Mouse Gene Pax3 (ENSMUST00000004994.15) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus paired box 3 (Pax3), transcript variant 2, mRNA. (from RefSeq NM_001159520)
Gencode Transcript: ENSMUST00000004994.15
Gencode Gene: ENSMUSG00000004872.15
Transcript (Including UTRs)
   Position: mm10 chr1:78,101,267-78,196,838 Size: 95,572 Total Exon Count: 9 Strand: -
Coding Region
   Position: mm10 chr1:78,102,801-78,196,749 Size: 93,949 Coding Exon Count: 9 

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: Q8BRF1_MOUSE
DESCRIPTION: SubName: Full=Paired box protein Pax-3; SubName: Full=Pax3 protein;
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Contains 1 paired 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


+  Comparative Toxicogenomics Database (CTD)
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -20.3089-0.228 Picture PostScript Text
3' UTR -390.901534-0.255 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
IPR022106 - Pax7
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00046 - Homeobox domain
PF00292 - 'Paired box' domain
PF12360 - Paired box protein 7

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on Q8BRF1
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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
  AK157760 - Mus musculus 9.5 days embryo parthenogenote cDNA, RIKEN full-length enriched library, clone:B130020L06 product:paired box gene 3, full insert sequence.
AK148354 - Mus musculus B16 F10Y cells cDNA, RIKEN full-length enriched library, clone:G370107F15 product:paired box gene 3, full insert sequence.
AK147919 - Mus musculus melanocyte cDNA, RIKEN full-length enriched library, clone:G270097N24 product:paired box gene 3, full insert sequence.
AK045018 - Mus musculus 9.5 days embryo parthenogenote cDNA, RIKEN full-length enriched library, clone:B130019I10 product:paired box gene 3, full insert sequence.
BC048699 - Mus musculus paired box gene 3, mRNA (cDNA clone MGC:59364 IMAGE:6518115), complete cds.
X59358 - Mouse Pax-3 gene for a DNA binding protein, involved in early neurogenesis.
AK012493 - Mus musculus 11 days embryo whole body cDNA, RIKEN full-length enriched library, clone:2700066P22 product:paired box gene 3, full insert sequence.
AK144973 - Mus musculus mammary gland RCB-0526 Jyg-MC(A) cDNA, RIKEN full-length enriched library, clone:G830016I19 product:paired box gene 3, full insert sequence.
AK044985 - Mus musculus 9.5 days embryo parthenogenote cDNA, RIKEN full-length enriched library, clone:B130017N14 product:paired box gene 3, full insert sequence.
AK014337 - Mus musculus 14, 17 days embryo head cDNA, RIKEN full-length enriched library, clone:3230402M02 product:paired box gene 3, full insert sequence.
AK214220 - Mus musculus cDNA, clone:Y2G0131B11, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000069689, based on BLAT search.
AK191274 - Mus musculus cDNA, clone:Y1G0105F24, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000069689, based on BLAT search.
AK183425 - Mus musculus cDNA, clone:Y0G0125N13, strand:unspecified.
AK195848 - Mus musculus cDNA, clone:Y1G0119N07, strand:unspecified.
AJ829760 - Mus musculus partial mRNA Pax3:Fhke fusion protein (Pax3:Fkhr gene).
AY743239 - Mus musculus PAX3/FKHR fusion (Pax3/Fkhr fusion) mRNA, Pax3/Fkhr fusion-P3Fa allele, partial cds.
S66429 - Pax-3 [mice, C3H/HeJ, mRNA Partial, 127 nt].
S66433 - Pax-3 (splotch(Sp2H)) [mice, Sp2H/Sp2H, mRNA Partial Mutant, 95 nt].
AK182746 - Mus musculus cDNA, clone:Y0G0123J18, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000004994, based on BLAT search.
AK178379 - Mus musculus cDNA, clone:Y0G0106H15, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000004994, based on BLAT search.
AK048723 - Mus musculus 0 day neonate cerebellum cDNA, RIKEN full-length enriched library, clone:C230022H20 product:paired box gene 3, full insert sequence.
AK083424 - Mus musculus 9 days embryo whole body cDNA, RIKEN full-length enriched library, clone:D030006B03 product:paired box gene 3, full insert sequence.
AK198372 - Mus musculus cDNA, clone:Y1G0127P16, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000004994, based on BLAT search.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
m_pmlPathway - Regulation of transcriptional activity by PML

+  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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