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Aliases for FOXN3 Gene

Aliases for FOXN3 Gene

  • Forkhead Box N3 2 3 5
  • Checkpoint Suppressor 1 2 3 4
  • C14orf116 3 4
  • CHES1 3 4
  • Chromosome 14 Open Reading Frame 116 2
  • Forkhead Box Protein N3 3
  • PRO1635 3

External Ids for FOXN3 Gene

Previous HGNC Symbols for FOXN3 Gene

  • C14orf116
  • CHES1

Previous GeneCards Identifiers for FOXN3 Gene

  • GC14M088692
  • GC14M089622
  • GC14M069797
  • GC14M089706
  • GC14M089882
  • GC14M090293
  • GC14M089149
  • GC14M089255
  • GC14M089315
  • GC14M090487
  • GC14M090815
  • GC14M091090

Summaries for FOXN3 Gene

Entrez Gene Summary for FOXN3 Gene

  • This gene is a member of the forkhead/winged helix transcription factor family. Checkpoints are eukaryotic DNA damage-inducible cell cycle arrests at G1 and G2. Checkpoint suppressor 1 suppresses multiple yeast checkpoint mutations including mec1, rad9, rad53 and dun1 by activating a MEC1-independent checkpoint pathway. Alternative splicing is observed at the locus, resulting in distinct isoforms. [provided by RefSeq, Jul 2008]

GeneCards Summary for FOXN3 Gene

FOXN3 (Forkhead Box N3) is a Protein Coding gene. Diseases associated with FOXN3 include Auditory Neuropathy. Among its related pathways are Mesodermal Commitment Pathway. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and protein C-terminus binding. An important paralog of this gene is FOXN2.

UniProtKB/Swiss-Prot for FOXN3 Gene

  • Acts as a transcriptional repressor. May be involved in DNA damage-inducible cell cycle arrests (checkpoints).

Gene Wiki entry for FOXN3 Gene

Additional gene information for FOXN3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for FOXN3 Gene

Genomics for FOXN3 Gene

Regulatory Elements for FOXN3 Gene

Enhancers for FOXN3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH14H089613 1.9 FANTOM5 Ensembl ENCODE dbSUPER 17.3 +1.6 1554 8.8 PKNOX1 ARNT SIN3A ARID4B YY1 GLIS2 ZNF143 ATF7 RUNX3 JUNB FOXN3 ENSG00000252655 TDP1 GC14P089586
GH14H089458 1.7 FANTOM5 Ensembl ENCODE dbSUPER 17.5 +160.0 159982 2.3 SOX13 FOXA2 SAP130 MAX DMAP1 ZNF384 CEBPG KMT2B RAD21 ZNF7 FOXN3 RN7SKP107 GC14P089486 FOXN3-AS1
GH14H089425 1.9 FANTOM5 Ensembl ENCODE dbSUPER 15.2 +190.2 190163 7.5 PKNOX1 ZNF133 FEZF1 YY1 FOS ATF7 RUNX3 JUNB TSHZ1 GLIS1 FOXN3 RN7SKP107 ENSG00000252655 FOXN3-AS1 GC14P089486
GH14H089718 1.3 FANTOM5 Ensembl ENCODE 20.7 -101.9 -101863 4.4 CTCF RFX1 MAX ATF2 GABPA POLR2A CTBP2 CREB1 ETV6 ATF7 FOXN3 ENSG00000252655 RN7SKP107 TDP1 RN7SKP255 CHORDC2P
GH14H089388 1.4 Ensembl ENCODE dbSUPER 18 +228.6 228554 4.4 ELF3 FOXA2 MLX ARID4B DMAP1 RAD21 RARA SLC30A9 FOS CREM FOXN3 RNU4-22P LOC105370614 ENSG00000258380 ENSG00000258699
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around FOXN3 on UCSC Golden Path with GeneCards custom track

Promoters for FOXN3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000071874 550 2401 ELF3 PKNOX1 TBL1XR1 RB1 ARNT SIN3A ARID4B RAD21 YY1 GLIS2

Genomic Locations for FOXN3 Gene

Genomic Locations for FOXN3 Gene
494,280 bases
Minus strand

Genomic View for FOXN3 Gene

Genes around FOXN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
FOXN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for FOXN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for FOXN3 Gene

Proteins for FOXN3 Gene

  • Protein details for FOXN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Forkhead box protein N3
    Protein Accession:
    Secondary Accessions:
    • Q96II7
    • Q9UIE7

    Protein attributes for FOXN3 Gene

    490 amino acids
    Molecular mass:
    53835 Da
    Quaternary structure:
    • Interacts through its C-terminus with the C-terminus of SNW1/SKIP.

