U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    FOXN3 forkhead box N3 [ Homo sapiens (human) ]

    Gene ID: 1112, updated on 5-Mar-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    FOXN3provided by HGNC
    Official Full Name
    forkhead box N3provided by HGNC
    Primary source
    HGNC:HGNC:1928
    See related
    Ensembl:ENSG00000053254 MIM:602628; AllianceGenome:HGNC:1928
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CHES1; PRO1635; C14orf116
    Summary
    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]
    Expression
    Ubiquitous expression in fat (RPKM 25.7), ovary (RPKM 24.3) and 25 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    14q31.3-q32.11
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (89156177..89619165, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (83379834..83842985, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (89622521..90085509, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903357 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89605771-89606692 Neighboring gene metallophosphoesterase 1 pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:89631335-89632266 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:89641541-89642042 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:89654698-89654882 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8848 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89671451-89671952 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89718876-89719531 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8849 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89760189-89760856 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89760857-89761524 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89762398-89762960 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89762961-89763522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89763523-89764084 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8851 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8850 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8853 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8854 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89775236-89775736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89775737-89776237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8856 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8857 Neighboring gene cyclase associated actin cytoskeleton regulatory protein 2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8858 Neighboring gene Sharpr-MPRA regulatory region 10244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89807187-89807686 Neighboring gene uncharacterized LOC101928817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5998 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89818959-89819674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8859 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8862 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8861 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8864 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8866 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89858093-89858593 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89865667-89866237 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89869264-89869764 Neighboring gene Sharpr-MPRA regulatory region 4092 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:89882738-89883271 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:89883272-89883804 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89891172-89891786 Neighboring gene uncharacterized LOC107984635 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:89894848-89896047 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr14:89898457-89899010 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:89906553-89907136 Neighboring gene FOXN3 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 349 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr14:89907723-89908306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89919266-89920166 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89929363-89929862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89932229-89933148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:89933149-89934068 Neighboring gene FOXN3 antisense RNA 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8867 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8868 Neighboring gene H3K27ac hESC enhancers GRCh37_chr14:90084905-90085406 and GRCh37_chr14:90085407-90085906 Neighboring gene uncharacterized LOC105370617 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:90091889-90092462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8869 Neighboring gene uncharacterized LOC105370616 Neighboring gene RN7SK pseudogene 107

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. FOXN3 inhibits cell proliferation and invasion via modulating the AKT/MDM2/p53 axis in human glioma. Wang C, et al. Aging (Albany NY), 2021 Sep 12. PMID 34511432, Free PMC Article
    2. The clinical and prognostic significance of FOXN3 downregulation in acute myeloid leukaemia. Zhang J, et al. Int J Lab Hematol, 2020 Jun. PMID 32078244, Free PMC Article
    3. Bispecific Forkhead Transcription Factor FoxN3 Recognizes Two Distinct Motifs with Different DNA Shapes. Rogers JM, et al. Mol Cell, 2019 Apr 18. PMID 30826165, Free PMC Article
    4. CHES1/FOXN3 regulates cell proliferation by repressing PIM2 and protein biosynthesis. Huot G, et al. Mol Biol Cell, 2014 Mar. PMID 24403608, Free PMC Article
    5. FOXN3 inhibits the progression of ovarian cancer through negatively regulating the expression of RPS15A. Yang H, et al. Hum Cell, 2023 May. PMID 37016167

