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PAX3 paired box 3 [ Homo sapiens (human) ]

Gene ID: 5077, updated on 12-Dec-2014
Official Symbol
PAX3provided by HGNC
Official Full Name
paired box 3provided by HGNC
Primary source
HGNC:HGNC:8617
See related
Ensembl:ENSG00000135903; HPRD:09421; MIM:606597; Vega:OTTHUMG00000133157
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
WS1; WS3; CDHS; HUP2
Summary
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]
See PAX3 in Epigenomics, MapViewer
Location:
2q35
Exon count:
10
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 2 NC_000002.12 (222199887..222298996, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (223064606..223163715, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene heat shock 70kDa protein 9 pseudogene 1 Neighboring gene ribosomal protein L23a pseudogene 28 Neighboring gene coiled-coil domain containing 140 Neighboring gene uncharacterized LOC440934 Neighboring gene sphingosine-1-phosphate phosphatase 2 Neighboring gene Nanog homeobox pseudogene 2

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Craniofacial deafness hand syndrome
MedGen: C1852510 OMIM: 122880 GeneReviews: Not available
Compare labs
Klein-Waardenberg's syndrome
MedGen: C0342680 OMIM: 148820 GeneReviews: Not available
Compare labs
Rhabdomyosarcoma alveolar
MedGen: C0206655 OMIM: 268220 GeneReviews: Not available
Compare labs
Waardenburg syndrome type 1
MedGen: C1847800 OMIM: 193500 GeneReviews: Waardenburg Syndrome Type I
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-11-02)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-11-02)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
NHGRI GWA Catalog
Genome-wide association study of three-dimensional facial morphology identifies a variant in PAX3 associated with nasion position.
NHGRI GWA Catalog
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • MGC120381, MGC120382, MGC120383, MGC120384, MGC134778

Gene Ontology Provided by GOA

Function Evidence Code Pubs
HMG box domain binding IEA
Inferred from Electronic Annotation
more info
 
RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
chromatin binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific DNA binding transcription factor activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
apoptotic process TAS
Traceable Author Statement
more info
PubMed 
cell proliferation IEA
Inferred from Electronic Annotation
more info
 
developmental pigmentation IEA
Inferred from Electronic Annotation
more info
 
heart development IEA
Inferred from Electronic Annotation
more info
 
mammary gland specification IEA
Inferred from Electronic Annotation
more info
 
muscle organ development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription from RNA polymerase II promoter IEA
Inferred from Electronic Annotation
more info
 
neural crest cell migration IEA
Inferred from Electronic Annotation
more info
 
neural tube closure IEA
Inferred from Electronic Annotation
more info
 
neuron fate commitment IEA
Inferred from Electronic Annotation
more info
 
organ morphogenesis TAS
Traceable Author Statement
more info
PubMed 
positive regulation of cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription from RNA polymerase II promoter IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
regulation of somitogenesis IEA
Inferred from Electronic Annotation
more info
 
sensory perception of sound TAS
Traceable Author Statement
more info
PubMed 
spinal cord association neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
transcription from RNA polymerase II promoter IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleus IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
paired box protein Pax-3
Names
paired box protein Pax-3
paired domain gene 3
paired domain gene HuP2
paired box homeotic gene 3

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011632.1 

    Range
    4986..104095
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000438.5NP_000429.2  paired box protein Pax-3 isoform PAX3a

    See proteins identical to NP_000429.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3A) differs in the 3' UTR, includes an alternate segment in the coding region, which causes a frameshift, and lacks several segments in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3a) has a shorter and distinct C-terminus, compared to isoform PAX3. Isoform PAX3a lacks the paired-type homeodomain.
    Source sequence(s)
    AC010980, BC101299, DA758804, S69369
    Consensus CDS
    CCDS46523.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000386817, OTTHUMP00000202745, ENST00000409828, OTTHUMT00000328669
    Conserved Domains (1) summary
    cd00131
    Location:34161
    PAX; Paired Box domain
  2. NM_001127366.2NP_001120838.1  paired box protein Pax-3 isoform PAX3i

    See proteins identical to NP_001120838.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3I) differs in the 3' UTR, uses an alternate in-frame splice site in the 5' coding region, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3i, also known as isoform PAX3dQ-) is longer and has a distinct C-terminus, compared to isoform PAX3.
    Source sequence(s)
    AC012591, AI382779, BC101299, DA758804
    Consensus CDS
    CCDS46522.1
    UniProtKB/Swiss-Prot
    P23760
    Conserved Domains (4) summary
    pfam12360
    Location:345390
    Pax7; Paired box protein 7
    cd00086
    Location:219276
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    cd00131
    Location:34160
    PAX; Paired Box domain
    pfam13551
    Location:56158
    HTH_29; Winged helix-turn helix
  3. NM_013942.4NP_039230.1  paired box protein Pax-3 isoform PAX3b

