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

Gene ID: 7507, updated on 2-Oct-2018

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; Vega:OTTHUMG00000020330
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

Genomic context

See XPA in Genome Data Viewer
Location:
9q22.33
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (97654398..97697409, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (100437191..100459691, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene tropomodulin 1 Neighboring gene thiosulfate sulfurtransferase like domain containing 2 Neighboring gene uncharacterized LOC105376171 Neighboring gene nuclear cap binding protein subunit 1 Neighboring gene keratin 18 pseudogene 13 Neighboring gene papillary thyroid carcinoma susceptibility candidate 2 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Xeroderma pigmentosum, type 1
MedGen: C0268135 OMIM: 278700 GeneReviews: Xeroderma Pigmentosum
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NHGRI GWAS Catalog

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

Pathways from BioSystems

  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • Dual Incision in GG-NER, organism-specific biosystem (from REACTOME)
    Dual Incision in GG-NER, organism-specific biosystemDouble incision at the damaged DNA strand excises the oligonucleotide that contains the lesion from the open bubble. The excised oligonucleotide is ~27-30 bases long. Incision 5' to the damage site, ...
  • Dual incision in TC-NER, organism-specific biosystem (from REACTOME)
    Dual incision in TC-NER, organism-specific biosystemIn transcription-coupled nucleotide excision repair (TC-NER), similar to global genome nucleotide excision repair (GG-NER), the oligonucleotide that contains the lesion is excised from the open bubbl...
  • Formation of Incision Complex in GG-NER, organism-specific biosystem (from REACTOME)
    Formation of Incision Complex in GG-NER, organism-specific biosystemAfter the XPC complex and the UV-DDB complex bind damaged DNA, a basal transcription factor TFIIH is recruited to the nucleotide excision repair (NER) site (Volker et al. 2001, Riedl et al. 2003). DN...
  • Formation of TC-NER Pre-Incision Complex, organism-specific biosystem (from REACTOME)
    Formation of TC-NER Pre-Incision Complex, organism-specific biosystemFormation of TC-NER pre-incision complex is initiated when the RNA polymerase II (RNA Pol II) complex stalls at a DNA damage site. The stalling is caused by misincorporation of a ribonucleotide oppos...
  • Global Genome Nucleotide Excision Repair (GG-NER), organism-specific biosystem (from REACTOME)
    Global Genome Nucleotide Excision Repair (GG-NER), organism-specific biosystemThe DNA damage in GG-NER is recognized by the joint action of two protein complexes. The first complex is composed of XPC, RAD23A or RAD23B and CETN2. The second complex, known as the UV-DDB complex,...
  • Nucleotide Excision Repair, organism-specific biosystem (from REACTOME)
    Nucleotide Excision Repair, organism-specific biosystemNucleotide excision repair (NER) was first described in the model organism E. coli in the early 1960s as a process whereby bulky base damage is enzymatically removed from DNA, facilitating the recove...
  • Nucleotide excision repair, organism-specific biosystem (from KEGG)
    Nucleotide excision repair, organism-specific biosystemNucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the ...
  • Nucleotide excision repair, conserved biosystem (from KEGG)
    Nucleotide excision repair, conserved biosystemNucleotide excision repair (NER) is a mechanism to recognize and repair bulky DNA damage caused by compounds, environmental carcinogens, and exposure to UV-light. In humans hereditary defects in the ...
  • Platinum drug resistance, organism-specific biosystem (from KEGG)
    Platinum drug resistance, organism-specific biosystemPlatinum-based drugs cisplatin, carboplatin and oxaliplatin are widely used in the therapy of solid malignancies, including testicular, ovarian, head and neck, colorectal, bladder and lung cancers. T...
  • Platinum drug resistance, conserved biosystem (from KEGG)
    Platinum drug resistance, conserved biosystemPlatinum-based drugs cisplatin, carboplatin and oxaliplatin are widely used in the therapy of solid malignancies, including testicular, ovarian, head and neck, colorectal, bladder and lung cancers. T...
  • Transcription-Coupled Nucleotide Excision Repair (TC-NER), organism-specific biosystem (from REACTOME)
    Transcription-Coupled Nucleotide Excision Repair (TC-NER), organism-specific biosystemDNA damage in transcribed strands of active genes is repaired through a specialized nucleotide excision repair (NER) pathway known as transcription-coupled nucleotide excision repair (TC-NER). TC-NER...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
damaged DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
damaged DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
DNA repair IDA
Inferred from Direct Assay
more info
PubMed 
DNA repair IMP
Inferred from Mutant Phenotype
more info
PubMed 
UV protection IDA
Inferred from Direct Assay
more info
PubMed 
UV protection IMP
Inferred from Mutant Phenotype
more info
PubMed 
UV-damage excision repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
base-excision repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
global genome nucleotide-excision repair TAS
Traceable Author Statement
more info
 
intrinsic apoptotic signaling pathway in response to DNA damage IEA
Inferred from Electronic Annotation
more info
 
multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
nucleotide-excision repair involved in interstrand cross-link repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleotide-excision repair, DNA damage recognition IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleotide-excision repair, DNA incision IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleotide-excision repair, DNA incision IMP
Inferred from Mutant Phenotype
more info
PubMed 
nucleotide-excision repair, DNA incision TAS
Traceable Author Statement
more info
 
nucleotide-excision repair, DNA incision, 5'-to lesion TAS
Traceable Author Statement
more info
 
nucleotide-excision repair, preincision complex assembly TAS
Traceable Author Statement
more info
 
nucleotide-excision repair, preincision complex stabilization TAS
Traceable Author Statement
more info
 
protein localization to nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of autophagy IEA
Inferred from Electronic Annotation
more info
 
response to auditory stimulus IEA
Inferred from Electronic Annotation
more info
 
response to oxidative stress IEA
Inferred from Electronic Annotation
more info
 
response to toxic substance IEA
Inferred from Electronic Annotation
more info
 
transcription-coupled nucleotide-excision repair TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
colocalizes_with DNA replication factor A complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
intercellular bridge IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleotide-excision repair factor 1 complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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)

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_000380.3NP_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
    Related
    ENSP00000364270.4, OTTHUMP00000021751, ENST00000375128.4, OTTHUMT00000053332
    Conserved Domains (1) summary
    TIGR00598
    Location:105273
    rad14; DNA repair protein
  2. NM_001354975.1NP_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_027302.1 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, OTTHUMT00000053334
  2. NR_149091.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL445531
  3. NR_149092.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL445531
  4. NR_149093.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL445531
  5. NR_149094.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL445531

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    97654398..97697409 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    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
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