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PAX1 paired box 1 [ Homo sapiens (human) ]

Gene ID: 5075, updated on 6-May-2024

Summary

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
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Genomic context

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

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

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

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.

Genomic

  1. NG_047065.1 RefSeqGene

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

mRNA and Protein(s)

  1. NM_001257096.2NP_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:98225
    PAX; Paired Box domain
  2. NM_006192.5NP_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:98225
    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)