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    PAX1 paired box 1 [ Homo sapiens (human) ]

    Gene ID: 5075, updated on 2-Nov-2024

    Summary

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    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; OTFCS2
    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
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    Genomic context

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    See PAX1 in Genome Data Viewer
    Location:
    20p11.22
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (21705664..21718481)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (21762357..21775174)
    RS_2024_09 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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. 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
    2. PAX1 methylation as a potential biomarker for cervical cancer screening. Kan YY, et al. Int J Gynecol Cancer, 2014 Jun. PMID 24844223
    3. PAX1 methylation as an auxiliary biomarker for cervical cancer screening: a meta-analysis. Nikolaidis C, et al. Cancer Epidemiol, 2015 Oct. PMID 26234429
    4. PAX1 methylation analysis by MS-HRM is useful in triage of high-grade squamous intraepithelial lesions. Wang ZM. Asian Pac J Cancer Prev, 2014. PMID 24568514
    5. PAX1 Methylation Hallmarks Promising Accuracy for Cervical Cancer Screening in Asians: Results from a Meta-Analysis. Kong LY, et al. Clin Lab, 2015. PMID 26642709

    See all (59) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Relationship between p16/ki67 immunoscores and PAX1/ZNF582 methylation status in precancerous and cancerous cervical lesions in high-risk HPV-positive women.
      Title: Relationship between p16/ki67 immunoscores and PAX1/ZNF582 methylation status in precancerous and cancerous cervical lesions in high-risk HPV-positive women.
    2. PAX1 represses canonical Wnt signaling pathway and plays dual roles during endoderm differentiation.
      Title: PAX1 represses canonical Wnt signaling pathway and plays dual roles during endoderm differentiation.
    3. 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.
    4. PAX1 expression in thymic epithelial neoplasms and morphologic mimics.
      Title: PAX1 expression in thymic epithelial neoplasms and morphologic mimics.
    5. Aberrant Epigenetic Alteration of PAX1 Expression Contributes to Parathyroid Tumorigenesis.
      Title: Aberrant Epigenetic Alteration of PAX1 Expression Contributes to Parathyroid Tumorigenesis.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. PAX1 is essential for development and function of the human thymus.
      Title: PAX1 is essential for development and function of the human thymus.
    Submit: New GeneRIF Correction See all GeneRIFs (38)

    Phenotypes

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    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

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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 embryo development ending in birth or egg hatching 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 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
    located_in chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    paired box protein Pax-1
    Names
    paired box gene 1
    paired domain gene HuP48

    NCBI Reference Sequences (RefSeq)

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    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_2024_08

    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.

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