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Aliases for PAX9 Gene

Aliases for PAX9 Gene

  • Paired Box 9 2 3 5
  • Paired Box Protein Pax-9 3
  • 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. Among its related pathways are Wnt / Hedgehog / Notch and Mesodermal Commitment Pathway. Gene Ontology (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 DNA binding. An important paralog of this gene is PAX1.

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

Additional gene information for PAX9 Gene

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

Genomics for PAX9 Gene

GeneHancer (GH) Regulatory Elements for PAX9 Gene

Promoters and enhancers for PAX9 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH14I036661 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE dbSUPER 558.3 +4.5 4473 2 PKNOX1 ATF1 SIN3A ATF7 ZNF202 SP3 NFYC ZNF623 PBX2 CTCF LOC105370455 PAX9 LOC644584 NKX2-8 RPL29P3 ENSG00000258690
GH14I036656 Enhancer 0.8 ENCODE dbSUPER 550.8 -1.0 -996 0.7 CTCF ZNF687 RNF2 SUZ12 SIN3A GATA3 MBD1 ZNF143 CTBP2 BCL6 PAX9 NKX2-8 RPL29P3 LOC105370455 RN7SKP257 GC14M036594
GH14I036655 Enhancer 0.8 ENCODE dbSUPER 550.8 -1.5 -1507 0.2 CTCF ZNF687 RNF2 SUZ12 SIN3A RAD21 GATA3 MBD1 ZNF143 CTBP2 PAX9 NKX2-8 RPL29P3 LOC105370455 RN7SKP257 GC14M036594 ENSG00000283098
GH14I036657 Promoter/Enhancer 0.8 EPDnew dbSUPER 550.8 0.0 -19 0.1 EZH2 PAX9 LOC105370455 RN7SKP257 GC14M036594
GH14I036658 Enhancer 0.7 ENCODE dbSUPER 550.8 +0.4 363 0.2 ZNF202 SUZ12 CTBP2 EZH2 PAX9 LOC105370455
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PAX9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PAX9 gene promoter:

Genomic Locations for PAX9 Gene

Genomic Locations for PAX9 Gene
chr14:36,657,568-36,679,715
(GRCh38/hg38)
Size:
22,148 bases
Orientation:
Plus strand
chr14:37,126,773-37,148,920
(GRCh37/hg19)

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:
    P55771-PAX9_HUMAN
    Recommended name:
    Paired box protein Pax-9
    Protein Accession:
    P55771
    Secondary Accessions:
    • Q99582
    • Q9UQR4

    Protein attributes for PAX9 Gene

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

neXtProt entry for PAX9 Gene

Post-translational modifications for PAX9 Gene

No Post-translational modifications

Other Protein References for PAX9 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

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

No data available for DME Specific Peptides for PAX9 Gene

Domains & Families for PAX9 Gene

Gene Families for PAX9 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for PAX9 Gene

Suggested Antigen Peptide Sequences for PAX9 Gene

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for PAX9 Gene

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.

Phenotypes From GWAS Catalog for PAX9 Gene

Gene Ontology (GO) - Molecular Function for PAX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IEA --
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IEA --
GO:0003677 DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IEA --
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:

Clone Products

  • Addgene plasmids for PAX9

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

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PAX9 gene
Compartment Confidence
nucleus 5
extracellular 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (3)
  • Mitochondria (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PAX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with PAX9: view

Pathways & Interactions for PAX9 Gene

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

Pathways by source for PAX9 Gene

1 Cell Signaling Technology pathway for PAX9 Gene
1 BioSystems pathway for PAX9 Gene

Gene Ontology (GO) - Biological Process for PAX9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006366 transcription by RNA polymerase II IEA --
GO:0007275 multicellular organism development IEA --
GO:0007492 endoderm development IEA --
genes like me logo Genes that share ontologies with PAX9: view

No data available for 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:

Clone Products

  • Addgene plasmids for PAX9

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

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b · 6c
SP1: - -
SP2:
SP3: - - -

Relevant External Links for PAX9 Gene

GeneLoc Exon Structure for
PAX9
ECgene alternative splicing isoforms for
PAX9

Expression for PAX9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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



Protein tissue co-expression partners for PAX9 Gene

NURSA nuclear receptor signaling pathways regulating expression of PAX9 Gene:

PAX9

SOURCE GeneReport for Unigene cluster for PAX9 Gene:

