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    XPA XPA, DNA damage recognition and repair factor [ Homo sapiens (human) ]

    Gene ID: 7507, updated on 23-Nov-2023

    Summary

    Official Symbol
    XPAprovided by HGNC
    Official Full Name
    XPA, DNA damage recognition and repair factorprovided by HGNC
    Primary source
    HGNC:HGNC:12814
    See related
    Ensembl:ENSG00000136936 MIM:611153; AllianceGenome:HGNC:12814
    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
    XP1; XPAC
    Summary
    This gene encodes a zinc finger protein plays a central role in nucleotide excision repair (NER), a specialized type of DNA repair. NER is responsible for repair of UV radiation-induced photoproducts and DNA adducts induced by chemical carcinogens and chemotherapeutic drugs. The encoded protein interacts with DNA and several NER proteins, acting as a scaffold to assemble the NER incision complex at sites of DNA damage. Mutations in this gene cause Xeroderma pigmentosum complementation group A (XP-A), an autosomal recessive skin disorder featuring hypersensitivity to sunlight and increased risk for skin cancer. [provided by RefSeq, Aug 2017]
    Expression
    Ubiquitous expression in thyroid (RPKM 6.2), fat (RPKM 4.7) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See XPA in Genome Data Viewer
    Location:
    9q22.33
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (97654398..97697340, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (109826339..109869281, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (100437191..100459622, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100278102-100278602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28665 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28666 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100293128-100293286 Neighboring gene tropomodulin 1 Neighboring gene Sharpr-MPRA regulatory region 7780 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100318031-100318532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100319241-100319742 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28667 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28668 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100335093-100335332 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28669 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28670 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28671 Neighboring gene Sharpr-MPRA regulatory region 9871 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:100396128-100396963 Neighboring gene thiosulfate sulfurtransferase like domain containing 2 Neighboring gene nuclear cap binding protein subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28674 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28675 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28676 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20102 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:100465986-100467185 Neighboring gene keratin 18 pseudogene 13 Neighboring gene papillary thyroid carcinoma susceptibility candidate 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28678 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:100520047-100521246 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:100534165-100534666 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:100534667-100535166 Neighboring gene VISTA enhancer hs1595 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20103 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:100571176-100572375 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:100589760-100589981 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:100613975-100614476 Neighboring gene forkhead box E1

    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
    Xeroderma pigmentosum group A
    MedGen: C0268135 OMIM: 278700 GeneReviews: Xeroderma Pigmentosum
    Compare labs

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies a novel susceptibility gene for serum TSH levels in Chinese populations.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    The FOXE1 locus is a major genetic determinant for radiation-related thyroid carcinoma in Chernobyl.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables damaged DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables damaged DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in DNA repair IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in DNA repair IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in UV protection IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in UV protection IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in UV-damage excision repair IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in base-excision repair IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in nucleotide-excision repair IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nucleotide-excision repair involved in interstrand cross-link repair IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in nucleotide-excision repair, DNA damage recognition IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein localization to nucleus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to auditory stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    part_of DNA replication factor A complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in intercellular bridge IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    part_of nucleotide-excision repair factor 1 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    DNA repair protein complementing XP-A cells
    Names
    xeroderma pigmentosum group A-complementing protein
    xeroderma pigmentosum, complementation group A

    NCBI Reference Sequences (RefSeq)

    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_011642.1 RefSeqGene

      Range
      5001..27501
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_471

    mRNA and Protein(s)

    1. NM_000380.4NP_000371.1  DNA repair protein complementing XP-A cells isoform 1

      See identical proteins and their annotated locations for NP_000371.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      BC014965, CB155090
      Consensus CDS
      CCDS6729.1
      UniProtKB/Swiss-Prot
      P23025, Q5T1U9, Q6LCW7, Q6LD02
      UniProtKB/TrEMBL
      F2Z2T2
      Related
      ENSP00000364270.5, ENST00000375128.5
      Conserved Domains (1) summary
      TIGR00598
      Location:105273
      rad14; DNA repair protein
    2. NM_001354975.2NP_001341904.1  DNA repair protein complementing XP-A cells isoform 2

      Status: REVIEWED

      Source sequence(s)
      AL445531
      Conserved Domains (1) summary
      TIGR00598
      Location:63231
      rad14; DNA repair protein

    RNA

    1. NR_027302.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has an additional exon in the CDS, which includes an upstream stop codon, as compared to variant 1. The transcript is a nonsense-mediated mRNA decay (NMD) candidate, so is unlikely to make a functional protein.
      Source sequence(s)
      AI961077, AL531629, BC014965, CB155090
      Related
      ENST00000462523.5
    2. NR_149091.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL445531
    3. NR_149092.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL445531
    4. NR_149093.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL445531
    5. NR_149094.2 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL445531

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      97654398..97697340 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006717278.2XP_006717341.1  DNA repair protein complementing XP-A cells isoform X1

      UniProtKB/TrEMBL
      F2Z2T2
      Conserved Domains (3) summary
      TIGR00598
      Location:105257
      rad14; DNA repair protein
      pfam01286
      Location:104133
      XPA_N; XPA protein N-terminal
      pfam05181
      Location:135186
      XPA_C; XPA protein C-terminus

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      109826339..109869281 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363756.1XP_054219731.1  DNA repair protein complementing XP-A cells isoform X1

      UniProtKB/TrEMBL
      F2Z2T2