    Alternative splice isoforms for FOXN3 Gene


neXtProt entry for FOXN3 Gene

Post-translational modifications for FOXN3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for FOXN3 Gene

Domains & Families for FOXN3 Gene

Gene Families for FOXN3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for FOXN3 Gene

Suggested Antigen Peptide Sequences for FOXN3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with FOXN3: view

No data available for UniProtKB/Swiss-Prot for FOXN3 Gene

Function for FOXN3 Gene

Molecular function for FOXN3 Gene

UniProtKB/Swiss-Prot Function:
Acts as a transcriptional repressor. May be involved in DNA damage-inducible cell cycle arrests (checkpoints).

Phenotypes From GWAS Catalog for FOXN3 Gene

Gene Ontology (GO) - Molecular Function for FOXN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003700 transcription factor activity, sequence-specific DNA binding IBA --
GO:0005515 protein binding IPI 16102918
GO:0008022 protein C-terminus binding IPI 16951149
GO:0043565 sequence-specific DNA binding IBA --
genes like me logo Genes that share ontologies with FOXN3: view

Phenotypes for FOXN3 Gene

genes like me logo Genes that share phenotypes with FOXN3: view

Animal Model Products

miRNA for FOXN3 Gene

Clone Products

  • Addgene plasmids for FOXN3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for FOXN3 Gene

Localization for FOXN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for FOXN3 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for FOXN3 gene
Compartment Confidence
nucleus 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytokinetic bridge (2)
  • Nucleus (2)
  • Plasma membrane (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for FOXN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IC,IBA 16102918
genes like me logo Genes that share ontologies with FOXN3: view

Pathways & Interactions for FOXN3 Gene

SuperPathways for FOXN3 Gene

SuperPathway Contained pathways
1 Mesodermal Commitment Pathway
genes like me logo Genes that share pathways with FOXN3: view

Pathways by source for FOXN3 Gene

1 BioSystems pathway for FOXN3 Gene

Gene Ontology (GO) - Biological Process for FOXN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007049 cell cycle IEA --
GO:0007095 mitotic G2 DNA damage checkpoint IGI 9154802
GO:0030154 cell differentiation IBA --
genes like me logo Genes that share ontologies with FOXN3: view

No data available for SIGNOR curated interactions for FOXN3 Gene

Drugs & Compounds for FOXN3 Gene

No Compound Related Data Available

Transcripts for FOXN3 Gene

Unigene Clusters for FOXN3 Gene

Forkhead box N3:
Representative Sequences:

Clone Products

  • Addgene plasmids for FOXN3

Alternative Splicing Database (ASD) splice patterns (SP) for FOXN3 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10
SP1: - - - -
SP2: - - -
SP4: -

Relevant External Links for FOXN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for FOXN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for FOXN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for FOXN3 Gene

NURSA nuclear receptor signaling pathways regulating expression of FOXN3 Gene:


SOURCE GeneReport for Unigene cluster for FOXN3 Gene:


Evidence on tissue expression from TISSUES for FOXN3 Gene

  • Muscle(4.3)
  • Lung(4)
  • Nervous system(3.9)
  • Liver(3.2)
  • Eye(2.2)
genes like me logo Genes that share expression patterns with FOXN3: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for FOXN3 Gene

Orthologs for FOXN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for FOXN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia FOXN3 33 34
  • 99.52 (n)
(Mus musculus)
Mammalia Foxn3 34
  • 95 (a)
(Canis familiaris)
Mammalia -- 34
  • 94 (a)
FOXN3 33
  • 92.01 (n)
-- 34
  • 90 (a)
(Monodelphis domestica)
Mammalia FOXN3 34
  • 92 (a)
(Bos Taurus)
Mammalia FOXN3 34
  • 88 (a)
(Ornithorhynchus anatinus)
Mammalia FOXN3 34
  • 86 (a)
(Gallus gallus)
Aves FOXN3 33 34
  • 83.13 (n)
(Anolis carolinensis)
Reptilia FOXN3 34
  • 87 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia foxn3 33
  • 77.69 (n)
(Danio rerio)
Actinopterygii foxn3 33 34
  • 77.69 (n)
fruit fly
(Drosophila melanogaster)
Insecta CHES-1-like 34
  • 12 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5413 34
  • 23 (a)
Species where no ortholog for FOXN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for FOXN3 Gene

