
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    1 with disease annotations
  • References
    1 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    96 phenotypes from 8 alleles in 8 genetic backgrounds
    45 phenotypes from multigenic genotypes
    42 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 die perinatally and exhibit altered and missing rhombomeric structures associated with abnormalities of cranial nerves and ganglia, defects in the skull, and both outer and inner ears, and anoxia at birth.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    92
  • GO References
    12
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
    1096
  • Tissues
    277
  • cDNA Data
    29
  • Literature Summary
    76
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 15394 NCBI Gene Model | MGI Sequence Detail 2727 C57BL/6J ±  kb
    transcript NM_010449 RefSeq | MGI Sequence Detail 2250 ZRU/MplStud  
    polypeptide P09022 UniProt | EBI | MGI Sequence Detail 331 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 62
      Genomic 11
      cDNA 30
      Primer pair 10
      Other 11

      Microarray probesets 3
    Other
    Accession IDs
    less
    MGD-MRK-10822, MGD-MRK-10871
    References
    more
    • Summaries
      All 166
      Developmental Gene Expression 76
      Diseases 1
      Gene Ontology 12
      Phenotypes 42
    • Earliest
      J:8427 Duboule D, et al., A new homeo-box is present in overlapping cosmid clones which define the mouse Hox-1 locus. EMBO J. 1986 Aug;5(8):1973-80
    • Latest
      J:337811 Petrelli B, et al., Genetically programmed retinoic acid deficiency during gastrulation phenocopies most known developmental defects due to acute prenatal alcohol exposure in FASD. Front Cell Dev Biol. 2023;11:1208279
    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
    11/12/2024
    MGI 6.24     		The Jackson Laboratory