Mouse Gene Pax9 (uc007npi.1) Description and Page Index
  Description: paired box protein Pax-9
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. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AK132404.1, X84000.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMN00849375, SAMN00849376 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: mm9 chr12:57,796,626-57,812,217 Size: 15,592 Total Exon Count: 4 Strand: +
Coding Region
   Position: mm9 chr12:57,796,848-57,810,894 Size: 14,047 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsCTDMicroarray ExpressionRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesModel Information
Data last updated: 2011-03-02

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:57,796,626-57,812,217)mRNA (may differ from genome)Protein (342 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAllen Brain Atlas
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkMGIPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: SubName: Full=Putative uncharacterized protein;
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Contains 1 paired domain.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  Microarray Expression Data
Expression ratio colors:

GNF Expression Atlas 2 Data from GNF1M Mouse Chip


Rinn et. al Sex Gene Expression Data on MOE430A Chip


GNF Expression Atlas Data from U74a Mouse Chip


Affymetrix All Exon Microarrays


-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -77.40222-0.349 Picture PostScript Text
3' UTR -328.021323-0.248 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

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on Q3V1K1
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 BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
Protein SequenceProtein SequenceProtein SequenceProtein Sequence  

-  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.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_011041, NP_035171, Q3V1K1, Q3V1K1_MOUSE
UCSC ID: uc007npi.1
RefSeq Accession: NM_011041
Protein: Q3V1K1 CCDS: CCDS25924.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_011041.2
exon count: 4CDS single in 3' UTR: no RNA size: 2574
ORF size: 1029CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2061.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.