Human Gene FOXN3 (ENST00000557258.6) from GENCODE V44
  Description: Homo sapiens forkhead box N3 (FOXN3), transcript variant 2, mRNA. (from RefSeq NM_005197)
RefSeq Summary (NM_005197): 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].
Gencode Transcript: ENST00000557258.6
Gencode Gene: ENSG00000053254.16
Transcript (Including UTRs)
   Position: hg38 chr14:89,156,177-89,417,233 Size: 261,057 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg38 chr14:89,162,414-89,412,476 Size: 250,063 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:89,156,177-89,417,233)mRNA (may differ from genome)Protein (468 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMGIneXtProtOMIM
PubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: FOXN3_HUMAN
DESCRIPTION: RecName: Full=Forkhead box protein N3; AltName: Full=Checkpoint suppressor 1;
FUNCTION: Acts as a transcriptional repressor. May be involved in DNA damage-inducible cell cycle arrests (checkpoints).
SUBUNIT: Interacts through its C-terminus with the C-terminus of SNW1/SKIP.
SUBCELLULAR LOCATION: Nucleus (Probable).
SIMILARITY: Contains 1 fork-head DNA-binding domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: FOXN3
Diseases sorted by gene-association score: auditory neuropathy (6)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D001564 Benzo(a)pyrene
  • D013749 Tetrachlorodibenzodioxin
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C012606 4-vinyl-1-cyclohexene dioxide
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D015127 9,10-Dimethyl-1,2-benzanthracene
  • D000082 Acetaminophen
  • D000393 Air Pollutants
  • D001554 Benzene
  • D020111 Chlorodiphenyl (54% Chlorine)
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 25.57 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 530.44 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -226.60377-0.601 Picture PostScript Text
3' UTR -1773.006237-0.284 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001766 - TF_fork_head
IPR018122 - TF_fork_head_CS
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00250 - Forkhead domain

ModBase Predicted Comparative 3D Structure on O00409
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0008022 protein C-terminus binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007049 cell cycle
GO:0007095 mitotic G2 DNA damage checkpoint
GO:0030154 cell differentiation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0097094 craniofacial suture morphogenesis

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  U68723 - Human checkpoint suppressor 1 mRNA, complete cds.
BC007506 - Homo sapiens forkhead box N3, mRNA (cDNA clone MGC:4149 IMAGE:3028787), complete cds.
AK225967 - Homo sapiens mRNA for checkpoint suppressor 1 variant, clone: FCC113E08.
AK308053 - Homo sapiens cDNA, FLJ98001.
KJ890908 - Synthetic construct Homo sapiens clone ccsbBroadEn_00302 FOXN3 gene, encodes complete protein.
EU831970 - Synthetic construct Homo sapiens clone HAIB:100066999; DKFZo008F1123 forkhead box N3 protein (FOXN3) gene, encodes complete protein.
EU832063 - Synthetic construct Homo sapiens clone HAIB:100067092; DKFZo004F1124 forkhead box N3 protein (FOXN3) gene, encodes complete protein.
AB528050 - Synthetic construct DNA, clone: pF1KB7750, Homo sapiens FOXN3 gene for forkhead box protein N3, without stop codon, in Flexi system.
AK055175 - Homo sapiens cDNA FLJ30613 fis, clone CTONG2000855.
AK123929 - Homo sapiens cDNA FLJ41935 fis, clone PERIC2005117.
BC010460 - Homo sapiens forkhead box N3, mRNA (cDNA clone IMAGE:4215125).
JD044805 - Sequence 25829 from Patent EP1572962.
JD540836 - Sequence 521860 from Patent EP1572962.
AF116643 - Homo sapiens PRO1635 mRNA, complete cds.
JD235492 - Sequence 216516 from Patent EP1572962.
JD110456 - Sequence 91480 from Patent EP1572962.
JD261777 - Sequence 242801 from Patent EP1572962.
JD261778 - Sequence 242802 from Patent EP1572962.
JD174837 - Sequence 155861 from Patent EP1572962.
JD377456 - Sequence 358480 from Patent EP1572962.
JD315365 - Sequence 296389 from Patent EP1572962.
JD312733 - Sequence 293757 from Patent EP1572962.
JD304241 - Sequence 285265 from Patent EP1572962.
JD231189 - Sequence 212213 from Patent EP1572962.
JD232635 - Sequence 213659 from Patent EP1572962.
JD457921 - Sequence 438945 from Patent EP1572962.
JD457922 - Sequence 438946 from Patent EP1572962.
JD264115 - Sequence 245139 from Patent EP1572962.
JD313275 - Sequence 294299 from Patent EP1572962.
JD171394 - Sequence 152418 from Patent EP1572962.
AK314098 - Homo sapiens cDNA, FLJ94781.
DQ891012 - Synthetic construct clone IMAGE:100003642; FLH168513.01X; RZPDo839A0294D chromosome 14 open reading frame 116 (C14orf116) gene, encodes complete protein.
KJ904436 - Synthetic construct Homo sapiens clone ccsbBroadEn_13830 FOXN3-like gene, encodes complete protein.
DQ894192 - Synthetic construct Homo sapiens clone IMAGE:100008652; FLH168511.01L; RZPDo839A0293D chromosome 14 open reading frame 116 (C14orf116) gene, encodes complete protein.
JD109408 - Sequence 90432 from Patent EP1572962.
JD165767 - Sequence 146791 from Patent EP1572962.
JD356070 - Sequence 337094 from Patent EP1572962.
BC010227 - Homo sapiens forkhead box N3, mRNA (cDNA clone IMAGE:4150549), with apparent retained intron.
JD073443 - Sequence 54467 from Patent EP1572962.
JD473706 - Sequence 454730 from Patent EP1572962.
JD390680 - Sequence 371704 from Patent EP1572962.
JD235171 - Sequence 216195 from Patent EP1572962.
JD184872 - Sequence 165896 from Patent EP1572962.
JD482548 - Sequence 463572 from Patent EP1572962.
JD086228 - Sequence 67252 from Patent EP1572962.
JD419837 - Sequence 400861 from Patent EP1572962.
JD305742 - Sequence 286766 from Patent EP1572962.
JD360129 - Sequence 341153 from Patent EP1572962.
JD385607 - Sequence 366631 from Patent EP1572962.
LF209626 - JP 2014500723-A/17129: Polycomb-Associated Non-Coding RNAs.
MA445203 - JP 2018138019-A/17129: Polycomb-Associated Non-Coding RNAs.
CU675677 - Synthetic construct Homo sapiens gateway clone IMAGE:100019541 5' read FOXN3 mRNA.

-  Other Names for This Gene
  Alternate Gene Symbols: C14orf116, CHES1, ENST00000557258.1, ENST00000557258.2, ENST00000557258.3, ENST00000557258.4, ENST00000557258.5, FOXN3_HUMAN, NM_005197, O00409, Q96II7, Q9UIE7, uc001xxn.1, uc001xxn.2, uc001xxn.3, uc001xxn.4, uc001xxn.5, uc001xxn.6
UCSC ID: ENST00000557258.6
RefSeq Accession: NM_005197
Protein: O00409 (aka FOXN3_HUMAN or FXN3_HUMAN)
CCDS: CCDS32138.1, CCDS41977.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.