Pax3 paired box 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Pax3provided by MGI
Official Full Name: paired box 3provided by MGI
Primary source: MGI:MGI:97487
See related: Ensembl:ENSMUSG00000004872 AllianceGenome:MGI:97487
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Sp; Pax-3; Splchl2; splotch
Summary: Enables several functions, including DNA-binding transcription factor activity, RNA polymerase II-specific; chromatin binding activity; and transcription coregulator binding activity. Acts upstream of or within several processes, including nervous system development; regulation of somitogenesis; and regulation of transcription by RNA polymerase II. Located in nucleus. Is expressed in several structures, including branchial arch; central nervous system; embryo mesenchyme; nose; and urinary system. Used to study Waardenburg syndrome; Waardenburg syndrome type 1; alveolar rhabdomyosarcoma; and neural tube defect. Human ortholog(s) of this gene implicated in Waardenburg syndrome; Waardenburg syndrome type 1; Waardenburg syndrome type 3; alveolar rhabdomyosarcoma; and craniofacial-deafness-hand syndrome. Orthologous to human PAX3 (paired box 3). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in CNS E11.5 (RPKM 7.2), whole brain E14.5 (RPKM 2.1) and 3 other tissues See more
Orthologs: human all
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Genomic context

Location:: 1 C4; 1 39.79 cM

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (78077904..78173773, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (78101267..78197136, complement)

Chromosome 1 - NC_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Loss of Pax3 causes reduction of melanocytes in the developing mouse cochlea.
Title: Loss of Pax3 causes reduction of melanocytes in the developing mouse cochlea.
Pax3 induces target-specific reinnervation through axon collateral expression of PSA-NCAM.
Title: Pax3 induces target-specific reinnervation through axon collateral expression of PSA-NCAM.
Pax3 lineage-specific deletion of Gpr161 is associated with spinal neural tube and craniofacial malformations during embryonic development.
Title: Pax3 lineage-specific deletion of Gpr161 is associated with spinal neural tube and craniofacial malformations during embryonic development.
PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors.
Title: PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors.
RNA-Seq analysis of a Pax3-expressing myoblast clone in-vitro and effect of culture surface stiffness on differentiation.
Title: RNA-Seq analysis of a Pax3-expressing myoblast clone in-vitro and effect of culture surface stiffness on differentiation.
Genetic interaction of Pax3 mutation and canonical Wnt signaling modulates neural tube defects and neural crest abnormalities.
Title: Genetic interaction of Pax3 mutation and canonical Wnt signaling modulates neural tube defects and neural crest abnormalities.
iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease modeling.
Title: iMyoblasts for ex vivo and in vivo investigations of human myogenesis and disease modeling.
Altered sacral neural crest development in Pax3 spina bifida mutants underlies deficits of bladder innervation and function.
Title: Altered sacral neural crest development in Pax3 spina bifida mutants underlies deficits of bladder innervation and function.
Pax3 inhibits Neuro-2a cells proliferation and neurite outgrowth.
Title: Pax3 inhibits Neuro-2a cells proliferation and neurite outgrowth.
Interleukin-21-mediated suppression of the Pax3-Id3 pathway exacerbates the development of Sjogren's syndrome via follicular helper T cells.
Title: Interleukin-21-mediated suppression of the Pax3-Id3 pathway exacerbates the development of Sjögren's syndrome via follicular helper T cells.

Submit: New GeneRIF Correction See all GeneRIFs (124)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically and radiation induced (1)
Chemically induced (ENU) (6) 1 citation
Endonuclease-mediated (2)
Radiation induced (4) 1 citation
Spontaneous (8) 1 citation
Targeted (27) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Pax3 (e-PCR), detects polymorphism
- UniSTS:265478

Pax3 (e-PCR), detects polymorphism
- UniSTS:265234

Pax3 (e-PCR), detects polymorphism
- UniSTS:265235

Pax3 (e-PCR), detects polymorphism
- UniSTS:238167

X59358 (e-PCR)
- UniSTS:158816

X59358 (e-PCR)
- UniSTS:125811

Pax3 (e-PCR), detects polymorphism
- UniSTS:256628

Pax3 (e-PCR), detects polymorphism
- UniSTS:243342

Pax3 (e-PCR), detects polymorphism
- UniSTS:536481

Pax3 (e-PCR), detects polymorphism
- UniSTS:144124

Pax3 (e-PCR), detects polymorphism
- UniSTS:144125

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IGI Inferred from Genetic Interaction more info	PubMed
enables HMG box domain binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info	PubMed
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription coregulator binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cardiac muscle cell differentiation	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within developmental pigmentation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mammary gland specification	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within muscle organ development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within myoblast migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within myoblast proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IGI Inferred from Genetic Interaction more info	PubMed
involved_in nervous system development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neural crest cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural tube closure	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural tube development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within neuron fate commitment	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within positive regulation of stem cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info	PubMed
acts_upstream_of_or_within regulation of somitogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of somitogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in skeletal muscle cell differentiation	NAS Non-traceable Author Statement more info	PubMed
acts_upstream_of_or_within skeletal muscle organ development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within spinal cord association neuron differentiation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of stem cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of transcription regulator complex	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: paired box protein Pax-3

Names: PAX3/FKHR fusion; paired box gene 3

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

NM_001159520.1 → NP_001152992.1 paired box protein Pax-3 isoform b

See identical proteins and their annotated locations for NP_001152992.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) contains an alternate splice site in the 3' coding region, compared to variant 1. This results in a distinct C-terminus and longer protein (isoform b), compared to isoform a.

Source sequence(s)

AC118213, AK044985, AK045018, AK157760

Consensus CDS

CCDS48294.1

UniProtKB/TrEMBL

Q3TZM4, Q8BRF1

Related

ENSMUSP00000004994.10, ENSMUST00000004994.16

Conserved Domains (3) summary

pfam00046
Location:222 → 275

Homeobox; Homeobox domain

pfam00292
Location:34 → 159

PAX; 'Paired box' domain

pfam12360
Location:347 → 391

Pax7; Paired box protein 7
NM_008781.4 → NP_032807.3 paired box protein Pax-3 isoform a

See identical proteins and their annotated locations for NP_032807.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript but encodes the shorter isoform (a).

Source sequence(s)

AC118213, AK045018, AK147919, AK148354, AK157760

Consensus CDS

CCDS15082.1

UniProtKB/Swiss-Prot

P24610, Q3UFQ9, Q8BRE7, Q9CXI6

UniProtKB/TrEMBL

Q3UGH9

Related

ENSMUSP00000084320.7, ENSMUST00000087086.7

Conserved Domains (3) summary

pfam00046
Location:222 → 275

Homeobox; Homeobox domain

pfam00292
Location:34 → 159

PAX; 'Paired box' domain

pfam12360
Location:347 → 391

Pax7; Paired box protein 7