Foxn3 MGI Mouse Gene Detail - MGI:1918625

Symbol

Foxn3
Name

forkhead box N3
Synonyms

5430426H20Rik, Ches1, Ches1l, HTLFL1

Feature Type

protein coding gene
IDs

MGI:1918625
NCBI Gene: 71375
Alliance

genome feature page
Transcription Start Sites

14 TSS

Sequence Map

Chr12:99156337-99529841 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 12, 49.93 cM, cytoband F1
Mapping Data

3 experiments

SNPs within 2kb

10457 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1918625	protein coding gene	Chr12:99156337-99529926 (-)
129S1/SvImJ	ENSMUSG00200017470	protein coding gene	Chr12:90926601-91125673 (-)
A/J	ENSMUSG00195020711	protein coding gene	Chr12:93491230-93690108 (-)
AKR/J	ENSMUSG00220017579	protein coding gene	Chr12:91383208-91582090 (-)
BALB/cJ	ENSMUSG00180031128	protein coding gene	Chr12:92642078-92840960 (-)
C3H/HeJ	ENSMUSG00175031280	protein coding gene	Chr12:95304975-95503825 (-)
C57BL/6NJ	ENSMUSG00215037605	protein coding gene	Chr12:91953376-92152246 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0018015	protein coding gene	Chr12:93803360-94059274 (-)
CAST/EiJ	ENSTCUG00005005849	protein coding gene	Chr12:91589745-91787436 (-)
CBA/J	ENSMUSG00210014457	protein coding gene	Chr12:92301153-92499988 (-)
DBA/2J	ENSMUSG00185045399	protein coding gene	Chr12:94083243-94282095 (-)
FVB/NJ	ENSMUSG00205017402	protein coding gene	Chr12:91454260-91653374 (-)
JF1/MsJ	ENSUMUG00000017555	protein coding gene	Chr12:98803102-98997891 (-)
LP/J	ENSMUSG00230004353	protein coding gene	Chr12:101191765-101390831 (-)
NOD/ShiLtJ	ENSMUSG00190004980	protein coding gene	Chr12:93647130-93845989 (+)
NZO/HlLtJ	ENSMUSG00225033079	protein coding gene	Chr12:102901849-103100754 (-)
PWK/PhJ	ENSLUMG00010011617	protein coding gene	Chr12:92297545-92495551 (-)
SPRET/EiJ	no annotation
WSB/EiJ	ENSIUOG00005002078	protein coding gene	Chr12:91278636-91477805 (-)

Human Ortholog

FOXN3, forkhead box N3

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

FOXN3, forkhead box N3
Synonyms

C14orf116, CHES1, PRO1635
Links

HGNC:1928

NCBI Gene ID: 1112

UniProt: O00409
Chr Location

14q31.3-q32.11; chr14:89124871-89619271 (-) GRCh38

MGI Vertebrate Homology

Foxn3 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: FOXN3
Gene Tree

Foxn3

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Phenotype Summary

27 phenotypes from 2 alleles in 2 genetic backgrounds
19 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

62
Chemically induced (other)

1
Endonuclease-mediated

7
Gene trapped

52
Transposon induced

2
Genomic Mutations

1 involving Foxn3
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

32 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Hypomorphic homozygous knockout affects the expression of osteogenic genes and leads to craniofacial abnormalities and reduces pre- and postnatal survival.

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All GO Annotations

13
GO References

6

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

786
Tissues

168
cDNA Data

17
Literature Summary

9

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase foxn3

ZFIN foxn3

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All Sequences

97
RefSeq

34
UniProt

5
CCDS

CCDS26103.1

Ensembl

ENSMUSG00000033713 (Evidence)
NCBI Gene

71375

			Length	Strain/Species	Flank
genomic	ENSMUSG00000033713	Ensembl Gene Model \| MGI Sequence Detail	373505	C57BL/6J	± kb
transcript	ENSMUST00000046859	Ensembl \| MGI Sequence Detail	7705	Not Applicable
polypeptide	ENSMUSP00000036035	Ensembl \| MGI Sequence Detail	457	Not Applicable

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UniProt

5 Sequences
Protein Ontology

PR:000007638 forkhead box protein N3

(term hierarchy)
InterPro Domains

IPR047119 Forkhead box protein N2/3-like

IPR047404 Forkhead box protein N3, 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

Q499D0 2 sites

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All nucleic 18

cDNA 17

Primer pair 1

Microarray probesets 8

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MGI:1276572, MGI:2144745, MGI:2145044

Summaries

All 62

Developmental Gene Expression 9

Gene Ontology 6

Phenotypes 19
Earliest

J:43593 Schorpp M, et al., Characterization of mouse and human nude genes. Immunogenetics. 1997;46(6):509-15
Latest

J:388958 Yu J, et al., Modulation of Lung Adenocarcinoma by Phosphorylated FOXN3-Mediated Transcriptional Inactivation of p53. Adv Sci (Weinh). 2026 Jul 7;:e76449

TSS for Foxn3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr117304	Chr12:99530215-99530218 (-)	-376 bp
Tssr117303	Chr12:99530178-99530194 (-)	-345 bp
Tssr117302	Chr12:99530162-99530176 (-)	-328 bp
Tssr117301	Chr12:99529977-99529988 (-)	-142 bp
Tssr117300	Chr12:99529821-99529910 (-)	-25 bp
Tssr117299	Chr12:99424154-99424177 (-)	105,675 bp
Tssr117298	Chr12:99411813-99411817 (-)	118,026 bp
Tssr117297	Chr12:99400673-99400679 (-)	129,165 bp
Tssr117296	Chr12:99386767-99386771 (-)	143,072 bp
Tssr117295	Chr12:99378855-99378870 (-)	150,978 bp
Tssr117294	Chr12:99359269-99359349 (-)	170,532 bp
Tssr117293	Chr12:99359172-99359255 (-)	170,627 bp
Tssr117290	Chr12:99342386-99342391 (-)	187,452 bp
Tssr117289	Chr12:99160975-99160979 (-)	368,864 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 09/08/2026 MGI 6.24