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Msx1 Gene Detail
Summary
  • Symbol
    Msx1
  • Name
    msh homeobox 1
  • Synonyms
    Hox-7, Hox7, Hox7.1, msh, muscle-segment homeobox
  • Feature Type
    protein coding gene
  • IDs
    MGI:97168
    NCBI Gene: 17701
  • Alliance
    genome feature page
  • Transcription Start Sites
    1 TSS
  • Regulated by
    Rr23 (1 regulatory region)
Location &
Maps
more
  • Sequence Map
    Chr5:37977835-37981929 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 5, 20.21 cM
  • Mapping Data
    28 experiments
Strain
Comparison
more
  • SNPs within 2kb
    136 from dbSNP Build 142
  • Strain Annotations
    19
  • RFLP
    7
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_97168
 protein coding gene Chr5:37977829-37981929 (-)
129S1/SvImJ ENSMUSG00200031777
 protein coding gene Chr5:33427188-33431285 (-)
A/J ENSMUSG00195028364
 protein coding gene Chr5:32883499-32887577 (-)
AKR/J ENSMUSG00220001929
 protein coding gene Chr5:32910338-32914415 (-)
BALB/cJ ENSMUSG00180023739
 protein coding gene Chr5:32686346-32690423 (-)
C3H/HeJ ENSMUSG00175018611
 protein coding gene Chr5:34670482-34674559 (-)
C57BL/6NJ ENSMUSG00215004961
 protein coding gene Chr5:33425718-33429817 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0027173
 protein coding gene Chr5:32691677-32695688 (-)
CAST/EiJ ENSTCUG00005022765
 protein coding gene Chr5:32890302-32894361 (-)
CBA/J ENSMUSG00210004399
 protein coding gene Chr5:33632492-33636569 (-)
DBA/2J ENSMUSG00185016458
 protein coding gene Chr5:35511088-35515185 (-)
FVB/NJ ENSMUSG00205016189
 protein coding gene Chr5:32393583-32397682 (-)
JF1/MsJ ENSUMUG00000053005
 protein coding gene Chr5:40098934-40102929 (-)
LP/J ENSMUSG00230002076
 protein coding gene Chr5:40154289-40158386 (-)
NOD/ShiLtJ ENSMUSG00190003108
 protein coding gene Chr5:32698215-32702313 (-)
NZO/HlLtJ ENSMUSG00225015781
 protein coding gene Chr5:45317123-45321189 (-)
PWK/PhJ ENSLUMG00010022794
 protein coding gene Chr5:32773452-32777433 (-)
SPRET/EiJ ENSMSPG00010031867
 protein coding gene Chr5:34017534-34021586 (-)
WSB/EiJ ENSIUOG00005016710
 protein coding gene Chr5:35603834-35607913 (-)



Homology
more
  • Human Ortholog
    MSX1, msh homeobox 1
  • Vertebrate Orthologs
    2
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    MSX1, msh homeobox 1
  • Synonyms
    ECTD3, HOX7, HYD1, STHAG1
  • Links
    NCBI Gene ID: 4487
    UniProt: P28360

  • Chr Location
    4p16.2; chr4:4859665-4863936 (+)  GRCh38
Human Diseases
more
  • Diseases
    2 with Msx1 mouse models; 6 with human MSX1 associations

Human Disease Mouse Models
      
IDs
 View 3 models
      
IDs
 View 1 model
      
IDs
IDs
IDs
IDs
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    2 with disease annotations
  • References
    4 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    57 phenotypes from 6 alleles in 10 genetic backgrounds
    99 phenotypes from multigenic genotypes
    127 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.
Mutants affect craniofacial neural crest-derived mesenchyme by controlling cell cycle progression. Homozygous null mutants die at birth with multiple craniofacial defects including cleft palate, reduced mandible and maxilla, and retarded tooth development.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    135
  • GO References
    44
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
    2650
  • Tissues
    1028
  • cDNA Data
    72
  • Literature Summary
    614
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 17701 NCBI Gene Model | MGI Sequence Detail 4095 C57BL/6J ±  kb
    transcript NM_010835 RefSeq | MGI Sequence Detail 1931 ZRU/MplStud  
    polypeptide P13297 UniProt | EBI | MGI Sequence Detail 303 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 207
      Genomic 15
      cDNA 89
      Primer pair 21
      Other 82
      Antibodies 5

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGD-MRK-10867, MGD-MRK-12570, MGI:2140786, MGI:2140836
    References
    more
    • Summaries
      All 794
      Developmental Gene Expression 614
      Diseases 4
      Gene Ontology 44
      Phenotypes 127
    • Earliest
      J:5021 Batchelor AL, et al., A comparison of the mutagenic effectiveness of chronic neutron- and gamma-irradiation of mouse spermatogonia. Mutat Res. 1966 Jun;3(3):218-29
    • Latest
      J:391313 He Y, et al., Human iPSC-derived heart valve-like assembloids model valve development and disease pathology. Cell Stem Cell. 2026 Aug 11;
    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)
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    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