Foxd3 MGI Mouse Gene Detail - MGI:1347473

Symbol

Foxd3
Name

forkhead box D3
Synonyms

CWH3, Genesis, Hfh2

Feature Type

protein coding gene
IDs

MGI:1347473
NCBI Gene: 15221
Alliance

genome feature page
Transcription Start Sites

5 TSS

Sequence Map

Chr4:99544536-99546859 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 4, 45.71 cM
Mapping Data

3 experiments

SNPs within 2kb

104 from dbSNP Build 142
Strain Annotations

19
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1347473	protein coding gene	Chr4:99544536-99546908 (+)
129S1/SvImJ	ENSMUSG00200026578	protein coding gene	Chr4:94527576-94529890 (+)
A/J	ENSMUSG00195007846	protein coding gene	Chr4:95066551-95068875 (+)
AKR/J	ENSMUSG00220006271	protein coding gene	Chr4:94531207-94533530 (+)
BALB/cJ	ENSMUSG00180031282	protein coding gene	Chr4:94011888-94014211 (+)
C3H/HeJ	ENSMUSG00175014958	protein coding gene	Chr4:94974082-94976405 (+)
C57BL/6NJ	ENSMUSG00215012617	protein coding gene	Chr4:94918354-94920678 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0026193	protein coding gene	Chr4:91809314-91811629 (+)
CAST/EiJ	ENSTCUG00005006883	protein coding gene	Chr4:94225604-94227927 (+)
CBA/J	ENSMUSG00210028069	protein coding gene	Chr4:94539593-94541916 (+)
DBA/2J	ENSMUSG00185021521	protein coding gene	Chr4:95314837-95317161 (+)
FVB/NJ	ENSMUSG00205011037	protein coding gene	Chr4:93526796-93529119 (+)
JF1/MsJ	ENSUMUG00000040120	protein coding gene	Chr4:95427088-95429410 (+)
LP/J	ENSMUSG00230017520	protein coding gene	Chr4:98637034-98639347 (+)
NOD/ShiLtJ	ENSMUSG00190023241	protein coding gene	Chr4:94000359-94002672 (+)
NZO/HlLtJ	ENSMUSG00225032511	protein coding gene	Chr4:103765306-103767631 (+)
PWK/PhJ	ENSLUMG00010017289	protein coding gene	Chr4:93129167-93131487 (+)
SPRET/EiJ	ENSMSPG00010007970	protein coding gene	Chr4:95360755-95363071 (+)
WSB/EiJ	ENSIUOG00005003059	protein coding gene	Chr4:94314771-94317094 (+)

Human Ortholog

FOXD3, forkhead box D3

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

FOXD3, forkhead box D3
Synonyms

AIS1, Genesis, HFH2, VAMAS2
Links

HGNC:3804

NCBI Gene ID: 27022

UniProt: Q9UJU5
Chr Location

1p31.3; chr1:63322567-63325128 (+) GRCh38

MGI Vertebrate Homology

Foxd3 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: FOXD3
Gene Tree

Foxd3

Diseases

1 with human FOXD3 associations

				Human Disease	Mouse Models
				vitiligo IDs vitiligo DOID:12306 EFO:0004208 ICD10CM:L80 ICD9CM:709.01 MESH:D014820 NCI:C26915 OMIM:193200 UMLS_CUI:C0042900

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

less

Phenotype Summary

43 phenotypes from 4 alleles in 4 genetic backgrounds
27 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

12
Chemically induced (other)

2
Endonuclease-mediated

2
Gene trapped

1
Radiation induced

1
Targeted

6
Genomic Mutations

4 involving Foxd3
Incidental Mutations

CvDC
Find Mice (IMSR)

12 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for null alleles dsiplay embryonic lethality with failure of primitive streak formation and gastrulation and failure to derive cultures of embryonic or trophoblast stem cells.

less

All GO Annotations

30
GO References

13

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.

less

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

1029
Tissues

290
cDNA Data

14
Literature Summary

80

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase foxd3

ZFIN foxd3

less

All Sequences

31
RefSeq

2
UniProt

2
CCDS

CCDS18383.1

Ensembl

ENSMUSG00000067261 (Evidence)
NCBI Gene

15221

			Length	Strain/Species	Flank
genomic	ENSMUSG00000067261	Ensembl Gene Model \| MGI Sequence Detail	2324	C57BL/6J	± kb
transcript	ENSMUST00000087285	Ensembl \| MGI Sequence Detail	2324	Not Applicable
polypeptide	ENSMUSP00000084541	Ensembl \| MGI Sequence Detail	469	Not Applicable

less

UniProt

2 Sequences
Protein Ontology

PR:000007611 forkhead box protein D3

(term hierarchy)
InterPro Domains

IPR050211 Forkhead box domain-containing protein

IPR047392 Forkhead box protein D3, forkhead domain

IPR001766 Fork head domain

IPR018122 Fork head domain conserved site1

IPR030456 Fork head domain conserved site 2

IPR036390 Winged helix DNA-binding domain superfamily

IPR036388 Winged helix-like DNA-binding domain superfamily
GlyGen

Q61060 1 site, 1 O-linked glycan (1 site)

less

All nucleic 22

cDNA 15

Primer pair 4

Other 3

Antibodies 6

Microarray probesets 3

less

MGD-MRK-16699, MGI:99903

Summaries

All 139

Developmental Gene Expression 80

Gene Ontology 13

Phenotypes 27
Earliest

J:20863 Clevidence DE, et al., Identification of nine tissue-specific transcription factors of the hepatocyte nuclear factor 3/forkhead DNA-binding-domain family. Proc Natl Acad Sci U S A. 1993 May 1;90(9):3948-52
Latest

J:381084 Moore Zajic EL, et al., NR6A1 is essential for neural crest cell specification, formation and survival. Nat Commun. 2026 Jan 29;17(1)

TSS for Foxd3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr37936	Chr4:99544366-99544391 (+)	-157 bp
Tssr37937	Chr4:99544401-99544413 (+)	-129 bp
Tssr37938	Chr4:99544565-99544577 (+)	35 bp
Tssr37939	Chr4:99544592-99544619 (+)	70 bp
Tssr37940	Chr4:99544899-99544909 (+)	368 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 09/15/2026 MGI 6.29