Foxn1 forkhead box N1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Foxn1provided by MGI
Official Full Name: forkhead box N1provided by MGI
Primary source: MGI:MGI:102949
See related: Ensembl:ENSMUSG00000002057 AllianceGenome:MGI:102949
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: nu; Whn; nude; Fkh19; Hfh11; HFH-11; D11Bhm185e
Summary: The protein encoded by this gene is part of the forkhead family or "winged-helix" transcription factors that are important in developmental processes, immune system regulation, metabolism, cancer and aging. This gene family has over 100 members, subdivided into classes (A-Q) based on phylogeny. The encoded protein is proposed to regulate development of the thymus and differentiation of keratinocytes. Mutations in this gene cause severe primary T-cell immunodeficiency and congenital alopecia. In mouse mutations of this gene underlie the phenotype of the nude mouse, which has been widely used as a model system in oncology, immunology, dermatology, and transplantation studies. In humans mutations in this gene have been correlated with T-cell immunodeficiency, the skin disorder congenital alopecia, and nail dystrophy. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Apr 2013]
Expression: Biased expression in thymus adult (RPKM 7.5), stomach adult (RPKM 0.8) and 1 other tissue See more
Orthologs: human all
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Genomic context

Location:: 11 B5; 11 46.74 cM

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (78248403..78277597, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (78357577..78386783, complement)

Chromosome 11 - NC_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Administration of recombinant FOXN1 protein attenuates Alzheimer's pathology in mice.
Title: Administration of recombinant FOXN1 protein attenuates Alzheimer's pathology in mice.
Dermal white adipose tissue development and metabolism: The role of transcription factor Foxn1.
Title: Dermal white adipose tissue development and metabolism: The role of transcription factor Foxn1.
Foxn1 overexpression promotes thymic epithelial progenitor cell proliferation and mTEC maintenance, but does not prevent thymic involution.
Title: Foxn1 overexpression promotes thymic epithelial progenitor cell proliferation and mTEC maintenance, but does not prevent thymic involution.
Limits to in vivo fate changes of epithelia in thymus and parathyroid by ectopic expression of transcription factors Gcm2 and Foxn1.
Title: Limits to in vivo fate changes of epithelia in thymus and parathyroid by ectopic expression of transcription factors Gcm2 and Foxn1.
Protection against autoimmunity is driven by thymic epithelial cell-mediated regulation of Treg development.
Title: Protection against autoimmunity is driven by thymic epithelial cell-mediated regulation of T(reg) development.
Delayed maturation of thymic epithelium in mice with specific deletion of beta-catenin gene in FoxN1 positive cells.
Title: Delayed maturation of thymic epithelium in mice with specific deletion of β-catenin gene in FoxN1 positive cells.
P63 targeted deletion under the FOXN1 promoter disrupts pre-and post-natal thymus development, function and maintenance as well as induces severe hair loss.
Title: P63 targeted deletion under the FOXN1 promoter disrupts pre-and post-natal thymus development, function and maintenance as well as induces severe hair loss.
Dermal White Adipose Tissue (dWAT) Is Regulated by Foxn1 and Hif-1alpha during the Early Phase of Skin Wound Healing.
Title: Dermal White Adipose Tissue (dWAT) Is Regulated by Foxn1 and Hif-1α during the Early Phase of Skin Wound Healing.
High-Oxygen Submersion Fetal Thymus Organ Cultures Enable FOXN1-Dependent and -Independent Support of T Lymphopoiesis.
Title: High-Oxygen Submersion Fetal Thymus Organ Cultures Enable FOXN1-Dependent and -Independent Support of T Lymphopoiesis.
Impairment of the Hif-1alpha regulatory pathway in Foxn1-deficient (Foxn1(-/-) ) mice affects the skin wound healing process.
Title: Impairment of the Hif-1α regulatory pathway in Foxn1-deficient (Foxn1(-/-) ) mice affects the skin wound healing process.

Submit: New GeneRIF Correction See all GeneRIFs (67)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Spontaneous (7) 1 citation
Targeted (13) 1 citation
Chemically induced (ENU) (1) 1 citation
Endonuclease-mediated (10) 1 citation

General gene information

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Markers

Foxn1 (e-PCR), detects polymorphism
- UniSTS:531516

BB241108 (e-PCR)
- UniSTS:208713

fb76e10.y1 (e-PCR)
- UniSTS:191305

X81593 (e-PCR)
- UniSTS:125866

X81593 (e-PCR)
- UniSTS:163509

D11Seg19 (e-PCR), detects polymorphism
- UniSTS:141792

Foxn1 (e-PCR), detects polymorphism
- UniSTS:548065

D11Seg20 (e-PCR), detects polymorphism
- UniSTS:141794

D11Seg23 (e-PCR), detects polymorphism
- UniSTS:141797

Foxn1 (e-PCR), detects polymorphism
- UniSTS:143339

Foxn1 (e-PCR), detects polymorphism
- UniSTS:526078

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in T cell homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in T cell lineage commitment	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in blood vessel morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within epidermis development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within hair follicle development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within keratinocyte differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in keratinocyte differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lymphocyte homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in lymphoid lineage cell migration into thymus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within multicellular organism development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within nail development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of epithelial cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of hair follicle development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of T cell differentiation in thymus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of positive thymic T cell selection	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within thymus development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in thymus development	ISO Inferred from Sequence Orthology more info
involved_in thymus epithelium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: forkhead box protein N1

Names: HNF-3/forkhead homolog 11; hepatocyte nuclear factor 3 forkhead homolog 11; winged-helix transcription factor nude

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001277290.1 → NP_001264219.1 forkhead box protein N1 isoform 2

See identical proteins and their annotated locations for NP_001264219.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site in the 5' coding region compared to variant 1. It encodes isoform 2 which is shorter compared to isoform 1.

