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Aliases for PAX9 Gene

Aliases for PAX9 Gene

  • Paired Box 9 2 3 5
  • Paired Domain Gene 9 3
  • Paired Box Gene 9 2
  • STHAG3 3

External Ids for PAX9 Gene

Previous GeneCards Identifiers for PAX9 Gene

  • GC14P034511
  • GC14P030988
  • GC14P035120
  • GC14P036200
  • GC14P037126
  • GC14P017241

Summaries for PAX9 Gene

Entrez Gene Summary for PAX9 Gene

  • 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]

GeneCards Summary for PAX9 Gene

PAX9 (Paired Box 9) is a Protein Coding gene. Diseases associated with PAX9 include tooth agenesis, selective, 3 and tooth agenesis. GO annotations related to this gene include RNA polymerase II regulatory region sequence-specific DNA binding and transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding. An important paralog of this gene is PAX4.

UniProtKB/Swiss-Prot for PAX9 Gene

  • Transcription factor required for normal development of thymus, parathyroid glands, ultimobranchial bodies, teeth, skeletal elements of skull and larynx as well as distal limbs.

Gene Wiki entry for PAX9 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PAX9 Gene

Genomics for PAX9 Gene

Regulatory Elements for PAX9 Gene

Genomic Location for PAX9 Gene

36,657,568 bp from pter
36,679,715 bp from pter
22,148 bases
Plus strand

Genomic View for PAX9 Gene

Genes around PAX9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PAX9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PAX9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PAX9 Gene

Proteins for PAX9 Gene

  • Protein details for PAX9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Paired box protein Pax-9
    Protein Accession:
    Secondary Accessions:
    • Q99582
    • Q9UQR4

    Protein attributes for PAX9 Gene

    341 amino acids
    Molecular mass:
    36310 Da
    Quaternary structure:
    • Interacts with KDM5B.

neXtProt entry for PAX9 Gene

Proteomics data for PAX9 Gene at MOPED

Post-translational modifications for PAX9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PAX9 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PAX9 (PAX9)

No data available for DME Specific Peptides for PAX9 Gene

Domains & Families for PAX9 Gene

Gene Families for PAX9 Gene

Protein Domains for PAX9 Gene

Suggested Antigen Peptide Sequences for PAX9 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 paired domain.
  • Contains 1 paired domain.
genes like me logo Genes that share domains with PAX9: view

Function for PAX9 Gene

Molecular function for PAX9 Gene

GENATLAS Biochemistry:
paired box (DNA binding) containing protein 9,with homeo domain,expressed in esophagus
UniProtKB/Swiss-Prot Function:
Transcription factor required for normal development of thymus, parathyroid glands, ultimobranchial bodies, teeth, skeletal elements of skull and larynx as well as distal limbs.

Gene Ontology (GO) - Molecular Function for PAX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 12657635
genes like me logo Genes that share ontologies with PAX9: view
genes like me logo Genes that share phenotypes with PAX9: view

Human Phenotype Ontology for PAX9 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PAX9 Gene

MGI Knock Outs for PAX9:

Animal Model Products

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PAX9 Gene

Localization for PAX9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PAX9 Gene

Subcellular locations from

Jensen Localization Image for PAX9 Gene COMPARTMENTS Subcellular localization image for PAX9 gene
Compartment Confidence
nucleus 5

No data available for Gene Ontology (GO) - Cellular Components for PAX9 Gene

Pathways & Interactions for PAX9 Gene

SuperPathways for PAX9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PAX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042481 regulation of odontogenesis IEA --
GO:0045892 negative regulation of transcription, DNA-templated IDA 12657635
GO:0045944 positive regulation of transcription from RNA polymerase II promoter IEA --
GO:0060325 face morphogenesis IEA --
genes like me logo Genes that share ontologies with PAX9: view

No data available for Pathways by source and SIGNOR curated interactions for PAX9 Gene

Drugs & Compounds for PAX9 Gene

(1) Drugs for PAX9 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with PAX9: view

Transcripts for PAX9 Gene

Unigene Clusters for PAX9 Gene

Paired box 9:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PAX9 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b · 6c
SP1: - -
SP3: - - -

Relevant External Links for PAX9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PAX9 Gene

mRNA expression in normal human tissues for PAX9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PAX9 Gene

This gene is overexpressed in Esophagus - Mucosa (x33.1) and Minor Salivary Gland (x9.3).

Protein differential expression in normal tissues from HIPED for PAX9 Gene

This gene is overexpressed in Liver, secretome (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PAX9 Gene

SOURCE GeneReport for Unigene cluster for PAX9 Gene Hs.132576

genes like me logo Genes that share expression patterns with PAX9: view

Protein tissue co-expression partners for PAX9 Gene

Primer Products

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for PAX9 Gene

Orthologs for PAX9 Gene

This gene was present in the common ancestor of animals.