    See proteins identical to NP_039230.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3B) differs in the 3' UTR, includes an alternate segment in the coding region, which causes a frameshift, and lacks several segments in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3a) has a shorter and distinct C-terminus, compared to isoform PAX3. Isoform PAX3b lacks the paired-type homeodomain.
    Source sequence(s)
    BC063547, BC101299, DA758804, S69370
    Consensus CDS
    CCDS2451.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000258387, OTTHUMP00000164209, ENST00000258387, OTTHUMT00000256859
    Conserved Domains (2) summary
    cd00131
    Location:34161
    PAX; Paired Box domain
    pfam13551
    Location:56159
    HTH_29; Winged helix-turn helix
  4. NM_181457.3NP_852122.1  paired box protein Pax-3 isoform PAX3

    See proteins identical to NP_852122.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3) encodes isoform PAX3 (also known as isoform PAX3c).
    Source sequence(s)
    AC012591, BC101299, BC101301, DA758804
    Consensus CDS
    CCDS42826.1
    UniProtKB/TrEMBL
    A0A024R470
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000386750, OTTHUMP00000224703, ENST00000409551, OTTHUMT00000375096
    Conserved Domains (4) summary
    pfam12360
    Location:346391
    Pax7; Paired box protein 7
    cd00086
    Location:220277
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    cd00131
    Location:34161
    PAX; Paired Box domain
    pfam13551
    Location:56159
    HTH_29; Winged helix-turn helix
  5. NM_181458.3NP_852123.1  paired box protein Pax-3 isoform PAX3d

    See proteins identical to NP_852123.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3D) differs in the 3' UTR, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3d) is longer and has a distinct C-terminus, compared to isoform PAX3.
    Source sequence(s)
    AC012591, AI382779, AK291278, BC101299, BC101301
    Consensus CDS
    CCDS42825.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000343052, OTTHUMP00000202746, ENST00000350526, OTTHUMT00000328670
    Conserved Domains (4) summary
    pfam12360
    Location:346391
    Pax7; Paired box protein 7
    cd00086
    Location:220277
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    cd00131
    Location:34161
    PAX; Paired Box domain
    pfam13551
    Location:56159
    HTH_29; Winged helix-turn helix
  6. NM_181459.3NP_852124.1  paired box protein Pax-3 isoform PAX3e

    See proteins identical to NP_852124.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3E) differs in the 3' UTR, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3e) is longer and has a distinct C-terminus, compared to isoform PAX3.
    Source sequence(s)
    AC012591, AI382779, BC101299, BC101301, DA758804
    Consensus CDS
    CCDS2448.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000375921, OTTHUMP00000205137, ENST00000392069, OTTHUMT00000334035
    Conserved Domains (4) summary
    pfam12360
    Location:346391
    Pax7; Paired box protein 7
    cd00086
    Location:220277
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    cd00131
    Location:34161
    PAX; Paired Box domain
    pfam13551
    Location:56159
    HTH_29; Winged helix-turn helix
  7. NM_181460.3NP_852125.1  paired box protein Pax-3 isoform PAX3h

    See proteins identical to NP_852125.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3H) differs in the 3' UTR, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3h) is shorter and has a distinct C-terminus, compared to variant PAX3.
    Source sequence(s)
    AC012591, AI382779, BC101299, BC101301, DA758804
    Consensus CDS
    CCDS2449.1
    UniProtKB/Swiss-Prot
    P23760
    Conserved Domains (4) summary
    pfam12360
    Location:346391
    Pax7; Paired box protein 7
    cd00086
    Location:220277
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    cd00131
    Location:34161
    PAX; Paired Box domain
    pfam13551
    Location:56159
    HTH_29; Winged helix-turn helix
  8. NM_181461.3NP_852126.1  paired box protein Pax-3 isoform PAX3g

    See proteins identical to NP_852126.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (PAX3G) differs in the 3' UTR, and contains an alternate splice pattern in the 3' coding region, compared to variant PAX3. The resulting protein (isoform PAX3g) is shorter and has a distinct C-terminus, compared to variant PAX3.
    Source sequence(s)
    AC012591, AI382779, BC101299, BC101301, DA758804
    Consensus CDS
    CCDS2450.1
    UniProtKB/Swiss-Prot
    P23760
    Related
    ENSP00000342092, OTTHUMP00000164207, ENST00000344493, OTTHUMT00000256857
    Conserved Domains (4) summary
    pfam12360
    Location:346391
    Pax7; Paired box protein 7
    cd00086
    Location:220277
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    cd00131
    Location:34161
    PAX; Paired Box domain
    pfam13551
    Location:56159
    HTH_29; Winged helix-turn helix

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000002.12 

    Range
    222199887..222298996
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006712559.1XP_006712622.1  

    Conserved Domains (4) summary
    pfam12360
    Location:345390
    Pax7; Paired box protein 7
    cd00086
    Location:219276
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    cd00131
    Location:34160
    PAX; Paired Box domain
    pfam13551
    Location:56158
    HTH_29; Winged helix-turn helix

Alternate CHM1_1.1

Genomic

  1. NC_018913.2 

    Range
    223071095..223170215
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000134.1 

    Range
    214918697..215017780
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)