Source sequence(s)

AI429806, BC108980, BX521706, CJ056441, W97983

UniProtKB/TrEMBL

Q32MU3

Conserved Domains (1) summary

pfam00250
Location:269 → 356

Forkhead; Forkhead domain
NM_008238.2 → NP_032264.1 forkhead box protein N1 isoform 1

See identical proteins and their annotated locations for NP_032264.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AI429806, AL591131, BC108981, BX521706, W97983

Consensus CDS

CCDS25102.1

UniProtKB/Swiss-Prot

Q61575

UniProtKB/TrEMBL

Q5SYK1

Related

ENSMUSP00000103929.2, ENSMUST00000108294.2

Conserved Domains (1) summary

pfam00250
Location:270 → 357

Forkhead; Forkhead domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000077.7 Reference GRCm39 C57BL/6J

Range

78248403..78277597 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006532266.5 → XP_006532329.1 forkhead box protein N1 isoform X1

See identical proteins and their annotated locations for XP_006532329.1

UniProtKB/Swiss-Prot

Q61575

UniProtKB/TrEMBL

Q5SYK1

Conserved Domains (1) summary

pfam00250
Location:270 → 357

Forkhead; Forkhead domain
XM_017314289.3 → XP_017169778.1 forkhead box protein N1 isoform X1

UniProtKB/Swiss-Prot

Q61575

UniProtKB/TrEMBL

Q5SYK1

Conserved Domains (1) summary

pfam00250
Location:270 → 357

Forkhead; Forkhead domain
XM_017314288.1 → XP_017169777.1 forkhead box protein N1 isoform X1

UniProtKB/Swiss-Prot

Q61575

UniProtKB/TrEMBL

Q5SYK1

Conserved Domains (1) summary

pfam00250
Location:270 → 357

Forkhead; Forkhead domain
XM_017314290.1 → XP_017169779.1 forkhead box protein N1 isoform X1

UniProtKB/Swiss-Prot

Q61575

UniProtKB/TrEMBL

Q5SYK1

Conserved Domains (1) summary

pfam00250
Location:270 → 357

Forkhead; Forkhead domain
XM_006532267.2 → XP_006532330.1 forkhead box protein N1 isoform X2

See identical proteins and their annotated locations for XP_006532330.1

UniProtKB/TrEMBL

Q32MU3

Conserved Domains (1) summary

pfam00250
Location:269 → 356

Forkhead; Forkhead domain
XM_017314285.1 → XP_017169774.1 forkhead box protein N1 isoform X1

UniProtKB/Swiss-Prot

Q61575

UniProtKB/TrEMBL

Q5SYK1

Conserved Domains (1) summary

pfam00250
Location:270 → 357

Forkhead; Forkhead domain
XM_017314284.2 → XP_017169773.1 forkhead box protein N1 isoform X3

Conserved Domains (1) summary

pfam00250
Location:269 → 356

Forkhead; Forkhead domain
XM_017314283.2 → XP_017169772.1 forkhead box protein N1 isoform X2

UniProtKB/TrEMBL

Q32MU3

Conserved Domains (1) summary

pfam00250
Location:269 → 356

Forkhead; Forkhead domain
XM_006532264.3 → XP_006532327.2 forkhead box protein N1 isoform X1

See identical proteins and their annotated locations for XP_006532327.2

UniProtKB/Swiss-Prot

Q61575

UniProtKB/TrEMBL

Q5SYK1

Conserved Domains (1) summary

pfam00250
Location:270 → 357

Forkhead; Forkhead domain
XM_006532268.3 → XP_006532331.2 forkhead box protein N1 isoform X5

Conserved Domains (1) summary

pfam00250
Location:116 → 203

Forkhead; Forkhead domain
XM_006532265.4 → XP_006532328.1 forkhead box protein N1 isoform X4

Conserved Domains (1) summary

pfam00250
Location:326 → 413

Forkhead; Forkhead domain
XM_017314286.2 → XP_017169775.1 forkhead box protein N1 isoform X1

UniProtKB/Swiss-Prot

Q61575

UniProtKB/TrEMBL

Q5SYK1

Conserved Domains (1) summary

pfam00250
Location:270 → 357

Forkhead; Forkhead domain
XM_017314292.2 → XP_017169781.1 forkhead box protein N1 isoform X1

UniProtKB/Swiss-Prot

Q61575

UniProtKB/TrEMBL

Q5SYK1

Conserved Domains (1) summary

pfam00250
Location:270 → 357

Forkhead; Forkhead domain
XM_017314291.2 → XP_017169780.1 forkhead box protein N1 isoform X1

UniProtKB/Swiss-Prot

Q61575

UniProtKB/TrEMBL

Q5SYK1

Conserved Domains (1) summary

pfam00250
Location:270 → 357

Forkhead; Forkhead domain
XM_017314287.1 → XP_017169776.1 forkhead box protein N1 isoform X1

UniProtKB/Swiss-Prot

Q61575

UniProtKB/TrEMBL

Q5SYK1

Conserved Domains (1) summary

pfam00250
Location:270 → 357

Forkhead; Forkhead domain