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Foxa1 Gene Detail
Summary
  • Symbol
    Foxa1
  • Name
    forkhead box A1
  • Synonyms
    Hnf-3a, Hnf3a, Tcf-3a, Tcf3a
  • Feature Type
    protein coding gene
  • IDs
    MGI:1347472
    NCBI Gene: 15375
  • Alliance
    genome feature page
  • Transcription Start Sites
    11 TSS
Location &
Maps
more
  • Sequence Map
    Chr12:57587414-57593702 bp, - strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 12, 24.70 cM
  • Mapping Data
    6 experiments
Strain
Comparison
more
  • SNPs within 2kb
    162 from dbSNP Build 142
  • Strain Annotations
    19
  • RFLP
    3
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1347472
 protein coding gene Chr12:57585750-57594815 (-)
129S1/SvImJ ENSMUSG00200029315
 protein coding gene Chr12:49506014-49511508 (-)
A/J ENSMUSG00195001561
 protein coding gene Chr12:52090805-52096308 (-)
AKR/J ENSMUSG00220026177
 protein coding gene Chr12:50115090-50120593 (-)
BALB/cJ ENSMUSG00180007417
 protein coding gene Chr12:51105057-51110560 (-)
C3H/HeJ ENSMUSG00175016531
 protein coding gene Chr12:54146097-54151600 (-)
C57BL/6NJ ENSMUSG00215013014
 protein coding gene Chr12:50431848-50437345 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0017772
 protein coding gene Chr12:53101095-53106542 (-)
CAST/EiJ ENSTCUG00005008877
 protein coding gene Chr12:50534873-50540385 (-)
CBA/J ENSMUSG00210009714
 protein coding gene Chr12:50620360-50625865 (-)
DBA/2J ENSMUSG00185001012
 protein coding gene Chr12:52565636-52571141 (-)
FVB/NJ ENSMUSG00205012548
 protein coding gene Chr12:50414189-50419688 (-)
JF1/MsJ ENSUMUG00000005853
 protein coding gene Chr12:56638046-56643542 (-)
LP/J ENSMUSG00230013832
 protein coding gene Chr12:59582851-59588341 (-)
NOD/ShiLtJ ENSMUSG00190015309
 protein coding gene Chr12:49614049-49619546 (-)
NZO/HlLtJ ENSMUSG00225040759
 protein coding gene Chr12:61724228-61729705 (-)
PWK/PhJ ENSLUMG00010002298
 protein coding gene Chr12:50700799-50706304 (-)
SPRET/EiJ ENSMSPG00010010791
 protein coding gene Chr12:52213949-52219455 (-)
WSB/EiJ ENSIUOG00005003352
 protein coding gene Chr12:50441597-50447088 (-)



Homology
more
  • Human Ortholog
    FOXA1, forkhead box A1
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    FOXA1, forkhead box A1
  • Synonyms
    HNF3A, TCF3A
  • Links
    NCBI Gene ID: 3169
    UniProt: P55317

  • Chr Location
    14q21.1; chr14:37589552-37596059 (-)  GRCh38
Human Diseases
more
  • Diseases
    6 with human FOXA1 associations

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

Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    19 phenotypes from 2 alleles in 3 genetic backgrounds
    14 phenotypes from multigenic genotypes
    52 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 exhibit abnormal feeding, hypoglycemia, impaired glucagon secretion, hypotryglyceridemia, wasting, and lethality between postnatal days 2 and 14.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    86
  • GO References
    25
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
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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
    1631
  • Tissues
    635
  • cDNA Data
    40
  • Literature Summary
    134
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000035451 Ensembl Gene Model | MGI Sequence Detail 6289 C57BL/6J ±  kb
    transcript ENSMUST00000044380 Ensembl | MGI Sequence Detail 3191 Not Applicable  
    polypeptide ENSMUSP00000041118 Ensembl | MGI Sequence Detail 468 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 84
      Genomic 5
      cDNA 42
      Primer pair 22
      Other 15
      Antibodies 13

      Microarray probesets 3
    Other
    Accession IDs
    less
    MGD-MRK-10804, MGD-MRK-14749, MGD-MRK-14755, MGD-MRK-16685, MGI:99890
    References
    more
    • Summaries
      All 272
      Developmental Gene Expression 134
      Gene Ontology 25
      Phenotypes 52
    • Earliest
      J:20860 Lai E, et al., Hepatocyte nuclear factor 3 alpha belongs to a gene family in mammals that is homologous to the Drosophila homeotic gene fork head. Genes Dev. 1991 Mar;5(3):416-27
    • Latest
      J:390780 Qasrawi F, et al., DeltaNP63 regulates epithelial stratification and differentiation in the murine ureter. Am J Physiol Renal Physiol. 2026 Aug 1;331(2):F286-F303
    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