Pax1 paired box 1 [Mus musculus (house mouse) ]

Gene ID: 18503, updated on 8-Mar-2025

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Gene Sequences (FASTA)

Transcript sequences (FASTA)

Protein sequences(FASTA)

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Summary

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Official Symbol: Pax1provided byMGI
Official Full Name: paired box 1provided byMGI
Primary source: MGI:MGI:97485
See related: Ensembl:ENSMUSG00000037034 AllianceGenome:MGI:97485
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: un; wt; hbs; Pax-1; hunchback; undulated
Summary: Enables DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in positive regulation of transcription by RNA polymerase II and sclerotome development. Acts upstream of or within several processes, including alpha-beta T cell differentiation; parathyroid gland development; and thymus development. Predicted to be located in nucleus. Predicted to be part of transcription regulator complex. Is expressed in several structures, including branchial pouch; central nervous system; embryo mesenchyme; foregut diverticulum; and musculoskeletal system. Human ortholog(s) of this gene implicated in branchiootorenal syndrome. Orthologous to human PAX1 (paired box 1). [provided by Alliance of Genome Resources, Mar 2025]
Expression: Biased expression in thymus adult (RPKM 22.9), testis adult (RPKM 3.3) and 2 other tissuesSee more
Orthologs: human all
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Genomic context

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See Pax1 inGenome Data Viewer

Location:: 2 G2; 2 72.63 cM

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (147203850..147216972)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (147361930..147375049)

Chromosome 2 - NC_000068.8 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?

Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality.
Title: Deletion of Pax1 scoliosis-associated regulatory elements leads to a female-biased tail abnormality.
Pax1 and Pax9 can transactivate regulatory sequences in the Bapx1 promoter to induce chondrogenic differentiation in the sclerotome.
Title: Pax1 and Pax9 activate Bapx1 to induce chondrogenic differentiation in the sclerotome.
Adult mice which carry a new allele of Pax1 have a lumbar scoliosis and kinky tails, a models for scoliosis
Title: The scoliosis (sco) mouse: a new allele of Pax1.
In addition to Hoxa3, this protein is required for both epithelial cell growth and differentiation throughout thymus and parathyroid organogenesis.
Title: Hoxa3 and pax1 regulate epithelial cell death and proliferation during thymus and parathyroid organogenesis.

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Variation

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Alleles

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

Chemically induced (ENU) (1)
Spontaneous (5) 1 citation
Targeted (6) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Pax1 (e-PCR), detects polymorphism
- UniSTS:526090

Pax1 (e-PCR), detects polymorphism
- UniSTS:238145

03.MMHAP66FLA3.seq (e-PCR)
- UniSTS:159046

M69222 (e-PCR)
- UniSTS:159047

PMC21138P1 (e-PCR)
- UniSTS:272012

D10Bir5 (e-PCR), detects polymorphism
- UniSTS:141485

Pax1 (e-PCR), detects polymorphism
- UniSTS:144123

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IMP Inferred from Mutant Phenotype more info	PubMed
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 RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within CD4-positive, alpha-beta T cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within CD8-positive, alpha-beta T cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within animal organ morphogenesis	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within bone morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in embryo development ending in birth or egg hatching	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within parathyroid gland development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within pattern specification process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in 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	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	TAS Traceable Author Statement more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in sclerotome development	IEP Inferred from Expression Pattern more info	PubMed
involved_in skeletal system development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within skeletal system development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within somitogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within thymus development	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in nucleus	IEA Inferred from Electronic Annotation more info
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-1

Names: paired box gene 1; wavy tail

NCBI Reference Sequences (RefSeq)

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NEWTry the newTranscript table

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 inGenomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_008780.2 →NP_032806.2 paired box protein Pax-1
See identical proteins and their annotated locations for NP_032806.2
Status: VALIDATED
Source sequence(s)
AL805918
Consensus CDS
CCDS16835.2
UniProtKB/Swiss-Prot
A2ALJ9,P09084,Q9R2B1
UniProtKB/TrEMBL
Q548R5
Related
ENSMUSP00000105594.3,ENSMUST00000109968.3
Conserved Domains (1)summary
cd00131
Location:89 →216
PAX; Paired Box domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

This section includes genomic Reference Sequences (RefSeqs) from all assemblies on which this gene is annotated, such as RefSeqs for chromosomes and scaffolds (contigs) from both reference and alternate assemblies. Model RNAs and proteins are also reported here.