U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

PAX1 paired box 1 [ Homo sapiens (human) ]

Gene ID: 5075, updated on 17-Mar-2024

Summary

Go to the top of the page Help
Official Symbol
PAX1provided by HGNC
Official Full Name
paired box 1provided by HGNC
Primary source
HGNC:HGNC:8615
See related
Ensembl:ENSG00000125813 MIM:167411; AllianceGenome:HGNC:8615
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
OFC2; HUP48
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. This gene plays a role in pattern formation during embryogenesis and may be essential for development of the vertebral column. This gene is silenced by methylation in ovarian and cervical cancers and may be a tumor suppressor gene. Mutations in this gene are also associated with vertebral malformations. [provided by RefSeq, Mar 2012]
Expression
Low expression observed in reference dataset See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See PAX1 in Genome Data Viewer
Location:
20p11.22
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (21705664..21718481)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (21762357..21775174)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (21686302..21699119)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene Beta cell long intergenic noncoding RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:21554890-21555390 Neighboring gene long intergenic non-protein coding RNA 1727 Neighboring gene long intergenic non-protein coding RNA 1726 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:21681724-21682329 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:21683541-21684145 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:21693479-21693978 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:21719865-21720366 Neighboring gene solute carrier family 25 member 6 pseudogene 1 Neighboring gene ribosomal protein L41 pseudogene 1

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Real time quantitative methylation detection of PAX1 gene in cervical cancer screening. Liu H, et al. Int J Gynecol Cancer, 2020 Oct. PMID 32616628
  2. PAX1 is essential for development and function of the human thymus. Yamazaki Y, et al. Sci Immunol, 2020 Feb 28. PMID 32111619, Free PMC Article
  3. Association between dense PAX1 promoter methylation and HPV16 infection in cervical squamous epithelial neoplasms of Xin Jiang Uyghur and Han women. Zhang L, et al. Gene, 2020 Jan 10. PMID 31589957
  4. Paired Box-1 (PAX1) Activates Multiple Phosphatases and Inhibits Kinase Cascades in Cervical Cancer. Su PH, et al. Sci Rep, 2019 Jun 24. PMID 31235851, Free PMC Article
  5. Genetic polymorphisms of PAX1 are functionally associated with different PUMC types of adolescent idiopathic scoliosis in a northern Chinese Han population. Liu G, et al. Gene, 2019 Mar 10. PMID 30572100

See all (55) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. High-grade cervical lesions diagnosed by JAM3/PAX1 methylation in high-risk human papillomavirus-infected patients.
    Title: High-grade cervical lesions diagnosed by JAM3/PAX1 methylation in high-risk human papillomavirus-infected patients.
  2. PAX1 expression in thymic epithelial neoplasms and morphologic mimics.
    Title: PAX1 expression in thymic epithelial neoplasms and morphologic mimics.
  3. Aberrant Epigenetic Alteration of PAX1 Expression Contributes to Parathyroid Tumorigenesis.
    Title: Aberrant Epigenetic Alteration of PAX1 Expression Contributes to Parathyroid Tumorigenesis.
  4. Real time quantitative methylation detection of PAX1 gene in cervical cancer screening.
    Title: Real time quantitative methylation detection of PAX1 gene in cervical cancer screening.
  5. The application value of PAX1 and ZNF582 gene methylation in high grade intraepithelial lesion and cervical cancer.
    Title: The application value of PAX1 and ZNF582 gene methylation in high grade intraepithelial lesion and cervical cancer.
  6. SOX1 and PAX1 Are Hypermethylated in Cervical Adenocarcinoma and Associated with Better Prognosis.
    Title: SOX1 and PAX1 Are Hypermethylated in Cervical Adenocarcinoma and Associated with Better Prognosis.
  7. Hypermethylated PAX1 and ZNF582 genes in the tissue sample are associated with aggressive progression of oral squamous cell carcinoma.
    Title: Hypermethylated PAX1 and ZNF582 genes in the tissue sample are associated with aggressive progression of oral squamous cell carcinoma.
  8. PAX1 is essential for development and function of the human thymus.
    Title: PAX1 is essential for development and function of the human thymus.
  9. Temporal and spatial expression of Sox9, Pax1, TGF-beta1 and type I and II collagen in human intervertebral disc development.
    Title: Temporal and spatial expression of Sox9, Pax1, TGF-β1 and type I and II collagen in human intervertebral disc development.
  10. Paired Box-1 (PAX1) Activates Multiple Phosphatases and Inhibits Kinase Cascades in Cervical Cancer.
    Title: Paired Box-1 (PAX1) Activates Multiple Phosphatases and Inhibits Kinase Cascades in Cervical Cancer.
Submit: New GeneRIF Correction See all GeneRIFs (36)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Otofaciocervical syndrome 2
MedGen: C5442121 OMIM: 615560 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Male-pattern baldness susceptibility locus at 20p11.
EBI GWAS Catalog
Six novel susceptibility Loci for early-onset androgenetic alopecia and their unexpected association with common diseases.
EBI GWAS Catalog
Susceptibility variants for male-pattern baldness on chromosome 20p11.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in anatomical structure development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in skeletal system development TAS
Traceable Author Statement
more info
 PubMed 
involved_in transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

Go to the top of the page Help
Preferred Names
paired box protein Pax-1
Names
paired box gene 1
paired domain gene HuP48

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript 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 in Genomic regions, transcripts, and products above.

Genomic

  1. NG_047065.1 RefSeqGene

    Range
    5006..17823
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001257096.2 → NP_001244025.1  paired box protein Pax-1 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. It encodes isoform 2, which has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AI167631, AL035562, BC143793
    Consensus CDS
    CCDS74709.1
    UniProtKB/TrEMBL
    A0A087WXV5
    Related
    ENSP00000481334.1, ENST00000613128.5
    Conserved Domains (1) summary
    cd00131
    Location:98 → 225
    PAX; Paired Box domain

  2. NM_006192.5 → NP_006183.2  paired box protein Pax-1 isoform 1

    See identical proteins and their annotated locations for NP_006183.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AI167631, AL035562, BC069134
    Consensus CDS
    CCDS13146.2
    UniProtKB/Swiss-Prot
    B4E0D6, P15863, Q642X9, Q6NTC0, Q9Y558
    Related
    ENSP00000381499.2, ENST00000398485.6
    Conserved Domains (1) summary
    cd00131
    Location:98 → 225
    PAX; Paired Box domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    21705664..21718481
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    21762357..21775174
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P15863.4 GenPept UniProtKB/Swiss-Prot:P15863

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous