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Alx1 Gene Detail
Summary
  • Symbol
    Alx1
  • Name
    ALX homeobox 1
  • Synonyms
    Cart1
  • Feature Type
    protein coding gene
  • IDs
    MGI:104621
    NCBI Gene: 216285
  • Alliance
    genome feature page
  • Transcription Start Sites
    4 TSS
  • Regulated by
    Rr844 (1 regulatory region)
Location &
Maps
more
  • Sequence Map
    Chr10:102834564-102865501 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 10, 53.56 cM
  • Mapping Data
    4 experiments
Strain
Comparison
more
  • SNPs within 2kb
    755 from dbSNP Build 142
  • Strain Annotations
    19
  • RFLP
    1
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_104621
 protein coding gene Chr10:102834564-102866076 (-)
129S1/SvImJ ENSMUSG00200019506
 protein coding gene Chr10:99328242-99359960 (-)
A/J ENSMUSG00195015210
 protein coding gene Chr10:99759958-99791660 (-)
AKR/J ENSMUSG00220024727
 protein coding gene Chr10:99347576-99379177 (-)
BALB/cJ ENSMUSG00180008762
 protein coding gene Chr10:99767149-99798851 (-)
C3H/HeJ ENSMUSG00175005745
 protein coding gene Chr10:99648461-99680143 (-)
C57BL/6NJ ENSMUSG00215006311
 protein coding gene Chr10:99353928-99385452 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0015776
 protein coding gene Chr10:96431352-96452630 (-)
CAST/EiJ ENSTCUG00005005697
 protein coding gene Chr10:98933036-98964972 (-)
CBA/J ENSMUSG00210022792
 protein coding gene Chr10:99539425-99571112 (-)
DBA/2J ENSMUSG00185018402
 protein coding gene Chr10:99709335-99741031 (-)
FVB/NJ ENSMUSG00205003256
 protein coding gene Chr10:99205943-99237542 (-)
JF1/MsJ ENSUMUG00000021154
 protein coding gene Chr10:101143096-101174836 (-)
LP/J ENSMUSG00230011907
 protein coding gene Chr10:101627541-101659253 (-)
NOD/ShiLtJ ENSMUSG00190022911
 protein coding gene Chr10:99833840-99865428 (-)
NZO/HlLtJ ENSMUSG00225040379
 protein coding gene Chr10:105858739-105890431 (-)
PWK/PhJ ENSLUMG00010005525
 protein coding gene Chr10:99421860-99453626 (-)
SPRET/EiJ ENSMSPG00010009022
 protein coding gene Chr10:101194665-101225742 (-)
WSB/EiJ ENSIUOG00005012979
 protein coding gene Chr10:99471242-99502759 (-)



Homology
more
  • Human Ortholog
    ALX1, ALX homeobox 1
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    ALX1, ALX homeobox 1
  • Synonyms
    CART1, FND3, HEL23
  • Links
    NCBI Gene ID: 8092
    UniProt: Q15699

  • Chr Location
    12q21.31; chr12:85280220-85301784 (+)  GRCh38
Human Diseases
more
  • Diseases
    1 with Alx1 mouse models; 1 with human ALX1 associations

Human Disease Mouse Models
      
IDs
 View 1 model
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
    52 phenotypes from 2 alleles in 5 genetic backgrounds
    37 phenotypes from multigenic genotypes
    15 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 a null allele show cranial neural tube and forebrain mesenchyme defects leading to acrania, meroanencephaly, and neonatal lethality. Homozygotes for another null allele die neonatally and display eye morphogenesis defects and craniofacial abnormalities, including frontonasal malformations, notching of the upper lip and cleft palate.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    54
  • 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
    859
  • Tissues
    137
  • cDNA Data
    26
  • Literature Summary
    56
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 216285 NCBI Gene Model | MGI Sequence Detail 30938 C57BL/6J ±  kb
    transcript NM_001421476 RefSeq | MGI Sequence Detail 2702 ZRU/MplStud  
    polypeptide Q8C8B0 UniProt | EBI | MGI Sequence Detail 326 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 47
      Genomic 1
      cDNA 28
      Primer pair 11
      Other 7
      Antibodies 1

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGD-MRK-26058, MGI:2143564
    References
    more
    • Summaries
      All 106
      Developmental Gene Expression 56
      Diseases 1
      Gene Ontology 12
      Phenotypes 15
    • Earliest
      J:137335 Roderick TH, Chromosomal inversions in studies of mammalian mutagenesis. Genetics. 1979 May;92(1 Pt 1 Suppl):s121-6
    • Latest
      J:383242 Huang Y, et al., A Twist1-regulated distal enhancer crucial for Alx1 gene expression and function during craniofacial development. Dev Biol. 2026 Jun;534:88-100
    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