Mouse Gene Pax7 (ENSMUST00000030508.13) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus paired box 7 (Pax7), mRNA. (from RefSeq NM_011039)
Gencode Transcript: ENSMUST00000030508.13
Gencode Gene: ENSMUSG00000028736.13
Transcript (Including UTRs)
   Position: mm10 chr4:139,737,062-139,833,528 Size: 96,467 Total Exon Count: 9 Strand: -
Coding Region
   Position: mm10 chr4:139,740,787-139,832,911 Size: 92,125 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Data last updated at UCSC: 2019-09-20

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr4:139,737,062-139,833,528)mRNA (may differ from genome)Protein (503 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Paired box protein Pax-7;
FUNCTION: Probable transcription factor. May have a role in myogenesis.
SUBUNIT: Can bind to DNA as a heterodimer with PAX3. Interacts with DAXX (By similarity).
DEVELOPMENTAL STAGE: Expressed specifically during the development of the nervous and muscular system.
SIMILARITY: Belongs to the paired homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
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

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 -288.10617-0.467 Picture PostScript Text
3' UTR -1283.023725-0.344 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
PF05920 - Homeobox KN domain
PF12360 - Paired box protein 7

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on P47239
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 orthologGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGD Ensembl  
Protein SequenceProtein Sequence Protein Sequence  
AlignmentAlignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000983 transcription factor activity, RNA polymerase II core promoter sequence-specific
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006338 chromatin remodeling
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007275 multicellular organism development
GO:0007517 muscle organ development
GO:0007519 skeletal muscle tissue development
GO:0009887 animal organ morphogenesis
GO:0010453 regulation of cell fate commitment
GO:0010468 regulation of gene expression
GO:0014813 skeletal muscle satellite cell commitment
GO:0021527 spinal cord association neuron differentiation
GO:0021904 dorsal/ventral neural tube patterning
GO:0031062 positive regulation of histone methylation
GO:0043393 regulation of protein binding
GO:0043403 skeletal muscle tissue regeneration
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048663 neuron fate commitment
GO:0048706 embryonic skeletal system development
GO:0051216 cartilage development
GO:0060415 muscle tissue morphogenesis
GO:2000288 positive regulation of myoblast proliferation

Cellular Component:
GO:0005634 nucleus
GO:0005667 transcription factor complex

-  Descriptions from all associated GenBank mRNAs
  AK133693 - Mus musculus adult male pituitary gland cDNA, RIKEN full-length enriched library, clone:5330440B08 product:paired box gene 7, full insert sequence.
AF254422 - Mus musculus paired box transcription factor PAX7 (Pax7) mRNA, complete cds.
BC156884 - Synthetic construct Mus musculus clone IMAGE:100062729, MGC:190944 paired box gene 7 (Pax7) mRNA, encodes complete protein.
BC156072 - Synthetic construct Mus musculus clone IMAGE:100062368, MGC:190857 paired box gene 7 (Pax7) mRNA, encodes complete protein.
U20792 - Mus musculus Pax7 mRNA, partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_011039, P47239, Pax-7, PAX7_MOUSE, Q9ES16, uc008vms.1, uc008vms.2
UCSC ID: uc008vms.2
RefSeq Accession: NM_011039
Protein: P47239 (aka PAX7_MOUSE)
CCDS: CCDS18850.1

-  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.