Hs.132576

Evidence on tissue expression from TISSUES for PAX9 Gene

  • Lung(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PAX9 Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • skeleton
Organs:
Head and neck:
  • chin
  • face
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • skull
  • tooth
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with PAX9: view

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
chimpanzee
(Pan troglodytes)
Mammalia PAX9 33 34
  • 98.14 (n)
oppossum
(Monodelphis domestica)
Mammalia PAX9 34
  • 94 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PAX9 33 34
  • 93.84 (n)
dog
(Canis familiaris)
Mammalia PAX9 33 34
  • 92.96 (n)
mouse
(Mus musculus)
Mammalia Pax9 33 16 34
  • 92.77 (n)
rat
(Rattus norvegicus)
Mammalia Pax9 33
  • 91.59 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PAX9 34
  • 90 (a)
OneToOne
chicken
(Gallus gallus)
Aves PAX-9 34
  • 88 (a)
OneToOne
PAX9 33
  • 82.75 (n)
lizard
(Anolis carolinensis)
Reptilia PAX9 34
  • 90 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pax9 33
  • 77.31 (n)
African clawed frog
(Xenopus laevis)
Amphibia pax9-A 33
zebrafish
(Danio rerio)
Actinopterygii pax9 33 34
  • 67.45 (n)
fruit fly
(Drosophila melanogaster)
Insecta Poxm 35 34
  • 85 (a)
sv 35
  • 70 (a)
Poxn 35
  • 67 (a)
worm
(Caenorhabditis elegans)
Secernentea K07C11.1 35
  • 72 (a)
egl-38 35
  • 67 (a)
K06B9.5 35
  • 55 (a)
pax-1 34
  • 37 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 40 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13184 33
Species where no ortholog for PAX9 was found in the sources mined by GeneCards:
  • 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

ENSEMBL:
Gene Tree for PAX9 (if available)
TreeFam:
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 Variation AA Info Type
rs104894467 pathogenic, Tooth agenesis, selective, 3 36,663,232(+) A/C/T coding_sequence_variant, missense_variant, stop_gained
rs104894468 pathogenic, Tooth agenesis, selective, 3 36,663,151(+) A/T coding_sequence_variant, missense_variant
rs104894469 pathogenic, Tooth agenesis, selective, 3, Tooth agenesis, selective, 3 (STHAG3) [MIM:604625] 36,663,043(+) G/A/T coding_sequence_variant, missense_variant
rs116676854 likely-benign, benign, Selective tooth agenesis, Partial congenital absence of teeth 36,663,515(+) C/A/G coding_sequence_variant, missense_variant
rs11847165 likely-benign, Selective tooth agenesis 36,677,270(+) C/T 3_prime_UTR_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
nsv952826 CNV deletion 24416366

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)

Additional Variant Information for PAX9 Gene

Human Gene Mutation Database (HGMD)
PAX9
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PAX9

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

Disorders for PAX9 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
tooth agenesis, selective, 3
  • sthag3
tooth agenesis
  • familial tooth agenesis
anodontia
  • anodontia of permanent dentition
tooth size
chromosome 14q11-q22 deletion syndrome
  • 14q11.2 microdeletion syndrome
- elite association - COSMIC cancer census association via MalaCards
Search PAX9 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

PAX9_HUMAN
  • 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.

Additional Disease Information for PAX9

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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. Maternal transmission effects of the PAX genes among cleft case-parent trios from four populations. (PMID: 19142206) Sull JW … Beaty TH (European journal of human genetics : EJHG 2009) 3 22 44 58
  2. PAX9 polymorphisms and susceptibility to sporadic tooth agenesis: a case-control study in southeast China. (PMID: 18353002) Pan Y … Huang Y (European journal of oral sciences 2008) 3 22 44 58
  3. PAX9 and TGFB3 are linked to susceptibility to nonsyndromic cleft lip with or without cleft palate in the Japanese: population-based and family-based candidate gene analyses. (PMID: 16247549) Ichikawa E … Yoshiura K (Journal of human genetics 2006) 3 22 44 58
  4. Association between PAX-9 promoter polymorphisms and hypodontia in humans. (PMID: 16137495) Peres RC … Line SR (Archives of oral biology 2005) 3 22 44 58
  5. A novel missense mutation in the paired domain of PAX9 causes non-syndromic oligodontia. (PMID: 14689302) Jumlongras D … Olsen BR (Human genetics 2004) 3 22 44 58

Products for PAX9 Gene

Sources for PAX9 Gene

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