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

Gene ID: 15218, updated on 8-Feb-2024

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
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Genomic context

See Foxn1 in Genome Data Viewer
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_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E906 Neighboring gene phosphatidylinositol glycan anchor biosynthesis, class S Neighboring gene unc-119 lipid binding chaperone Neighboring gene STARR-positive B cell enhancer mm9_chr11:78173491-78173792 Neighboring gene predicted gene, 30367 Neighboring gene solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2, opposite strand Neighboring gene solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 2 Neighboring gene solute carrier family 46, member 1 Neighboring gene sterile alpha and HEAT/Armadillo motif containing 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

General gene information

Markers

Clone Names

  • MGC124316, MGC124317

Gene Ontology Provided by MGI

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

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)

  1. NM_001277290.1NP_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:269356
    Forkhead; Forkhead domain
  2. NM_008238.2NP_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:270357
    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

  1. NC_000077.7 Reference GRCm39 C57BL/6J

    Range
    78248403..78277597 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006532266.5XP_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:270357
    Forkhead; Forkhead domain
  2. XM_017314289.3XP_017169778.1  forkhead box protein N1 isoform X1

    UniProtKB/Swiss-Prot
    Q61575
    UniProtKB/TrEMBL
    Q5SYK1
    Conserved Domains (1) summary
    pfam00250
    Location:270357
    Forkhead; Forkhead domain
  3. XM_017314288.1XP_017169777.1  forkhead box protein N1 isoform X1

    UniProtKB/Swiss-Prot
    Q61575
    UniProtKB/TrEMBL
    Q5SYK1
    Conserved Domains (1) summary
    pfam00250
    Location:270357
    Forkhead; Forkhead domain
  4. XM_017314290.1XP_017169779.1  forkhead box protein N1 isoform X1

    UniProtKB/Swiss-Prot
    Q61575
    UniProtKB/TrEMBL
    Q5SYK1
    Conserved Domains (1) summary
    pfam00250
    Location:270357
    Forkhead; Forkhead domain
  5. XM_006532267.2XP_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:269356
    Forkhead; Forkhead domain
  6. XM_017314285.1XP_017169774.1  forkhead box protein N1 isoform X1

    UniProtKB/Swiss-Prot
    Q61575
    UniProtKB/TrEMBL
    Q5SYK1
    Conserved Domains (1) summary
    pfam00250
    Location:270357
    Forkhead; Forkhead domain
  7. XM_017314284.2XP_017169773.1  forkhead box protein N1 isoform X3

    Conserved Domains (1) summary
    pfam00250
    Location:269356
    Forkhead; Forkhead domain
  8. XM_017314283.2XP_017169772.1  forkhead box protein N1 isoform X2

    UniProtKB/TrEMBL
    Q32MU3
    Conserved Domains (1) summary
    pfam00250
    Location:269356
    Forkhead; Forkhead domain
  9. XM_006532264.3XP_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:270357
    Forkhead; Forkhead domain
  10. XM_006532268.3XP_006532331.2  forkhead box protein N1 isoform X5

    Conserved Domains (1) summary
    pfam00250
    Location:116203
    Forkhead; Forkhead domain
  11. XM_006532265.4XP_006532328.1  forkhead box protein N1 isoform X4

    Conserved Domains (1) summary
    pfam00250
    Location:326413
    Forkhead; Forkhead domain
  12. XM_017314286.2XP_017169775.1  forkhead box protein N1 isoform X1

    UniProtKB/Swiss-Prot
    Q61575
    UniProtKB/TrEMBL
    Q5SYK1
    Conserved Domains (1) summary
    pfam00250
    Location:270357
    Forkhead; Forkhead domain
  13. XM_017314292.2XP_017169781.1  forkhead box protein N1 isoform X1

    UniProtKB/Swiss-Prot
    Q61575
    UniProtKB/TrEMBL
    Q5SYK1
    Conserved Domains (1) summary
    pfam00250
    Location:270357
    Forkhead; Forkhead domain
  14. XM_017314291.2XP_017169780.1  forkhead box protein N1 isoform X1

    UniProtKB/Swiss-Prot
    Q61575
    UniProtKB/TrEMBL
    Q5SYK1
    Conserved Domains (1) summary
    pfam00250
    Location:270357
    Forkhead; Forkhead domain
  15. XM_017314287.1XP_017169776.1  forkhead box protein N1 isoform X1

    UniProtKB/Swiss-Prot
    Q61575
    UniProtKB/TrEMBL
    Q5SYK1
    Conserved Domains (1) summary
    pfam00250
    Location:270357
    Forkhead; Forkhead domain