Orthologs for PAX9 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia PAX9 35
  • 93.84 (n)
  • 98.24 (a)
PAX9 36
  • 98 (a)
(Canis familiaris)
Mammalia PAX9 35
  • 92.96 (n)
  • 97.65 (a)
PAX9 36
  • 97 (a)
(Mus musculus)
Mammalia Pax9 35
  • 92.77 (n)
  • 98.53 (a)
Pax9 16
Pax9 36
  • 98 (a)
(Pan troglodytes)
Mammalia PAX9 35
  • 98.14 (n)
  • 97.94 (a)
PAX9 36
  • 99 (a)
(Rattus norvegicus)
Mammalia Pax9 35
  • 91.59 (n)
  • 97.65 (a)
(Monodelphis domestica)
Mammalia PAX9 36
  • 94 (a)
(Ornithorhynchus anatinus)
Mammalia PAX9 36
  • 90 (a)
(Gallus gallus)
Aves PAX9 35
  • 82.75 (n)
  • 90 (a)
PAX-9 36
  • 88 (a)
(Anolis carolinensis)
Reptilia PAX9 36
  • 90 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pax9 35
  • 77.31 (n)
  • 84.94 (a)
African clawed frog
(Xenopus laevis)
Amphibia pax9-A 35
(Danio rerio)
Actinopterygii pax9 35
  • 67.45 (n)
  • 74.19 (a)
pax9 36
  • 74 (a)
fruit fly
(Drosophila melanogaster)
Insecta Poxm 37
  • 85 (a)
Poxn 37
  • 67 (a)
sv 37
  • 70 (a)
Poxm 36
  • 44 (a)
(Caenorhabditis elegans)
Secernentea egl-38 37
  • 67 (a)
K06B9.5 37
  • 55 (a)
K07C11.1 37
  • 72 (a)
pax-1 36
  • 37 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13184 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 40 (a)
Species with no ortholog for PAX9:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PAX9 Gene

Gene Tree for PAX9 (if available)
Gene Tree for PAX9 (if available)

Paralogs for PAX9 Gene

Paralogs for PAX9 Gene

(8) SIMAP similar genes for PAX9 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with PAX9: view

Variants for PAX9 Gene

Sequence variations from dbSNP and Humsavar for PAX9 Gene

SNP ID Clin Chr 14 pos Sequence Context AA Info Type
VAR_015698 Tooth agenesis selective 3 (STHAG3)
rs4904210 - 36,666,548(+) CGCAC(C/G)CGGTG reference, missense
rs1955734 -- 36,669,423(+) TAACT(C/T)GAATG intron-variant
rs2295218 -- 36,665,286(+) GCAAC(A/T)TTTCC intron-variant
rs2295219 -- 36,665,712(+) ATATA(C/T)ATTTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PAX9 Gene

Variant ID Type Subtype PubMed ID
nsv819585 CNV Gain 19587683
nsv819749 CNV Loss 19587683

Variation tolerance for PAX9 Gene

Residual Variation Intolerance Score: 26.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.23; 84.95% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PAX9 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PAX9 Gene

Disorders for PAX9 Gene

MalaCards: The human disease database

(6) MalaCards diseases for PAX9 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
tooth agenesis, selective, 3
  • hypodontia/oligodontia 3
tooth agenesis
  • familial tooth agenesis
  • anodontia nos
cleft lip
  • cheiloschisis
mouth disease
  • mouth diseases
- elite association - COSMIC cancer census association via MalaCards
Search PAX9 in MalaCards View complete list of genes associated with diseases


  • Tooth agenesis selective 3 (STHAG3) [MIM:604625]: A form of selective tooth agenesis, a common anomaly characterized by the congenital absence of one or more teeth. Selective tooth agenesis without associated systemic disorders has sometimes been divided into 2 types: oligodontia, defined as agenesis of 6 or more permanent teeth, and hypodontia, defined as agenesis of less than 6 teeth. The number in both cases does not include absence of third molars (wisdom teeth). {ECO:0000269 PubMed:12786960}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PAX9

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with PAX9: view

No data available for Genatlas for PAX9 Gene

Publications for PAX9 Gene

  1. Chromosomal localization of seven PAX genes and cloning of a novel family member, PAX-9. (PMID: 7981748) Stapleton P. … Busslinger M. (Nat. Genet. 1993) 2 3 4 67
  2. A 223-kb de novo deletion of PAX9 in a patient with oligodontia. (PMID: 20485064) Haldeman-Englert C.R. … Ming J.E. (J Craniofac Surg 2010) 3 23
  3. Tooth dimensions in hypodontia with a known PAX9 mutation. (PMID: 18653171) Brook A.H. … Smith R.N. (Arch. Oral Biol. 2009) 3 23
  4. Identification and functional analysis of two novel PAX9 mutations. (PMID: 18701815) Wang Y. … Kapadia H. (Cells Tissues Organs (Print) 2009) 3 23
  5. Maternal transmission effects of the PAX genes among cleft case-parent trios from four populations. (PMID: 19142206) Sull J.W. … Beaty T.H. (Eur. J. Hum. Genet. 2009) 3 23

Products for PAX9 Gene

Sources for PAX9 Gene

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