Gene Tree for FOXN3 (if available)
Gene Tree for FOXN3 (if available)

Paralogs for FOXN3 Gene

Paralogs for FOXN3 Gene Pseudogenes for FOXN3 Gene

genes like me logo Genes that share paralogs with FOXN3: view

Variants for FOXN3 Gene

Sequence variations from dbSNP and Humsavar for FOXN3 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
rs1000006538 -- 89,526,245(+) TAATA(C/T)TGTAT intron-variant
rs1000008413 -- 89,241,565(+) TAAAG(C/T)GGAGT intron-variant
rs1000009008 -- 89,234,487(+) GGCCT(A/G)GTGGG intron-variant
rs1000009946 -- 89,385,888(+) GAGGA(A/G)AACAA intron-variant
rs1000013753 -- 89,567,204(+) TCTCT(G/T)CCCCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for FOXN3 Gene

Variant ID Type Subtype PubMed ID
nsv976363 CNV duplication 23825009
nsv974479 CNV deletion 23825009
nsv85548 CNV deletion 16902084
nsv85015 CNV deletion 16902084
nsv832852 CNV gain 17160897
nsv832851 CNV gain 17160897
nsv565515 CNV loss 21841781
nsv565514 CNV loss 21841781
nsv528176 CNV loss 19592680
nsv526326 CNV loss 19592680
nsv512369 CNV loss 21212237
nsv480412 CNV novel sequence insertion 20440878
nsv442354 CNV loss 18776908
nsv1152147 CNV deletion 26484159
nsv1143615 CNV deletion 24896259
nsv1115976 CNV insertion 24896259
nsv1069811 CNV deletion 25765185
nsv1069810 CNV deletion 25765185
nsv1054841 CNV gain 25217958
nsv1039774 CNV loss 25217958
esv3892574 CNV loss 25118596
esv3635297 CNV gain 21293372
esv3635296 CNV loss 21293372
esv3635295 CNV loss 21293372
esv3635294 CNV gain 21293372
esv3635292 CNV loss 21293372
esv3635291 CNV loss 21293372
esv3581382 CNV loss 25503493
esv3581381 CNV loss 25503493
esv3581380 CNV loss 25503493
esv3581379 CNV loss 25503493
esv2761851 CNV loss 21179565
esv275436 CNV loss 21479260
esv27509 CNV loss 19812545
esv2749002 CNV deletion 23290073
esv2749001 CNV deletion 23290073
esv2672523 CNV deletion 23128226
esv2668092 CNV deletion 23128226
esv2666528 CNV deletion 23128226
esv1600275 CNV deletion 17803354
esv1552920 CNV deletion 17803354
esv1516315 CNV deletion 17803354
esv1491660 CNV deletion 17803354
esv1482284 CNV deletion 17803354
esv1459170 CNV deletion 17803354
esv1407895 CNV deletion 17803354
esv1378771 CNV deletion 17803354
esv1286606 CNV insertion 17803354
esv1206899 CNV deletion 17803354
dgv1121n106 CNV deletion 24896259
dgv1120n106 CNV deletion 24896259

Variation tolerance for FOXN3 Gene

Residual Variation Intolerance Score: 28% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.34; 26.52% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for FOXN3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for FOXN3 Gene

Disorders for FOXN3 Gene

MalaCards: The human disease database

(1) MalaCards diseases for FOXN3 Gene - From: HGMD and GeneCards

Disorder Aliases PubMed IDs
auditory neuropathy
  • auditory dys-synchrony
- elite association - COSMIC cancer census association via MalaCards
Search FOXN3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for FOXN3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with FOXN3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for FOXN3 Gene

Publications for FOXN3 Gene

  1. Reconstitution of a MEC1-independent checkpoint in yeast by expression of a novel human fork head cDNA. (PMID: 9154802) Pati D … Plon SE (Molecular and cellular biology 1997) 2 3 4 22 60
  2. CHES1/FOXN3 interacts with Ski-interacting protein and acts as a transcriptional repressor. (PMID: 16102918) Scott KL … Plon SE (Gene 2005) 3 4 22 60
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60
  4. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PMID: 20634891) Jugessur A … Murray JC (PloS one 2010) 3 45 60
  5. Multiple endocrine neoplasia type 1 interacts with forkhead transcription factor CHES1 in DNA damage response. (PMID: 16951149) Busygina V … Bale AE (Cancer research 2006) 3 22 60

Products for FOXN3 Gene

Sources for FOXN3 Gene

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