Mouse Gene Pax6 (ENSMUST00000111086.10) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus paired box 6 (Pax6), transcript variant 1, mRNA. (from RefSeq NM_001244198)
RefSeq Summary (NM_001244198): This gene encodes a homeobox-containing protein that functions as a regulator of transcription. It plays a key role in the development of neural tissues, particularly the eye. Activity of this protein is also required for expression of glucagon in the pancreas. This gene is regulated by multiple enhancers located up to tens or hundreds of kilobases upstream and downstream of the transcription start sites. Mutations in this gene or deletion of these regulatory elements results in severe defects in eye development. Alternative splicing and the use of alternative promoters results in multiple transcript variants, some of which encode proteins that lack the N-terminal paired domain. [provided by RefSeq, Jul 2015].
Gencode Transcript: ENSMUST00000111086.10
Gencode Gene: ENSMUSG00000027168.21
Transcript (Including UTRs)
   Position: mm10 chr2:105,668,900-105,697,364 Size: 28,465 Total Exon Count: 13 Strand: +
Coding Region
   Position: mm10 chr2:105,680,298-105,696,355 Size: 16,058 Coding Exon Count: 11 

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
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-  Comments and Description Text from UniProtKB
  ID: PAX6_MOUSE
DESCRIPTION: RecName: Full=Paired box protein Pax-6; AltName: Full=Oculorhombin;
FUNCTION: Transcription factor with important functions in the development of the eye, nose, central nervous system and pancreas. Required for the differentiation of pancreatic islet alpha cells. Competes with PAX4 in binding to a common element in the glucagon, insulin and somatostatin promoters. Regulates specification of the ventral neuron subtypes by establishing the correct progenitor domains (By similarity).
SUBUNIT: Interacts with MAF and MAFB. Interacts with TRIM11; this interaction leads to ubiquitination and proteasomal degradation, as well as inhibition of transactivation, possibly in part by preventing PAX6 binding to consensus DNA sequences.
SUBCELLULAR LOCATION: Nucleus.
DEVELOPMENTAL STAGE: Expressed in the developing eye, nose, brain and pancreas. At 9 dpc, expressed in the telencephalon, diencephalon, neural tube, optic vesicle and pancreas. Throughout development, expression continues in the dorsal and ventral pancreas. Expressed during cortical neurogenesis from 11 to 18 dpc. High levels in the early radial glial progenitors from 11 to 14 dpc and gradually decrease thereafter (at protein level). During corticogenesis, the protein level declines faster than that of the mRNA, due to proteasomal degradation. In newborn animals, becomes restricted to endocrine cells of the islets of Langerhans.
PTM: Ubiquitinated by TRIM11, leading to ubiquitination and proteasomal degradation.
DISEASE: Note=Defects in Pax6 are the cause of a condition known as small eye (Sey) which results in the complete lack of eyes and nasal primordia.
SIMILARITY: Belongs to the paired homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
SIMILARITY: Contains 1 paired domain.
SEQUENCE CAUTION: Sequence=AAA40109.1; Type=Erroneous initiation;

-  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


+  Comparative Toxicogenomics Database (CTD)
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -87.50281-0.311 Picture PostScript Text
3' UTR -236.501009-0.234 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
IPR017970 - Homeobox_CS
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like
IPR001523 - Paired_dom
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00046 - Homeobox domain
PF00292 - 'Paired box' domain

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on P63015
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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.
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
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-  Descriptions from all associated GenBank mRNAs
  AK028059 - Mus musculus adult male cerebellum cDNA, RIKEN full-length enriched library, clone:1500038E17 product:paired box gene 6, full insert sequence.
AK032616 - Mus musculus adult male olfactory brain cDNA, RIKEN full-length enriched library, clone:6430706M13 product:paired box gene 6, full insert sequence.
BC036957 - Mus musculus paired box gene 6, mRNA (cDNA clone MGC:46875 IMAGE:4504106), complete cds.
AF457141 - Mus musculus Pax6 paired-less isoform mRNA, complete cds.
AF457142 - Mus musculus Pax6 protein isoform mRNA, complete cds; alternatively spliced.
BC069912 - Mus musculus paired box gene 6, mRNA (cDNA clone IMAGE:6309201).
AY064175 - Mus musculus Pax6 paired-less isoform mRNA, complete cds.
X63963 - M.musculus pax-6 mRNA for paired box protein.
AK045805 - Mus musculus adult male corpora quadrigemina cDNA, RIKEN full-length enriched library, clone:B230311L02 product:paired box gene 6, full insert sequence.
BC011272 - Mus musculus paired box gene 6, mRNA (cDNA clone MGC:18454 IMAGE:4008490), complete cds.
AJ292077 - Mus musculus partial mRNA for paired box protein (Pax6 gene), clone PAX6-9Neu.
AJ307468 - Mus musculus mRNA for paired box protein (Pax-6 gene).
AF443223 - Mus musculus PAX6 mRNA, partial cds, alternatively spliced.
M77842 - Mus musculus oculorhombin (Sey) mRNA, complete cds.
AK139054 - Mus musculus 7 days neonate cerebellum cDNA, RIKEN full-length enriched library, clone:A730006J20 product:paired box gene 6, full insert sequence.
HW661303 - JP 2014522668-A/27: DOWNREGULATION OF miR-7 FOR PROMOTION OF BETA CELL DIFFERENTIATION AND INSULIN PRODUCTION.
JC277325 - Sequence 27 from Patent WO2013021389.
KX987998 - UNVERIFIED: Mus musculus strain AKR paired box 6-like mRNA, complete sequence.

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

+  Other Names for This Gene
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-  Gene Model Information
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+  Methods, Credits, and Use Restrictions
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