Foxi3 MGI Mouse Gene Detail - MGI:3511278

Symbol

Foxi3
Name

forkhead box I3

Feature Type

protein coding gene
IDs

MGI:3511278
NCBI Gene: 232077
Alliance

genome feature page
Transcription Start Sites

1 TSS

Sequence Map

Chr6:70933590-70938050 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 6, 32.14 cM
Mapping Data

1 experiment

SNPs within 2kb

183 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_3511278	protein coding gene	Chr6:70933515-70938050 (+)
129S1/SvImJ	ENSMUSG00200011460	protein coding gene	Chr6:67836669-67841129 (+)
A/J	ENSMUSG00195041090	protein coding gene	Chr6:67598652-67603114 (+)
AKR/J	ENSMUSG00220039674	protein coding gene	Chr6:66545291-66549739 (+)
BALB/cJ	ENSMUSG00180033028	protein coding gene	Chr6:67953689-67958149 (+)
C3H/HeJ	ENSMUSG00175012015	protein coding gene	Chr6:109494820-109499278 (-)
C57BL/6NJ	ENSMUSG00215040051	protein coding gene	Chr6:67926338-67930800 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0028479	protein coding gene	Chr6:67851494-67855940 (+)
CAST/EiJ	ENSTCUG00005031594	protein coding gene	Chr6:68076199-68080670 (+)
CBA/J	ENSMUSG00210034276	protein coding gene	Chr6:67751509-67755969 (+)
DBA/2J	ENSMUSG00185040526	protein coding gene	Chr6:68311528-68315988 (+)
FVB/NJ	ENSMUSG00205031794	protein coding gene	Chr6:67049180-67053640 (+)
JF1/MsJ	ENSUMUG00000018427	protein coding gene	Chr6:67344334-67348781 (+)
LP/J	ENSMUSG00230021126	protein coding gene	Chr6:69431731-69436181 (+)
NOD/ShiLtJ	ENSMUSG00190030796	protein coding gene	Chr6:67284585-67289032 (+)
NZO/HlLtJ	ENSMUSG00225006714	protein coding gene	Chr6:71405618-71410078 (+)
PWK/PhJ	ENSLUMG00010019857	protein coding gene	Chr6:66715427-66719912 (+)
SPRET/EiJ	ENSMSPG00010024806	protein coding gene	Chr6:68628262-68632748 (+)
WSB/EiJ	ENSIUOG00005023076	protein coding gene	Chr6:68307157-68311613 (+)

Human Ortholog

FOXI3, forkhead box I3

Vertebrate Orthologs

5

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

FOXI3, forkhead box I3
Synonyms

CFM2
Links

HGNC:35123

NCBI Gene ID: 344167

UniProt: A8MTJ6
Chr Location

2p11.2; chr2:88446787-88452693 (-) GRCh38

MGI Vertebrate Homology

Foxi3 stringent orthology
1 human;1 mouse;1 rat;3 zebrafish
HCOP

vertebrate homology predictions: FOXI3
Gene Tree

Foxi3

Diseases

1 with Foxi3 mouse models

Human Disease

Mouse Models

Goldenhar syndrome

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

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Phenotype Summary

50 phenotypes from 5 alleles in 7 genetic backgrounds
4 phenotypes from multigenic genotypes
15 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

15
Endonuclease-mediated

11
Targeted

4
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

22 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous null mice start dying after E9.5. Those born die neonatally, lack a mouth and whiskers, and show branchial arch-derived skeletal defects, including a reduced mandible, total absence of inner, middle and external ear structures, and increased cranial neural crest cell apoptosis.

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All GO Annotations

19
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.

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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

778
Tissues

100
cDNA Data

4
Literature Summary

16

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA FOXI3

Xenbase foxi3, foxi3.2

ZFIN foxi3a, foxi3b

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All Sequences

31
RefSeq

2
UniProt

2
CCDS

CCDS51804.1

Ensembl

ENSMUSG00000055874 (Evidence)
NCBI Gene

232077

			Length	Strain/Species	Flank
genomic	232077	NCBI Gene Model \| MGI Sequence Detail	4461	C57BL/6J	± kb
transcript	NM_001101464	RefSeq \| MGI Sequence Detail	1206	mixed
polypeptide	D3Z120	UniProt \| EBI \| MGI Sequence Detail	399	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000007627 forkhead box protein I3

(term hierarchy)
InterPro Domains

IPR050211 Forkhead box domain-containing protein

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

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All nucleic 8

Genomic 1

cDNA 4

Primer pair 2

Other 1

Antibodies 1

Microarray probesets 1

Summaries

All 43

Developmental Gene Expression 16

Diseases 1

Gene Ontology 13

Phenotypes 15
Earliest

J:93815 Ohyama T, et al., Expression of mouse Foxi class genes in early craniofacial development. Dev Dyn. 2004 Nov;231(3):640-6
Latest

J:378035 Mohtadi Hamadani Y, et al., Stem cell specification and niche formation in developing incisor requires actomyosin forces. Stem Cells. 2025 Nov 26;

TSS for Foxi3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr56981	Chr6:70933440-70933444 (+)	-148 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 09/01/2026 MGI 6.24