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XPC XPC complex subunit, DNA damage recognition and repair factor [ Homo sapiens (human) ]

Gene ID: 7508, updated on 21-Apr-2019

Summary

Official Symbol
XPCprovided by HGNC
Official Full Name
XPC complex subunit, DNA damage recognition and repair factorprovided by HGNC
Primary source
HGNC:HGNC:12816
See related
Ensembl:ENSG00000154767 MIM:613208
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
XP3; RAD4; XPCC; p125
Summary
The protein encoded by this gene is a key component of the XPC complex, which plays an important role in the early steps of global genome nucleotide excision repair (NER). The encoded protein is important for damage sensing and DNA binding, and shows a preference for single-stranded DNA. Mutations in this gene or some other NER components can result in Xeroderma pigmentosum, a rare autosomal recessive disorder characterized by increased sensitivity to sunlight with the development of carcinomas at an early age. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2017]
Expression
Ubiquitous expression in ovary (RPKM 17.1), kidney (RPKM 15.8) and 25 other tissues See more
Orthologs

Genomic context

See XPC in Genome Data Viewer
Location:
3p25.1
Exon count:
18
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (14145145..14178672, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (14186647..14220172, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 4 Neighboring gene transmembrane protein 43 Neighboring gene uncharacterized LOC107986063 Neighboring gene LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated Neighboring gene uncharacterized LOC105376958

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 FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • DNA Damage Recognition in GG-NER, organism-specific biosystem (from REACTOME)
    DNA Damage Recognition in GG-NER, organism-specific biosystemIn global genome nucleotide excision repair (GG-NER), the DNA damage is recognized by two protein complexes. The first complex consists of XPC, RAD23A or RAD23B, and CETN2. This complex probes the DN...
  • 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...
  • 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...
  • 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,...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • 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 ...
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • SUMO E3 ligases SUMOylate target proteins, organism-specific biosystem (from REACTOME)
    SUMO E3 ligases SUMOylate target proteins, organism-specific biosystemSUMO proteins are conjugated to lysine residues of target proteins via an isopeptide bond with the C-terminal glycine of SUMO (reviewed in Zhao 2007, Gareau and Lima 2010, Hannoun et al. 2010, Citro ...
  • SUMOylation, organism-specific biosystem (from REACTOME)
    SUMOylation, organism-specific biosystemSmall Ubiquitin-like MOdifiers (SUMOs) are a family of 3 proteins (SUMO1,2,3) that are reversibly conjugated to lysine residues of target proteins via a glycine-lysine isopeptide bond (reviewed in Ha...
  • SUMOylation of DNA damage response and repair proteins, organism-specific biosystem (from REACTOME)
    SUMOylation of DNA damage response and repair proteins, organism-specific biosystemSeveral factors that participate in DNA damage response and repair are SUMOylated (reviewed in Dou et al. 2011, Bekker-Jensen and Mailand 2011, Ulrich 2012, Psakhye and Jentsch 2012, Bologna and Ferr...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
bubble DNA binding TAS
Traceable Author Statement
more info
PubMed 
damaged DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
heteroduplex DNA loop binding TAS
Traceable Author Statement
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IDA
Inferred from Direct Assay
more info
PubMed 
single-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
DNA repair TAS
Traceable Author Statement
more info
PubMed 
UV-damage excision repair IDA
Inferred from Direct Assay
more info
PubMed 
global genome nucleotide-excision repair TAS
Traceable Author Statement
more info
 
intra-S DNA damage checkpoint IEA
Inferred from Electronic Annotation
more info
 
nucleotide-excision repair IDA
Inferred from Direct Assay
more info
PubMed 
nucleotide-excision repair, DNA damage recognition IDA
Inferred from Direct Assay
more info
PubMed 
nucleotide-excision repair, DNA damage recognition TAS
Traceable Author Statement
more info
 
nucleotide-excision repair, DNA duplex unwinding TAS
Traceable Author Statement
more info
 
nucleotide-excision repair, preincision complex assembly TAS
Traceable Author Statement
more info
 
regulation of mitotic cell cycle phase transition IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to UV-B IEA
Inferred from Electronic Annotation
more info
 
response to auditory stimulus IEA
Inferred from Electronic Annotation
more info
 
response to drug IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
XPC complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
mitochondrion IDA
Inferred from Direct Assay
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleotide-excision repair complex IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

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

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_011763.1 RefSeqGene

    Range
    5001..38526
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_472

mRNA and Protein(s)

  1. NM_001354726.1NP_001341655.1  DNA repair protein complementing XP-C cells isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC093495, FJ695192, KJ534962
    Conserved Domains (1) summary
    TIGR00605
    Location:1674
    rad4; DNA repair protein rad4
  2. NM_001354727.1NP_001341656.1  DNA repair protein complementing XP-C cells isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate exon and contains another alternate exon compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC093495, FJ695192
    Conserved Domains (1) summary
    TIGR00605
    Location:147865
    rad4; DNA repair protein rad4
  3. NM_001354729.1NP_001341658.1  DNA repair protein complementing XP-C cells isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate in-frame splice junction in the 5' end compared to variant 1. The resulting isoform (5) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC093495, FJ695192, KJ534962
    Conserved Domains (1) summary
    TIGR00605
    Location:141861
    rad4; DNA repair protein rad4
  4. NM_001354730.1NP_001341659.1  DNA repair protein complementing XP-C cells isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (6) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC093495, FJ695192, KJ534962
    Conserved Domains (1) summary
    cl26537
    Location:147785
    BHD_3; Rad4 beta-hairpin domain 3
  5. NM_004628.4NP_004619.3  DNA repair protein complementing XP-C cells

    See identical proteins and their annotated locations for NP_004619.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AI091587, AK222844, D21089
    Consensus CDS
    CCDS46763.1
    UniProtKB/Swiss-Prot
    Q01831
    UniProtKB/TrEMBL
    X5DRB1
    Related
    ENSP00000285021.7, ENST00000285021.11
    Conserved Domains (6) summary
    smart01032
    Location:751825
    BHD_3; Rad4 beta-hairpin domain 3
    smart01030
    Location:630681
    BHD_1; Rad4 beta-hairpin domain 1
    smart01031
    Location:684743
    BHD_2; Rad4 beta-hairpin domain 2
    TIGR00605
    Location:147867
    rad4; DNA repair protein rad4
    pfam03835
    Location:531626
    Rad4; Rad4 transglutaminase-like domain
    cl00936
    Location:355499
    RecX; RecX family

RNA

  1. NR_148950.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC093495, FJ695192
  2. NR_148951.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC093495, FJ695192

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    14145145..14178672 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001740256.2 RNA Sequence

  2. XR_002959580.1 RNA Sequence

  3. XR_002959581.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001145769.1: Suppressed sequence

    Description
    NM_001145769.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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