Mouse Gene Pax5 (ENSMUST00000014174.13) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus paired box 5 (Pax5), mRNA. (from RefSeq NM_008782)
Gencode Transcript: ENSMUST00000014174.13
Gencode Gene: ENSMUSG00000014030.15
Transcript (Including UTRs)
   Position: mm10 chr4:44,524,757-44,710,487 Size: 185,731 Total Exon Count: 10 Strand: -
Coding Region
   Position: mm10 chr4:44,531,506-44,710,408 Size: 178,903 Coding Exon Count: 10 

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 (chr4:44,524,757-44,710,487)mRNA (may differ from genome)Protein (391 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
MGIPubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Paired box protein Pax-5; AltName: Full=B-cell-specific transcription factor; Short=BSAP;
FUNCTION: May play an important role in B-cell differentiation as well as neural development and spermatogenesis. Involved in the regulation of the CD19 gene, a B-lymphoid-specific target gene.
SUBUNIT: Interacts with ETS1, altering its DNA-binding properties (By similarity). Interacts with DAXX and TLE4. Binds DNA as a monomer.
INTERACTION: Q9UER7:DAXX (xeno); NbExp=4; IntAct=EBI-296260, EBI-77321;
DEVELOPMENTAL STAGE: Expressed at early B-cell differentiation, in the developing CNS and in adult testis.
PTM: O-glycosylated (Probable).
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)
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -9.3079-0.118 Picture PostScript Text
3' UTR -2199.206749-0.326 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
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-  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     
Protein SequenceProtein Sequence    

-  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
GO:0005515 protein binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
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:0007283 spermatogenesis
GO:0007399 nervous system development
GO:0007568 aging
GO:0009887 animal organ morphogenesis
GO:0021670 lateral ventricle development
GO:0021987 cerebral cortex development
GO:0030154 cell differentiation
GO:0030534 adult behavior
GO:0035914 skeletal muscle cell differentiation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048701 embryonic cranial skeleton morphogenesis
GO:0051573 negative regulation of histone H3-K9 methylation
GO:0071542 dopaminergic neuron differentiation

Cellular Component:
GO:0001650 fibrillar center
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex
GO:0005829 cytosol
GO:0043231 intracellular membrane-bounded organelle

+  Descriptions from all associated GenBank mRNAs
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-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q02650 (Reactome details) participates in the following event(s):

R-MMU-8938951 RUNX1 binds PAX5 (BSAP)
R-MMU-8939245 RUNX1 regulates transcription of genes involved in BCR signaling
R-MMU-8878171 Transcriptional regulation by RUNX1
R-MMU-212436 Generic Transcription Pathway
R-MMU-73857 RNA Polymerase II Transcription
R-MMU-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: NM_008782, Pax-5, PAX5_MOUSE, Q02650, uc008srx.1, uc008srx.2
UCSC ID: uc008srx.2
RefSeq Accession: NM_008782
Protein: Q02650 (aka PAX5_MOUSE)
CCDS: CCDS18125.1

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