Mouse Gene Pax9 (ENSMUST00000153250.9) from GENCODE VM33
  Description: Nucleus (By similarity). (from UniProt Q3V1K1)
RefSeq Summary (NM_011041): This gene is a member of the paired box (PAX) family of transcription factors. Members of this gene family typically contain a paired box domain, an octapeptide, and a paired-type homeodomain. These genes play critical roles during fetal development and cancer growth. Mice lacking this gene exhibit impaired development of organs, musculature and the skeleton, including absent and abnormally developed teeth, and neonatal lethality. Mutations in the human gene are associated with selective tooth agenesis-3. [provided by RefSeq, Sep 2015]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on transcript alignments.
Gencode Transcript: ENSMUST00000153250.9
Gencode Gene: ENSMUSG00000001497.19
Transcript (Including UTRs)
   Position: mm39 chr12:56,738,552-56,759,492 Size: 20,941 Total Exon Count: 5 Strand: +
Coding Region
   Position: mm39 chr12:56,742,646-56,756,692 Size: 14,047 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-15 19:06:27

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:56,738,552-56,759,492)mRNA (may differ from genome)Protein (342 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblExonPrimerGeneCardsMGIPubMed
SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: Q3V1K1_MOUSE
DESCRIPTION: SubName: Full=Putative uncharacterized 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

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 -148.30403-0.368 Picture PostScript Text
3' UTR -674.602800-0.241 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 Q3V1K1
FrontTopSide
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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     
GenBankRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding

Biological Process:
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:0007492 endoderm development
GO:0009887 animal organ morphogenesis
GO:0042476 odontogenesis
GO:0042481 regulation of odontogenesis
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0060325 face morphogenesis
GO:0071363 cellular response to growth factor stimulus

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK132404 - Mus musculus 14 days embryo liver cDNA, RIKEN full-length enriched library, clone:4432412B16 product:paired box gene 9, full insert sequence.
AK034985 - Mus musculus 12 days embryo embryonic body between diaphragm region and neck cDNA, RIKEN full-length enriched library, clone:9430070E09 product:paired box gene 9, full insert sequence.
X84000 - M.musculus mRNA for Pax9.
BC005794 - Mus musculus paired box gene 9, mRNA (cDNA clone MGC:11500 IMAGE:3707718), complete cds.
BC006930 - Mus musculus paired box gene 9, mRNA (cDNA clone IMAGE:3599040), with apparent retained intron.
LF203952 - JP 2014500723-A/11455: Polycomb-Associated Non-Coding RNAs.
MA439529 - JP 2018138019-A/11455: Polycomb-Associated Non-Coding RNAs.
LF199155 - JP 2014500723-A/6658: Polycomb-Associated Non-Coding RNAs.
MA434732 - JP 2018138019-A/6658: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: AK132404, ENSMUST00000153250.1, ENSMUST00000153250.2, ENSMUST00000153250.3, ENSMUST00000153250.4, ENSMUST00000153250.5, ENSMUST00000153250.6, ENSMUST00000153250.7, ENSMUST00000153250.8, Q3V1K1, Q3V1K1_MOUSE, uc288gmx.1, uc288gmx.2
UCSC ID: ENSMUST00000153250.9
RefSeq Accession: NM_011041
Protein: Q3V1K1

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