Foxa2 MGI Mouse Gene Detail - MGI:1347476

Symbol

Foxa2
Name

forkhead box A2
Synonyms

Hnf-3b, Hnf3b, HNF3-beta, HNF3beta, Tcf-3b, Tcf3b

Feature Type

protein coding gene
IDs

MGI:1347476
NCBI Gene: 15376
Alliance

gene page
Transcription Start Sites

5 TSS
Regulated by

Rr210, Rr213, Rr212 ... (6 regulatory regions)

Sequence Map

Chr2:147884797-147888889 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 73.38 cM
Mapping Data

6 experiments

SNPs within 2kb

159 from dbSNP Build 142
Strain Annotations

18
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1347476	protein coding gene	Chr2:147884797-147888889 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0026605	protein coding gene	Chr2:152358345-152362437 (-)
A/J	MGP_AJ_G0026569	protein coding gene	Chr2:146166634-146170727 (-)
AKR/J	MGP_AKRJ_G0026543	protein coding gene	Chr2:150400211-150404303 (-)
BALB/cJ	MGP_BALBcJ_G0026581	protein coding gene	Chr2:146591503-146595596 (-)
C3H/HeJ	MGP_C3HHeJ_G0026324	protein coding gene	Chr2:150888610-150892703 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0027026	protein coding gene	Chr2:156809520-156813612 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0024404	protein coding gene	Chr2:140187959-140192069 (-)
CAST/EiJ	MGP_CASTEiJ_G0025785	protein coding gene	Chr2:151256698-151260787 (-)
CBA/J	MGP_CBAJ_G0026304	protein coding gene	Chr2:162559230-162563323 (-)
DBA/2J	MGP_DBA2J_G0026438	protein coding gene	Chr2:145427795-145431885 (-)
FVB/NJ	MGP_FVBNJ_G0026402	protein coding gene	Chr2:143935221-143939309 (-)
LP/J	MGP_LPJ_G0026542	protein coding gene	Chr2:152487697-152491789 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0026422	protein coding gene	Chr2:166621263-166625452 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0027081	protein coding gene	Chr2:150386235-150390325 (-)
PWK/PhJ	MGP_PWKPhJ_G0025521	protein coding gene	Chr2:145119098-145123188 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0025322	protein coding gene	Chr2:149370819-149374900 (-)
WSB/EiJ	MGP_WSBEiJ_G0025859	protein coding gene	Chr2:151335438-151339525 (-)

Human Ortholog

FOXA2, forkhead box A2

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

FOXA2, forkhead box A2
Synonyms

HNF3B, HNF-3-beta, TCF3B
Links

HGNC:5022

NCBI Gene ID: 3170

neXtProt AC: NX_Q9Y261

UniProt: Q9Y261
Chr Location

20p11.21; chr20:22580998-22585490 (-) GRCh38

MGI Vertebrate Homology

Foxa2 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: FOXA2
Gene Tree

Foxa2

Diseases

1 with human FOXA2 associations

				Human Disease	Mouse Models
				type 2 diabetes mellitus IDs type 2 diabetes mellitus DOID:9352 ICD10CM:E11 KEGG:04930 MESH:D003924 NCI:C26747 OMIM:125853 OMIM:601283 OMIM:601407 OMIM:603694 OMIM:608036 UMLS_CUI:C0011860

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

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Phenotype Summary

115 phenotypes from 9 alleles in 16 genetic backgrounds
55 phenotypes from multigenic genotypes
162 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

24
Chemically induced (other)

1
Endonuclease-mediated

4
Radiation induced

1
Targeted

16
Transgenic

2
Genomic Mutations

2 involving Foxa2
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

28 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Embryos homozygous for targeted null mutations fail to form a distinct node, lack a notochord, and die by embryonic day 10 or 11. Mutants also exhibit defects of somite and neural tube organization, and lack a floor plate and motor neurons.

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All GO Annotations

120
GO References

42

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

3047
Tissues

762
cDNA Data

41
Literature Summary

757

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase foxa2

ZFIN foxa2

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All Sequences

48
RefSeq

6
UniProt

3
CCDS

CCDS16836.1, CCDS71157.1

Ensembl

ENSMUSG00000037025 (Evidence)
NCBI Gene

15376

			Length	Strain/Species	Flank
genomic	15376	NCBI Gene Model \| MGI Sequence Detail	4093	C57BL/6J	± kb
transcript	NM_001291067	RefSeq \| MGI Sequence Detail	2138	ZRU/MplStud
polypeptide	P35583	UniProt \| EBI \| MGI Sequence Detail	459	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000007603 hepatocyte nuclear factor 3-beta

(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 156

Genomic 9

cDNA 51

Primer pair 30

Other 66

Microarray probesets 3

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MGD-MRK-10805, MGD-MRK-14750, MGD-MRK-14756, MGD-MRK-16684, MGI:99889

Summaries

All 968

Developmental Gene Expression 757

Gene Ontology 42

Phenotypes 162
Earliest

J:109968 Roderick TH, et al., Nineteen paracentric chromosomal inversions in mice. Genetics. 1974 Jan;76(1):109-17
Latest

J:364278 Brooks ER, et al., A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate. Elife. 2025 Apr 7;13

Foxa2 expression regulated by:

Feature	Feature Type	Location	Reference
Rr210, regulatory region 210	enhancer	Chr2:147707569-147709551	J:316612
Rr213, regulatory region 213	enhancer	Chr2:147718180-147719287	J:316612
Rr212, regulatory region 212	enhancer	Chr2:147727915-147728589	J:316612
Rr211, regulatory region 211	enhancer	Chr2:147878714-147879140	J:176642
Rr241, regulatory region 241	enhancer	Chr2:147902314-147902834	J:176642
Rr595, regulatory region 595	enhancer	Chr2, Syntenic	J:358609

TSS for Foxa2:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr26644	Chr2:147888974-147889005 (-)	-101 bp
Tssr26643	Chr2:147888904-147888911 (-)	-19 bp
Tssr26642	Chr2:147888258-147888263 (-)	628 bp
Tssr26641	Chr2:147888132-147888161 (-)	742 bp
Tssr26640	Chr2:147887811-147887825 (-)	1,071 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 03/25/2025 MGI 6.24