Mouse Gene Pax1 (ENSMUST00000109968.3) from GENCODE VM32
  Description: Mus musculus paired box 1 (Pax1), mRNA. (from RefSeq NM_008780)
Gencode Transcript: ENSMUST00000109968.3
Gencode Gene: ENSMUSG00000037034.17
Transcript (Including UTRs)
   Position: mm39 chr2:147,206,914-147,216,973 Size: 10,060 Total Exon Count: 5 Strand: +
Coding Region
   Position: mm39 chr2:147,206,968-147,215,725 Size: 8,758 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2022-12-30 19:23:49

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr2:147,206,914-147,216,973)mRNA (may differ from genome)Protein (446 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Paired box protein Pax-1;
FUNCTION: This protein is a transcriptional activator. It may play a role in the formation of segmented structures of the embryo. May play an important role in the normal development of the vertebral column.
DISEASE: Note=Undulated (un) homozygous mice exhibits vertebral malformations along the entire rostro-caudal axis. This is due to a single mutation in the paired box region.
SIMILARITY: Contains 1 paired domain.
SEQUENCE CAUTION: Sequence=AAA37793.1; Type=Erroneous gene model prediction; Sequence=AAA39888.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -5.4054-0.100 Picture PostScript Text
3' UTR -354.901248-0.284 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
IPR009057 - Homeodomain-like
IPR001523 - Paired_dom
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00292 - 'Paired box' domain

ModBase Predicted Comparative 3D Structure on P09084
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 BrowserNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBank Ensembl   
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:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding

Biological Process:
GO:0001501 skeletal system development
GO:0001756 somitogenesis
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007389 pattern specification process
GO:0008283 cell proliferation
GO:0009887 animal organ morphogenesis
GO:0043367 CD4-positive, alpha-beta T cell differentiation
GO:0043374 CD8-positive, alpha-beta T cell differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048538 thymus development
GO:0060017 parathyroid gland development
GO:0060349 bone morphogenesis
GO:0061056 sclerotome development

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

-  Descriptions from all associated GenBank mRNAs
  AB080657 - Mus musculus Pax1 mRNA, partial cds, clone:5832438N23.
AB080656 - Mus musculus Pax1 mRNA, partial cds, clone:A430036B21.
AK134066 - Mus musculus adult male thymus cDNA, RIKEN full-length enriched library, clone:5830427P13 product:paired box gene 1, full insert sequence.
M69222 - Mouse Pax-1 protein (Pax-1) mRNA, complete cds.
BC140989 - Mus musculus paired box gene 1, mRNA (cDNA clone MGC:175950 IMAGE:9055601), complete cds.
AK041531 - Mus musculus 3 days neonate thymus cDNA, RIKEN full-length enriched library, clone:A630019K16 product:paired box gene 1, full insert sequence.

-  Other Names for This Gene
  Alternate Gene Symbols: A2ALJ9, ENSMUST00000109968.1, ENSMUST00000109968.2, NM_008780, P09084, Pax-1, PAX1_MOUSE, Q9R2B1, uc008msx.1, uc008msx.2, uc008msx.3, uc008msx.4, uc008msx.5
UCSC ID: ENSMUST00000109968.3
RefSeq Accession: NM_008780
Protein: P09084 (aka PAX1_MOUSE)

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