Foxa1 MGI Mouse Gene Detail - MGI:1347472

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

gene page
Transcription Start Sites

11 TSS

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

SNPs within 2kb

162 from dbSNP Build 142
Strain Annotations

18
RFLP

3

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1347472	protein coding gene	Chr12:57585750-57594815 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0019761	protein coding gene	Chr12:56733807-56739295 (-)
A/J	MGP_AJ_G0019720	protein coding gene	Chr12:54642114-54648620 (-)
AKR/J	MGP_AKRJ_G0019695	protein coding gene	Chr12:56374954-56380452 (-)
BALB/cJ	MGP_BALBcJ_G0019700	protein coding gene	Chr12:55014567-55020067 (-)
C3H/HeJ	MGP_C3HHeJ_G0019505	protein coding gene	Chr12:56466550-56472065 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0020152	protein coding gene	Chr12:58406052-58411534 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017772	protein coding gene	Chr12:53101095-53106542 (-)
CAST/EiJ	MGP_CASTEiJ_G0019057	protein coding gene	Chr12:51392306-51397813 (-)
CBA/J	MGP_CBAJ_G0019474	protein coding gene	Chr12:60483328-60488828 (-)
DBA/2J	MGP_DBA2J_G0019590	protein coding gene	Chr12:54560397-54566214 (-)
FVB/NJ	MGP_FVBNJ_G0019578	protein coding gene	Chr12:53844908-53850404 (-)
LP/J	MGP_LPJ_G0019662	protein coding gene	Chr12:56695191-56700674 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0019616	protein coding gene	Chr12:62029715-62035199 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0020186	protein coding gene	Chr12:55832197-55837671 (-)
PWK/PhJ	MGP_PWKPhJ_G0018824	protein coding gene	Chr12:48956741-48962439 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0018617	protein coding gene	Chr12:50263344-50268847 (-)
WSB/EiJ	MGP_WSBEiJ_G0019108	protein coding gene	Chr12:56366433-56371921 (-)

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

HGNC:5021

NCBI Gene ID: 3169

neXtProt AC: NX_P55317

UniProt: P55317
Chr Location

14q21.1; chr14:37589552-37596059 (-) GRCh38

MGI Vertebrate Homology

Foxa1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: FOXA1
Gene Tree

Foxa1

Diseases

6 with human FOXA1 associations

				Human Disease	Mouse Models
				breast cancer IDs breast cancer DOID:1612 DOID:1648 DOID:4241 ICD10CM:C50 ICD9CM:174.8 MESH:D001943 NCI:C9335 OMIM:114480 UMLS_CUI:C0006142
				esophagus squamous cell carcinoma IDs esophagus squamous cell carcinoma DOID:3748 MESH:D000077277 NCI:C4024 UMLS_CUI:C0279626
				hepatocellular carcinoma IDs hepatocellular carcinoma DOID:684 DOID:5005 EFO:0000182 ICD10CM:C22.0 MESH:D006528 NCI:C3099 OMIM:114550 ORDO:88673 UMLS_CUI:C2239176
				lung cancer IDs lung cancer DOID:1324 DOID:13075 DOID:1322 DOID:9881 ICD10CM:C34.1 ICD10CM:C34.2 ICD10CM:C34.3 ICD9CM:162.3 ICD9CM:162.4 ICD9CM:162.5 ICD9CM:162.8 OMIM:211980 OMIM:608935 OMIM:612571 OMIM:612593 OMIM:614210 UMLS_CUI:C0024624 UMLS_CUI:C0153491 UMLS_CUI:C0153492 UMLS_CUI:C0153493
				lung carcinoma IDs lung carcinoma DOID:3905 EFO:0001071 NCI:C4878 UMLS_CUI:C0684249
				stomach cancer IDs stomach cancer DOID:10534 DOID:10539 DOID:10542 DOID:10543 DOID:4713 ICD10CM:C16 ICD10CM:C16.2 ICD10CM:C16.5 ICD10CM:C16.6 ICD9CM:151 ICD9CM:151.4 ICD9CM:151.5 ICD9CM:151.6 ICD9CM:151.9 MESH:D013274 NCI:C3387 NCI:C9331 OMIM:613659 UMLS_CUI:C0024623 UMLS_CUI:C0038356 UMLS_CUI:C0153421 UMLS_CUI:C0153422 UMLS_CUI:C0153423

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

19 phenotypes from 2 alleles in 3 genetic backgrounds
14 phenotypes from multigenic genotypes
48 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

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.

All Mutations and Alleles

11
Chemically induced (other)

1
Endonuclease-mediated

3
Targeted

7
Genomic Mutations

1 involving Foxa1
Incidental Mutations

APF , CvDC
Find Mice (IMSR)

21 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygotes for targeted null mutations exhibit abnormal feeding, hypoglycemia, impaired glucagon secretion, hypotryglyceridemia, wasting, and lethality between postnatal days 2 and 14.

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All GO Annotations

79
GO References

23

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.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

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

1672
Tissues

602
cDNA Data

38
Literature Summary

122

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase foxa1

ZFIN foxa1

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All Sequences

45
RefSeq

12
UniProt

2
CCDS

CCDS25926.1

Ensembl

ENSMUSG00000035451 (Evidence)
NCBI Gene

15375

			Length	Strain/Species	Flank
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

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UniProt

2 Sequences
Protein Ontology

PR:000007602 hepatocyte nuclear factor 3-alpha

(term hierarchy)
InterPro Domains

IPR050211 Forkhead box domain-containing protein

IPR018533 Forkhead box protein, C-terminal

IPR001766 Fork head domain

IPR018122 Fork head domain conserved site1

IPR030456 Fork head domain conserved site 2

IPR013638 Fork-head N-terminal

IPR036390 Winged helix DNA-binding domain superfamily

IPR036388 Winged helix-like DNA-binding domain superfamily

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All nucleic 76

Genomic 5

cDNA 40

Primer pair 17

Other 14

Microarray probesets 3

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MGD-MRK-10804, MGD-MRK-14749, MGD-MRK-14755, MGD-MRK-16685, MGI:99890

Summaries

All 222

Developmental Gene Expression 122

Gene Ontology 23

Phenotypes 48
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:357386 Swisa A, et al., The evolutionarily ancient FOXA transcription factors shape the murine gut microbiome via control of epithelial glycosylation. Dev Cell. 2024 May 29;

TSS for Foxa1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr116433	Chr12:57593663-57593709 (-)	16 bp
Tssr116432	Chr12:57593567-57593579 (-)	129 bp
Tssr116431	Chr12:57593479-57593492 (-)	216 bp
Tssr116430	Chr12:57593251-57593290 (-)	431 bp
Tssr116429	Chr12:57592935-57592944 (-)	762 bp
Tssr116428	Chr12:57592913-57592927 (-)	782 bp
Tssr116427	Chr12:57592773-57592802 (-)	914 bp
Tssr116426	Chr12:57590895-57590912 (-)	2,798 bp
Tssr116425	Chr12:57590136-57590148 (-)	3,560 bp
Tssr116424	Chr12:57589126-57589136 (-)	4,571 bp
Tssr116423	Chr12:57589053-57589063 (-)	4,644 bp

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 Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 12/10/2024 MGI 6.24