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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
  • GC14M091383
  • GC14M091669

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. Among its related pathways are Mesodermal Commitment Pathway. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity 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

GeneHancer (GH) Regulatory Elements for FOXN3 Gene

Promoters and enhancers for FOXN3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH14J089613 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 667.3 +1.6 1553 8.8 PKNOX1 FOXA2 ARNT ARID4B SIN3A ZNF48 YY1 ETS1 GLIS2 ZNF143 FOXN3 LOC105370617 ENSG00000252655 TDP1 GC14P089623 RN7SKP107 GC14P089586 ENSG00000259053
GH14J089414 Promoter/Enhancer 2.5 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 655.8 +202.0 202030 4.7 HDGF PKNOX1 FOXA2 SMAD1 ARID4B SIN3A FEZF1 DMAP1 YY1 ZNF207 FOXN3 FOXN3-AS1 NRDE2 ZC3H14 ENSG00000252655 RPL21P11 TDP1 LOC105370614 ENSG00000258380 ENSG00000259053
GH14J089458 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 17.5 +160.0 159982 2.3 FOXA2 DMAP1 RAD21 YY1 ATF7 CREM MIXL1 RXRA CEBPB PPARG FOXN3 RN7SKP107 GC14P089486 FOXN3-AS1 ENSG00000259053
GH14J089718 Enhancer 1.2 FANTOM5 Ensembl ENCODE 20.7 -101.9 -101863 4.4 CTCF TFAP4 MAX EBF1 POLR2A EGR1 ATF7 ETV6 RUNX3 RFX1 FOXN3 ENSG00000252655 RN7SKP107 TDP1 RN7SKP255 CHORDC2P ENSG00000259053
GH14J089425 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 15.2 +190.2 190162 7.5 PKNOX1 SMAD1 ZNF133 FEZF1 IRF4 YY1 ATF7 FOS RUNX3 RXRA NRDE2 FOXN3 RN7SKP107 ENSG00000252655 RPL21P11 FOXN3-AS1 GC14P089486 ENSG00000259053
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around FOXN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the FOXN3 gene promoter:
  • FOXO4
  • AP-2alphaA
  • AP-2alpha isoform 4
  • AP-2alpha isoform 3
  • AP-2alpha isoform 2
  • AP-2alpha
  • Bach2
  • AREB6
  • C/EBPalpha

Genomic Locations for FOXN3 Gene

Genomic Locations for FOXN3 Gene
494,280 bases
Minus strand
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:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding ISM 19274049
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IBA --
GO:0005515 protein binding IPI 16102918
GO:0008022 protein C-terminus binding IPI 16951149
genes like me logo Genes that share ontologies with FOXN3: view
genes like me logo Genes that share phenotypes with FOXN3: view

Animal Model Products

miRNA for FOXN3 Gene

miRTarBase miRNAs that target FOXN3

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)
  • 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 IBA,IC 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:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0007049 cell cycle IEA --
GO:0007095 mitotic G2 DNA damage checkpoint IGI 9154802
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

mRNA/cDNA 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 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 34 33
  • 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 34 33
  • 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 34 33
  • 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)
Evolutionary constrained regions (ECRs) for FOXN3: view image

Paralogs for FOXN3 Gene

Paralogs for FOXN3 Gene

(10) SIMAP similar genes for FOXN3 Gene using alignment to 10 proteins:

  • G3V3A7_HUMAN
  • G3V4N5_HUMAN
  • G3V5C7_HUMAN
  • H0YJ22_HUMAN
  • H0YJ43_HUMAN
  • H0YJ54_HUMAN
  • H0YJ94_HUMAN
  • H0YJY0_HUMAN 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 Variation AA Info Type
rs1000006538 -- 89,526,245(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000008413 -- 89,241,565(-) C/T intron_variant
rs1000009008 -- 89,234,487(-) G/A intron_variant
rs1000009946 -- 89,385,888(-) G/A intron_variant
rs1000013753 -- 89,567,204(-) T/G genic_upstream_transcript_variant, intron_variant

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

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

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)

Additional Variant Information for FOXN3 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for FOXN3 Gene

Additional Disease Information for FOXN3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for FOXN3 Gene.

No data available for MalaCards , 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 58
  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 58
  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 44 58
  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 44 58
  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 58

Products for FOXN3 Gene

Sources for FOXN3 Gene

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