Mouse Gene Foxn3 (ENSMUST00000177451.7) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Acts as a transcriptional repressor. May be involved in DNA damage-inducible cell cycle arrests (checkpoints) (By similarity). (from UniProt Q499D0)
Gencode Transcript: ENSMUST00000177451.7
Gencode Gene: ENSMUSG00000033713.12
Transcript (Including UTRs)
   Position: mm10 chr12:99,195,094-99,393,072 Size: 197,979 Total Exon Count: 6 Strand: -
Coding Region
   Position: mm10 chr12:99,196,267-99,388,903 Size: 192,637 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:99,195,094-99,393,072)mRNA (may differ from genome)Protein (457 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsMGIPubMed
SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: FOXN3_MOUSE
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) (By similarity).
SUBUNIT: Interacts through its C-terminus with the C-terminus of SNW1/SKIP (By similarity).
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


-  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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -189.80335-0.567 Picture PostScript Text
3' UTR -348.101173-0.297 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

SCOP Domains:
46785 - "Winged helix" DNA-binding domain

ModBase Predicted Comparative 3D Structure on Q499D0
FrontTopSide
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.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA 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: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
  BC099971 - Mus musculus forkhead box N3, mRNA (cDNA clone MGC:107530 IMAGE:30008715), complete cds.
AK046748 - Mus musculus 4 days neonate thymus cDNA, RIKEN full-length enriched library, clone:B630006M02 product:checkpoint suppressor 1, full insert sequence.
AK017346 - Mus musculus 6 days neonate head cDNA, RIKEN full-length enriched library, clone:5430426H20 product:checkpoint suppressor 1, full insert sequence.
AK180878 - Mus musculus cDNA, clone:Y0G0116D06, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000046859, based on BLAT search.
AK208910 - Mus musculus cDNA, clone:Y2G0113D08, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000046859, based on BLAT search.
LF199285 - JP 2014500723-A/6788: Polycomb-Associated Non-Coding RNAs.
MA434862 - JP 2018138019-A/6788: Polycomb-Associated Non-Coding RNAs.
AK077921 - Mus musculus 13 days embryo male testis cDNA, RIKEN full-length enriched library, clone:6030443H13 product:checkpoint suppressor 1, full insert sequence.
AK198961 - Mus musculus cDNA, clone:Y1G0129L08, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000046859, based on BLAT search.
AK148970 - Mus musculus 2 days neonate sympathetic ganglion cDNA, RIKEN full-length enriched library, clone:7120469I24 product:checkpoint suppressor 1, full insert sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: AK046748, Ches1, FOXN3_MOUSE, Q499D0, Q8C5N8, Q9CU83, uc007ors.1
UCSC ID: uc007ors.1
RefSeq Accession: NM_183186
Protein: Q499D0 (aka FOXN3_MOUSE)
CCDS: CCDS26103.1

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

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