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Gene Detail
paired box 9
Synonyms Pax-9
Feature Type protein coding gene
Genetic Map
Chromosome 12
24.53 cM
Detailed Genetic Map ± 1 cM

Mapping data(6)
Sequence Map
Chr12:56691767-56712707 bp, + strand
From VEGA annotation of GRCm38

  20941 bp   ±  kb flank

VEGA Genome Browser | Ensembl Genome Browser | UCSC Browser | NCBI Map Viewer

Mouse Genome Browser
HomoloGene:31360  Vertebrate Homology Class
1 human; 1 mouse; 1 rat; 1 chimpanzee; 1 rhesus macaque; 1 cattle; 1 dog; 1 chicken; 1 western clawed frog; 1 zebrafish

Protein SuperFamily: paired box protein PAX
Gene Tree: Pax9

Human Homolog PAX9, paired box 9
NCBI Gene ID 5083
neXtProt AC  NX_P55771
Human Synonyms  STHAG3
Human Chr (Location)  14q13.3; chr14:36657568-36677807 (+)  GRCh38
Disease Associations  (1) Diseases Associated with Human PAX9
alleles, and
All mutations/alleles(8) : Targeted(8)
Incidental mutations (data from Mutagenetix , APF )
Homozygous inactivation of this gene results in abnormal tooth development and absent teeth and may lead to lack of pharyngeal pouch derivatives, athymia, craniofacial and limb anomalies, a small tympanic ring, various defects of the skeleton and musculature, and neonatal lethality.
Human Diseases Modeled Using Mouse Pax9 (1)    Alleles Annotated to Human Diseases(2)   
Pax9 interacts with 385 markers (Mir1a-1, Mir1a-2, Mir1b, ...)
Gene Ontology
All GO classifications: (21 annotations)
Process cellular response to growth factor stimulus, endoderm development, ...
Component nucleus, transcription factor complex
Function DNA binding, protein binding, ...
External Resources: FuncBase
Literature Summary: (133 records)
Data Summary: Results (373)    Tissues (203)    Images (120)
Theiler Stages: 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28
Assay TypeResults
Immunohistochemistry 5
RNA in situ 349
In situ reporter (knock in) 2
Northern blot 8
RNase protection 9
cDNA source data(11)
External Resources: Allen Institute   GEO   Expression Atlas
All nucleic(26) Genomic(2) cDNA(13) Primer pair(1) Other(10)
Microarray probesets(5)
Other database
VEGA Gene ModelOTTMUSG00000023206 (Evidence)
Ensembl Gene ModelENSMUSG00000001497 (Evidence)
Entrez Gene18511 (Evidence)
NIA Mouse Gene IndexU013975
Consensus CDS ProjectCCDS25924.1
International Mouse Knockout Project StatusPax9
Representative SequencesLengthStrain/SpeciesFlank
genomic OTTMUSG00000023206 VEGA Gene Model | MGI Sequence Detail 20941 C57BL/6J ±  kb
transcript OTTMUST00000056158 VEGA | MGI Sequence Detail 4232 Not Applicable 
polypeptide OTTMUSP00000026953 VEGA | MGI Sequence Detail 342 Not Applicable 

For the selected sequences
All sequences(33) RefSeq(10) UniProt(3)
Polymorphisms RFLP(2) : SNPs within 2kb(160 from dbSNP Build 137)
InterPro IPR009057 Homeodomain-like
InterPro IPR001523 Paired domain
InterPro IPR011991 Winged helix-turn-helix DNA-binding domain
Protein Ontology PR:000012321 paired box protein Pax-9
References (Earliest) J:4336 Stapleton P, et al., Chromosomal localization of seven PAX genes and cloning of a novel family member, PAX-9. Nat Genet. 1993 Apr;3(4):292-8
(Latest) J:207523 Edlund RK, et al., Foxi transcription factors promote pharyngeal arch development by regulating formation of FGF signaling centers. Dev Biol. 2014 Jun 1;390(1):1-13
All references(173)
Disease annotation references (1)
accession IDs
MGD-MRK-13152, MGD-MRK-13161

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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last database update
MGI 5.19
The Jackson Laboratory