Foxn4 MGI Mouse Gene Detail - MGI:2151057

Symbol

Foxn4
Name

forkhead box N4

Feature Type

protein coding gene
IDs

MGI:2151057
NCBI Gene: 116810
Alliance

genome feature page
Transcription Start Sites

6 TSS

Sequence Map

Chr5:114392225-114411868 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 5, 55.99 cM
Mapping Data

1 experiment

SNPs within 2kb

674 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2151057	protein coding gene	Chr5:114392225-114412486 (-)
129S1/SvImJ	ENSMUSG00200020627	protein coding gene	Chr5:108132996-108152663 (-)
A/J	ENSMUSG00195035413	protein coding gene	Chr5:107645925-107665594 (-)
AKR/J	ENSMUSG00220042431	protein coding gene	Chr5:107162253-107181920 (-)
BALB/cJ	ENSMUSG00180043707	protein coding gene	Chr5:107783564-107803232 (-)
C3H/HeJ	ENSMUSG00175042216	protein coding gene	Chr5:109771272-109790943 (-)
C57BL/6NJ	ENSMUSG00215031528	protein coding gene	Chr5:107792304-107811947 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0027592	protein coding gene	Chr5:107212689-107232948 (-)
CAST/EiJ	ENSTCUG00005031509	protein coding gene	Chr5:106971094-106990757 (-)
CBA/J	ENSMUSG00210034324	protein coding gene	Chr5:108523377-108543047 (-)
DBA/2J	ENSMUSG00185053379	protein coding gene	Chr5:111568946-111588620 (-)
FVB/NJ	ENSMUSG00205050909	protein coding gene	Chr5:107421048-107440720 (-)
JF1/MsJ	ENSUMUG00000051176	protein coding gene	Chr5:114412978-114433162 (-)
LP/J	ENSMUSG00230042909	protein coding gene	Chr5:115671155-115690817 (-)
NOD/ShiLtJ	ENSMUSG00190047781	protein coding gene	Chr5:107460361-107480001 (-)
NZO/HlLtJ	ENSMUSG00225014275	protein coding gene	Chr5:123318416-123338085 (-)
PWK/PhJ	ENSLUMG00010035714	protein coding gene	Chr5:106316938-106337132 (-)
SPRET/EiJ	ENSMSPG00010040456	protein coding gene	Chr5:109599287-109618902 (-)
WSB/EiJ	ENSIUOG00005041875	protein coding gene	Chr5:110163646-110183322 (-)

Human Ortholog

FOXN4, forkhead box N4

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

FOXN4, forkhead box N4
Links

HGNC:21399

NCBI Gene ID: 121643

UniProt: Q96NZ1
Chr Location

12q24.11; chr12:109277978-109309284 (-) GRCh38

MGI Vertebrate Homology

Foxn4 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: FOXN4
Gene Tree

Foxn4

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Phenotype Summary

18 phenotypes from 2 alleles in 2 genetic backgrounds
26 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

9
Chemically induced (other)

1
Endonuclease-mediated

2
Radiation induced

1
Targeted

5
Genomic Mutations

2 involving Foxn4
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

32 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous null mice display postnatal lethality and abnormal retina morphology with a total loss of horizontal cells and decreased amacrine cell number.

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All GO Annotations

25
GO References

12

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

906
Tissues

238
cDNA Data

13
Literature Summary

46

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase foxn4

ZFIN foxn4

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All Sequences

48
RefSeq

8
UniProt

4
CCDS

CCDS19562.1

Ensembl

ENSMUSG00000042002 (Evidence)
NCBI Gene

116810

			Length	Strain/Species	Flank
genomic	ENSMUSG00000042002	Ensembl Gene Model \| MGI Sequence Detail	19644	C57BL/6J	± kb
transcript	ENSMUST00000044790	Ensembl \| MGI Sequence Detail	3016	Not Applicable
polypeptide	ENSMUSP00000047951	Ensembl \| MGI Sequence Detail	521	Not Applicable

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UniProt

4 Sequences
Protein Ontology

PR:000007639 forkhead box protein N4

(term hierarchy)
InterPro Domains

IPR049624 Forkhead box protein N1/4

IPR001766 Fork head domain

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 18

Genomic 1

cDNA 14

Primer pair 2

Other 1

Antibodies 1

Microarray probesets 3

Summaries

All 85

Developmental Gene Expression 46

Gene Ontology 12

Phenotypes 26
Earliest

J:134667 Roderick TH, et al., Two radiation-induced chromosomal inversions in mice (Mus musculus). Proc Natl Acad Sci U S A. 1970 Oct;67(2):961-7
Latest

J:354849 Wutikeli H, et al., Role of Elavl-like RNA-binding protein in retinal development and signal transduction. Biochim Biophys Acta Mol Basis Dis. 2024 Sep 20;1871(1):167518

TSS for Foxn4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr52701	Chr5:114412306-114412330 (-)	-450 bp
Tssr52700	Chr5:114412094-114412142 (-)	-250 bp
Tssr52699	Chr5:114411894-114411899 (-)	-29 bp
Tssr1601	Chr5:114411851-114411863 (-)	11 bp
Tssr52698	Chr5:114411833-114411847 (-)	28 bp
Tssr52697	Chr5:114409223-114409225 (-)	2,644 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 09/01/2026 MGI 6.24