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. FOXN3 inhibits the progression of ovarian cancer through negatively regulating the expression of RPS15A.
      Title: FOXN3 inhibits the progression of ovarian cancer through negatively regulating the expression of RPS15A.
    2. FOXN3 inhibits cell proliferation and invasion via modulating the AKT/MDM2/p53 axis in human glioma.
      Title: FOXN3 inhibits cell proliferation and invasion via modulating the AKT/MDM2/p53 axis in human glioma.
    3. miR-574-5p Targets FOXN3 to Regulate the Invasion of Nasopharyngeal Carcinoma Cells via Wnt/beta-Catenin Pathway.
      Title: miR-574-5p Targets FOXN3 to Regulate the Invasion of Nasopharyngeal Carcinoma Cells via Wnt/β-Catenin Pathway.
    4. FOXN3 suppresses the growth and invasion of papillary thyroid cancer through the inactivation of Wnt/beta-catenin pathway.
      Title: FOXN3 suppresses the growth and invasion of papillary thyroid cancer through the inactivation of Wnt/β-catenin pathway.
    5. MicroRNA-574-5p directly targets FOXN3 to mediate thyroid cancer progression via Wnt/beta-catenin signaling pathway.
      Title: MicroRNA-574-5p directly targets FOXN3 to mediate thyroid cancer progression via Wnt/β-catenin signaling pathway.
    6. The clinical and prognostic significance of FOXN3 downregulation in acute myeloid leukaemia.
      Title: The clinical and prognostic significance of FOXN3 downregulation in acute myeloid leukaemia.
    7. FOXN3 was notably downregulated in osteosarcoma (OS) tissues and the expression of FOXN3 was negatively correlated with tumor size, metastasis and TNM stage. Also, FOXN3 suppressed the proliferation, migration and invasion of osteosarcoma cells. Furthermore, FOXN3 was demonstrated to transcriptionally suppress SIRT6 expression, thereby inhibiting MMP9 secretion.
      Title: FOXN3 is downregulated in osteosarcoma and transcriptionally regulates SIRT6, and suppresses migration and invasion in osteosarcoma.
    8. liver FOXN3 and glucagon control fasting glucose.
      Title: A Hepatocyte FOXN3-α Cell Glucagon Axis Regulates Fasting Glucose.
    9. these results identified a negative cross-regulatory loop between ERalpha and CHES1 that was required for growth of breast cancer cells, it might uncover novel insight into molecular mechanism of CHES1 involved in breast cancer and provide new avenues for molecular-targeted therapy in hormone-regulated breast cancer.
      Title: Checkpoint suppressor 1 suppresses transcriptional activity of ERα and breast cancer cell proliferation via deacetylase SIRT1.
    10. We present co-crystal structures of the FoxN3 DNA binding domain bound to the FKH and FHL sites, respectively. FoxN3 adopts a similar conformation to recognize both motifs, making contacts with different DNA bases using the same amino acids. However, the DNA structure is different in the two complexes
      Title: Bispecific Forkhead Transcription Factor FoxN3 Recognizes Two Distinct Motifs with Different DNA Shapes.
    Submit: New GeneRIF Correction See all GeneRIFs (26)

    Phenotypes

    Go to the top of the page Help

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
    EBI GWAS Catalog
    Weight loss after gastric bypass is associated with a variant at 15q26.1.
    EBI GWAS Catalog

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in craniofacial suture morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitotic G2 DNA damage checkpoint signaling IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IC
    Inferred by Curator
    more info
    		 PubMed 

    General protein information

    Go to the top of the page Help
    Preferred Names
    forkhead box protein N3
    Names
    checkpoint suppressor 1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001085471.2 → NP_001078940.1  forkhead box protein N3 isoform 1

      See identical proteins and their annotated locations for NP_001078940.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AI084011, AL137230, AL138478, BP213901, U68723
      Consensus CDS
      CCDS41977.1
      UniProtKB/Swiss-Prot
      O00409, Q96II7, Q9UIE7
      Related
      ENSP00000343288.4, ENST00000345097.8
      Conserved Domains (1) summary
      pfam00250
      Location:114 → 201
      Forkhead; Forkhead domain

    2. NM_005197.4 → NP_005188.2  forkhead box protein N3 isoform 2

      See identical proteins and their annotated locations for NP_005188.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon and differs in the 5' UTR, compared to variant 1, resulting in a shorter protein (isoform 2).
      Source sequence(s)
      AI084011, AL138478, AL356805, BC007506, CB989352
      Consensus CDS
      CCDS32138.1
      UniProtKB/Swiss-Prot
      O00409
      Related
      ENSP00000452005.1, ENST00000557258.6
      Conserved Domains (1) summary
      pfam00250
      Location:114 → 200
      Forkhead; Forkhead domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      89156177..89619165 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      83379834..83842985 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O00409.1 GenPept UniProtKB/Swiss-Prot:O00409

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous