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Aliases for PAX3 Gene

Aliases for PAX3 Gene

  • Paired Box 3 2 3
  • HUP2 3 4 6
  • CDHS 3 6
  • WS3 3 6
  • WS1 3 6
  • Paired Box Gene 3 (Waardenburg Syndrome 1) 2
  • Paired Box Homeotic Gene 3 3
  • Paired Box Protein Pax-3 3
  • Paired Domain Gene HuP2 3
  • Waardenburg Syndrome 1 2
  • Paired Domain Gene 3 3

External Ids for PAX3 Gene

Previous HGNC Symbols for PAX3 Gene

  • WS1

Previous GeneCards Identifiers for PAX3 Gene

  • GC02M221089
  • GC02M221788
  • GC02M223029
  • GC02M223267
  • GC02M222890
  • GC02M222772
  • GC02M214918
  • GC02M223064

Summaries for PAX3 Gene

Entrez Gene Summary for PAX3 Gene

  • This gene is a member of the paired box (PAX) family of transcription factors. Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. These genes play critical roles during fetal development. Mutations in paired box gene 3 are associated with Waardenburg syndrome, craniofacial-deafness-hand syndrome, and alveolar rhabdomyosarcoma. The translocation t(2;13)(q35;q14), which represents a fusion between PAX3 and the forkhead gene, is a frequent finding in alveolar rhabdomyosarcoma. Alternative splicing results in transcripts encoding isoforms with different C-termini. [provided by RefSeq, Jul 2008]

GeneCards Summary for PAX3 Gene

PAX3 (Paired Box 3) is a Protein Coding gene. Diseases associated with PAX3 include waardenburg syndrome, type 1 and waardenburg syndrome, type 3. Among its related pathways are Neural Crest Differentiation and Transcriptional misregulation in cancer. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and chromatin binding. An important paralog of this gene is PAX4.

UniProtKB/Swiss-Prot for PAX3 Gene

  • Transcription factor that may regulate cell proliferation, migration and apoptosis. Involved in neural development and myogenesis.

Gene Wiki entry for PAX3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PAX3 Gene

Genomics for PAX3 Gene

Regulatory Elements for PAX3 Gene

Genomic Location for PAX3 Gene

222,199,887 bp from pter
222,298,996 bp from pter
99,110 bases
Minus strand

Genomic View for PAX3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PAX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PAX3 Gene

Proteins for PAX3 Gene

  • Protein details for PAX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Paired box protein Pax-3
    Protein Accession:
    Secondary Accessions:
    • G5E9C1
    • Q16448
    • Q494Z3
    • Q494Z4
    • Q53T90
    • Q6GSJ9
    • Q86UQ2
    • Q86UQ3

    Protein attributes for PAX3 Gene

    479 amino acids
    Molecular mass:
    52968 Da
    Quaternary structure:
    • Can bind to DNA as a homodimer or a heterodimer with PAX7. Interacts with PAXBP1; the interaction links PAX3 to a WDR5-containing histone methyltransferase complex. Interacts with DAXX. Interacts with TBX18.

    Three dimensional structures from OCA and Proteopedia for PAX3 Gene

    Alternative splice isoforms for PAX3 Gene

neXtProt entry for PAX3 Gene

Proteomics data for PAX3 Gene at MOPED

Post-translational modifications for PAX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PAX3 Gene

Domains for PAX3 Gene

Gene Families for PAX3 Gene

  • PAX :Paired boxes
  • PRD :Homeoboxes / PRD class

Graphical View of Domain Structure for InterPro Entry



  • P23760
  • Contains 1 homeobox DNA-binding domain.
  • Contains 1 paired domain.
  • Belongs to the paired homeobox family.
genes like me logo Genes that share domains with PAX3: view

Function for PAX3 Gene

Molecular function for PAX3 Gene

GENATLAS Biochemistry: paired box (DNA binding) containing protein 3 (HuP2),with an homeo domain,mouse Pax3,splotch homolog,involved in neurogenesis and in melanogenesis through MITF transactivation ? and other processes (see BARMS2,WS1,WS2,WS3),interacting with HIRA,activating MYOD1 gene
UniProtKB/Swiss-Prot Function: Transcription factor that may regulate cell proliferation, migration and apoptosis. Involved in neural development and myogenesis.

Gene Ontology (GO) - Molecular Function for PAX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0003682 chromatin binding IEA --
GO:0003700 sequence-specific DNA binding transcription factor activity TAS 9500554
GO:0003705 RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity IEA --
GO:0005515 protein binding IPI 11029584
genes like me logo Genes that share ontologies with PAX3: view
genes like me logo Genes that share phenotypes with PAX3: view

Animal Models for PAX3 Gene

MGI Knock Outs for PAX3:

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for PAX3 Gene

Localization for PAX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PAX3 Gene

Subcellular locations from

Jensen Localization Image for PAX3 Gene COMPARTMENTS Subcellular localization image for PAX3 gene
Compartment Confidence
nucleus 5
cytoskeleton 2
extracellular 1

Gene Ontology (GO) - Cellular Components for PAX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus --
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with PAX3: view

Pathways for PAX3 Gene

genes like me logo Genes that share pathways with PAX3: view

Pathways by source for PAX3 Gene

1 Qiagen pathway for PAX3 Gene
1 Cell Signaling Technology pathway for PAX3 Gene
1 KEGG pathway for PAX3 Gene

Gene Ontology (GO) - Biological Process for PAX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IEA --
GO:0001755 neural crest cell migration IEA --
GO:0001843 neural tube closure IEA --
GO:0006325 chromatin organization TAS --
GO:0006355 regulation of transcription, DNA-templated --
genes like me logo Genes that share ontologies with PAX3: view

Compounds for PAX3 Gene

(6) Novoseek inferred chemical compound relationships for PAX3 Gene

Compound -log(P) Hits PubMed IDs
n-ethylmaleimide 5.73 1
oligonucleotide 0 2
tyrosine 0 2
cysteine 0 3
cycloheximide 0 1
genes like me logo Genes that share compounds with PAX3: view

Transcripts for PAX3 Gene

Unigene Clusters for PAX3 Gene

Paired box 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PAX3 Gene

No ASD Table

Relevant External Links for PAX3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PAX3 Gene

mRNA expression in normal human tissues for PAX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PAX3 Gene

This gene is overexpressed in Minor Salivary Gland (12.3), Brain - Cerebellum (6.8), and Muscle - Skeletal (4.0).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for PAX3 Gene

SOURCE GeneReport for Unigene cluster for PAX3 Gene Hs.42146

genes like me logo Genes that share expressions with PAX3: view

No data available for mRNA Expression by UniProt/SwissProt for PAX3 Gene

Orthologs for PAX3 Gene

This gene was present in the common ancestor of animals.

Orthologs for PAX3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PAX3 35
  • 99.59 (n)
  • 100 (a)
PAX3 36
  • 100 (a)
(Bos Taurus)
Mammalia PAX3 35
  • 93.72 (n)
  • 99.38 (a)
PAX3 36
  • 99 (a)
(Canis familiaris)
Mammalia PAX3 35
  • 90.64 (n)
  • 97.92 (a)
PAX3 36
  • 96 (a)
(Mus musculus)
Mammalia Pax3 35
  • 91.79 (n)
  • 98.76 (a)
Pax3 16
Pax3 36
  • 99 (a)
(Monodelphis domestica)
Mammalia PAX3 36
  • 98 (a)
(Ornithorhynchus anatinus)
Mammalia PAX3 36
  • 97 (a)
(Rattus norvegicus)
Mammalia Pax3 35
  • 90.75 (n)
  • 98.76 (a)
(Gallus gallus)
Aves PAX3 35
  • 85.51 (n)
  • 96.69 (a)
PAX3 36
  • 89 (a)
(Anolis carolinensis)
Reptilia PAX3 36
  • 98 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pax3 35
  • 81.34 (n)
  • 92.81 (a)
(Danio rerio)
Actinopterygii pax3a 35
  • 71.33 (n)
  • 79.24 (a)
pax3a 36
  • 72 (a)
pax3b 36
  • 68 (a)
fruit fly
(Drosophila melanogaster)
Insecta gsb 36
  • 44 (a)
gsb-n 36
  • 43 (a)
prd 36
  • 34 (a)
Poxn 37
  • 67 (a)
(Caenorhabditis elegans)
Secernentea pax-3 36
  • 45 (a)
K07C11.1 37
  • 61 (a)
egl-38 37
  • 59 (a)
K06B9.5 37
  • 69 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 36 (a)
Species with no ortholog for PAX3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 PAX3 Gene

Gene Tree for PAX3 (if available)
Gene Tree for PAX3 (if available)

Paralogs for PAX3 Gene

Paralogs for PAX3 Gene

Selected SIMAP similar genes for PAX3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with PAX3: view

Variants for PAX3 Gene

Sequence variations from dbSNP and Humsavar for PAX3 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type MAF
rs752172 -- 222,227,498(+) gaggc(A/G)ggagg intron-variant
rs762606 -- 222,202,487(-) TTTAT(C/G)ACTAG intron-variant
rs930140 -- 222,283,573(-) TCTGA(A/G)GATTG intron-variant
rs984042 -- 222,237,144(-) TCCTA(A/G)GATTG intron-variant
rs984043 -- 222,237,007(-) ATAGA(G/T)TCAAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PAX3 Gene

Variant ID Type Subtype PubMed ID
nsv834549 CNV Gain 17160897
nsv834550 CNV Gain 17160897
nsv516764 CNV Loss 19592680

Relevant External Links for PAX3 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PAX3 Gene

Disorders for PAX3 Gene

(4) OMIM Diseases for PAX3 Gene (606597)


  • Waardenburg syndrome 1 (WS1) [MIM:193500]: WS1 is an autosomal dominant disorder characterized by non-progressive sensorineural deafness, pigmentary disturbances such as frontal white blaze of hair, heterochromia of irides, white eyelashes, leukoderma, and wide bridge of nose owing to lateral displacement of the inner canthus of each eye (dystopia canthorum). WS1 shows variable clinical expression and some affected individuals do not manifest hearing impairment or iris pigmentation disturbances. Dystopia canthorum is the most consistent sign and is found in 98% of the patients. {ECO:0000269 PubMed:10779847, ECO:0000269 PubMed:12949970, ECO:0000269 PubMed:1303193, ECO:0000269 PubMed:1347148, ECO:0000269 PubMed:1347149, ECO:0000269 PubMed:7825605, ECO:0000269 PubMed:7833953, ECO:0000269 PubMed:7981674, ECO:0000269 PubMed:8447316, ECO:0000269 PubMed:8490648, ECO:0000269 PubMed:8533800, ECO:0000269 PubMed:8589691, ECO:0000269 PubMed:8845842, ECO:0000269 PubMed:9067759, ECO:0000269 PubMed:9452070, ECO:0000269 PubMed:9541113, ECO:0000269 Ref.34}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Waardenburg syndrome 3 (WS3) [MIM:148820]: WS3 is an autosomal dominant disorder characterized by sensorineural deafness, pigmentary disturbances, dystopia canthorum and limb anomalies such as hypoplasia of the musculoskeletal system, flexion contractures, fusion of the carpal bones, syndactylies. {ECO:0000269 PubMed:12949970, ECO:0000269 PubMed:7726174, ECO:0000269 Ref.35}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Craniofacial-deafness-hand syndrome (CDHS) [MIM:122880]: Thought to be an autosomal dominant disease which comprises absence or hypoplasia of the nasal bones, hypoplastic maxilla, small and short nose with thin nares, limited movement of the wrist, short palpebral fissures, ulnar deviation of the fingers, hypertelorism and profound sensory-neural deafness. {ECO:0000269 PubMed:8664898}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Rhabdomyosarcoma 2 (RMS2) [MIM:268220]: A form of rhabdomyosarcoma, a highly malignant tumor of striated muscle derived from primitive mesenchymal cells and exhibiting differentiation along rhabdomyoblastic lines. Rhabdomyosarcoma is one of the most frequently occurring soft tissue sarcomas and the most common in children. It occurs in four forms: alveolar, pleomorphic, embryonal and botryoidal rhabdomyosarcomas. Note=The gene represented in this entry is involved in disease pathogenesis. A chromosomal aberration involving PAX3 is found in rhabdomyosarcoma. Translocation (2;13)(q35;q14) with FOXO1. The resulting protein is a transcriptional activator.
  • Note=A chromosomal aberration involving PAX3 is a cause of rhabdomyosarcoma. Translocation t(2;2)(q35;p23) with NCOA1 generates the NCOA1-PAX3 oncogene consisting of the N-terminus part of PAX3 and the C-terminus part of NCOA1. The fusion protein acts as a transcriptional activator. Rhabdomyosarcoma is the most common soft tissue carcinoma in childhood, representing 5-8% of all malignancies in children.

(33) Novoseek inferred disease relationships for PAX3 Gene

Disease -log(P) Hits PubMed IDs
waardenburgs syndrome 97.1 52
waardenburg syndrome, type i 94.8 12
rhabdomyosarcoma alveolar 94.5 33
craniofacial-deafness-hand syndrome 93.1 4
klein-waardenburg syndrome 91.3 1

Relevant External Links for PAX3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with PAX3: view

Publications for PAX3 Gene

  1. Isolation of two isoforms of the PAX3 gene transcripts and their tissue-specific alternative expression in human adult tissues. (PMID: 7545913) Tsukamoto K. … Niikawa N. (Hum. Genet. 1994) 3 4 23
  2. A frameshift mutation in the HuP2 paired domain of the probable human homolog of murine Pax-3 is responsible for Waardenburg syndrome type 1 in an Indonesian family. (PMID: 1303193) Morell R. … Asher J.H. Jr. (Hum. Mol. Genet. 1992) 3 4 23
  3. Waardenburg's syndrome patients have mutations in the human homologue of the Pax-3 paired box gene. (PMID: 1347148) Tassabehji M. … Strachan T. (Nature 1992) 3 4 23
  4. Homozygosity for Waardenburg syndrome. (PMID: 7726174) Zlotogora J. … Abeliovich D. (Am. J. Hum. Genet. 1995) 3 4 23
  5. Further elucidation of the genomic structure of PAX3, and identification of two different point mutations within the PAX3 homeobox that cause Waardenburg syndrome type 1 in two families. (PMID: 7825605) Lalwani A.K. … Wilcox E.R. (Am. J. Hum. Genet. 1995) 3 4 23

Products for PAX3 Gene

Sources for PAX3 Gene

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