Mouse Gene Foxa2 (ENSMUST00000109964.7) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus forkhead box A2 (Foxa2), transcript variant 3, mRNA. (from RefSeq NM_001291067)
Gencode Transcript: ENSMUST00000109964.7
Gencode Gene: ENSMUSG00000037025.11
Transcript (Including UTRs)
   Position: mm10 chr2:148,042,877-148,045,948 Size: 3,072 Total Exon Count: 2 Strand: -
Coding Region
   Position: mm10 chr2:148,043,514-148,045,913 Size: 2,400 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-20

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr2:148,042,877-148,045,948)mRNA (may differ from genome)Protein (465 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI

-  Comments and Description Text from UniProtKB
DESCRIPTION: SubName: Full=Hepatocyte nuclear factor 3-beta;
SIMILARITY: Contains 1 fork-head DNA-binding domain.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -4.3035-0.123 Picture PostScript Text
3' UTR -172.30637-0.270 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
IPR013638 - Fork-head_N
IPR018533 - Forkhead_box_C
IPR001766 - TF_fork_head
IPR018122 - TF_fork_head_CS
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00250 - Forkhead domain
PF08430 - Forkhead N-terminal region
PF09354 - HNF3 C-terminal domain

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

ModBase Predicted Comparative 3D Structure on G5E8P5
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
No orthologGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
 Protein Sequence Protein Sequence  
 Alignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0008134 transcription factor binding
GO:0019904 protein domain specific binding
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0010719 negative regulation of epithelial to mesenchymal transition
GO:0030193 regulation of blood coagulation
GO:0031018 endocrine pancreas development
GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0071542 dopaminergic neuron differentiation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0030054 cell junction

-  Descriptions from all associated GenBank mRNAs
  LF204794 - JP 2014500723-A/12297: Polycomb-Associated Non-Coding RNAs.
L10409 - Mouse fork head related protein (HNF-3beta) mRNA, complete cds.
X74937 - M.musculus HNF-3beta mRNA.
U04197 - Mus musculus HNF3 beta transcription factor (HNF3b) mRNA, partial cds.
BC160375 - Synthetic construct Mus musculus clone IMAGE:100064119, MGC:193490 forkhead box A2 (Foxa2) mRNA, encodes complete protein.
AB231453 - Mus musculus liver hepatoma CRL-1830 Hepa1-6 cDNA, clone:VZZZZZZA02.
LF193637 - JP 2014500723-A/1140: Polycomb-Associated Non-Coding RNAs.
LF202455 - JP 2014500723-A/9958: Polycomb-Associated Non-Coding RNAs.
LF203573 - JP 2014500723-A/11076: Polycomb-Associated Non-Coding RNAs.
MA440371 - JP 2018138019-A/12297: Polycomb-Associated Non-Coding RNAs.
MA429214 - JP 2018138019-A/1140: Polycomb-Associated Non-Coding RNAs.
MA438032 - JP 2018138019-A/9958: Polycomb-Associated Non-Coding RNAs.
MA439150 - JP 2018138019-A/11076: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
mmu04950 - Maturity onset diabetes of the young

-  Other Names for This Gene
  Alternate Gene Symbols: G5E8P5, G5E8P5_MOUSE, NM_001291067, uc008mta.1, uc008mta.2
UCSC ID: uc008mta.2
RefSeq Accession: NM_001291065
Protein: G5E8P5 CCDS: CCDS16836.1, CCDS71157.1

-  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.