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Xpa XPA, DNA damage recognition and repair factor [ Rattus norvegicus (Norway rat) ]

Gene ID: 298074, updated on 17-Aug-2024

Summary

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Official Symbol
Xpaprovided by RGD
Official Full Name
XPA, DNA damage recognition and repair factorprovided by RGD
Primary source
RGD:1308769
See related
EnsemblRapid:ENSRNOG00000009576 AllianceGenome:RGD:1308769
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable DNA binding activity; protein domain specific binding activity; and protein homodimerization activity. Involved in response to auditory stimulus. Located in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in xeroderma pigmentosum and xeroderma pigmentosum group A. Orthologous to human XPA (XPA, DNA damage recognition and repair factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Thymus (RPKM 33.2), Kidney (RPKM 29.9) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Xpa in Genome Data Viewer
Location:
5q22
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (65227281..65275784, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (60431673..60475726, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (61749767..61793641, complement)

Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120102866 Neighboring gene tudor domain containing 7 Neighboring gene tropomodulin 1 Neighboring gene thiosulfate sulfurtransferase like domain containing 2 Neighboring gene nuclear cap binding protein subunit 1 Neighboring gene sorbitol dehydrogenase, pseudogene 4 Neighboring gene forkhead box E1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Localization and distribution of neurons that co-express xeroderma pigmentosum-A and epidermal growth factor receptor within Rosenthal's canal. Guthrie OW. Acta Histochem, 2015 Oct. PMID 26493720
  2. Mutational analysis of the structure and function of the xeroderma pigmentosum group A complementing protein. Identification of essential domains for nuclear localization and DNA excision repair. Miyamoto I, et al. J Biol Chem, 1992 Jun 15. PMID 1601884
  3. Elevated frequencies of benzo(a)pyrene-induced Hprt mutations in internal tissue of XPA-deficient mice. Bol SA, et al. Cancer Res, 1998 Jul 1. PMID 9661901
  4. Immunohistochemical analysis of nucleotide excision repair factors XPA and XPB in adult rat brain. Yang SZ, et al. Anat Rec (Hoboken), 2008 Jul. PMID 18543291
  5. Preincision complex-I from the excision nuclease reaction among cochlear spiral limbus and outer hair cells. Guthrie OW. J Mol Histol, 2008 Dec. PMID 18979173

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. This current study tested the hypothesis that noise stress would alter the expression pattern of EGFR/XPA within the auditory nerve. In both the apical and middle cochlear coils, the noise stress depleted EGFR+XPA expression. Furthermore, there was a reduction in the proportion of neurons that expressed XPA-alone in the middle coils.
    Title: Noise Stress Induces an Epidermal Growth Factor Receptor/Xeroderma Pigmentosum-A Response in the Auditory Nerve.
  2. A population of spiral ganglion neurons that constitutively express XPA may also express the EGFR in rat.
    Title: Localization and distribution of neurons that co-express xeroderma pigmentosum-A and epidermal growth factor receptor within Rosenthal's canal.
  3. This study showed that spontaneous Xpa mutations causing cerebellar pathology are impaired in motor functions during the neonatal period.
    Title: Behavioral effects of neonatal lesions on the cerebellar system.
  4. XP mRNA levels were up to 95% (XPA) and 69% (XPC) of the respective maximum expression capacity of each gene; in addition, these cochlear levels were up to sixfold (XPC) and threefold (XPA)
    Title: Real-time quantification of Xeroderma pigmentosum mRNA from the mammalian cochlea.
  5. study examined XPA and XPC immunoreactivity among outer hair cells and spiral limbus cells; data show that outer hair cells failed to acclimate to cisplatin treatment cycles by regulating XPA and XPC immunoreactivity
    Title: Preincision complex-I from the excision nuclease reaction among cochlear spiral limbus and outer hair cells.
  6. nucleotide excision repair (NER) factors XPA and XPB exist in the nuclei of neurons in the brain, suggesting that the NER may play important roles in the process of DNA repair in adult brain neurons
    Title: Immunohistochemical analysis of nucleotide excision repair factors XPA and XPB in adult rat brain.
Submit: New GeneRIF Correction

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables damaged DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables damaged DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein domain specific binding ISO
Inferred from Sequence Orthology
more info
  
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
  
enables sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within DNA repair ISO
Inferred from Sequence Orthology
more info
  
involved_in DNA repair ISO
Inferred from Sequence Orthology
more info
  
involved_in UV protection ISO
Inferred from Sequence Orthology
more info
  
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
  
acts_upstream_of_or_within intrinsic apoptotic signaling pathway in response to DNA damage ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within multicellular organism growth ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within nucleotide-excision repair ISO
Inferred from Sequence Orthology
more info
  
involved_in nucleotide-excision repair ISO
Inferred from Sequence Orthology
more info
  
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
  
acts_upstream_of_or_within positive regulation of transcription initiation by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in protein localization to nucleus ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within regulation of autophagy ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within response to UV ISO
Inferred from Sequence Orthology
more info
  
involved_in response to auditory stimulus IEP
Inferred from Expression Pattern
more info
 PubMed 
acts_upstream_of_or_within response to oxidative stress ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within response to toxic substance ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of DNA replication factor A complex ISO
Inferred from Sequence Orthology
more info
  
located_in intercellular bridge IEA
Inferred from Electronic Annotation
more info
  
located_in intercellular bridge ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
part_of nucleotide-excision repair factor 1 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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

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.

mRNA and Protein(s)

  1. NM_001106656.1 → NP_001100126.1  DNA repair protein complementing XP-A cells isoform 2

    See identical proteins and their annotated locations for NP_001100126.1

    Status: PROVISIONAL

    Source sequence(s)
    CH473962
    UniProtKB/TrEMBL
    A6IJB2, D4A981
    Related
    ENSRNOP00000059280.1, ENSRNOT00000064685.3
    Conserved Domains (2) summary
    pfam01286
    Location:104 → 133
    XPA_N; XPA protein N-terminal
    pfam05181
    Location:135 → 186
    XPA_C; XPA protein C-terminus

  2. NM_001399041.1 → NP_001385970.1  DNA repair protein complementing XP-A cells isoform 1

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000005
    UniProtKB/TrEMBL
    A0A8I6G6T5, A6IJB3
    Related
    ENSRNOP00000100893.1, ENSRNOT00000127599.1
    Conserved Domains (1) summary
    TIGR00598
    Location:105 → 273
    rad14; DNA repair protein

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086023.1 Reference GRCr8

    Range
    65227281..65275784 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039109456.2 → XP_038965384.1  DNA repair protein complementing XP-A cells isoform X3

    Conserved Domains (1) summary
    cd21076
    Location:120 → 226
    DBD_XPA; DNA-binding domain found in DNA repair protein complementing XP-A cells (XPA) and similar proteins

  2. XM_063287331.1 → XP_063143401.1  DNA repair protein complementing XP-A cells isoform X6

  3. XM_063287332.1 → XP_063143402.1  DNA repair protein complementing XP-A cells isoform X6

  4. XM_006238035.4 → XP_006238097.1  DNA repair protein complementing XP-A cells isoform X1

    Related
    ENSRNOP00000108065.1, ENSRNOT00000141451.1
    Conserved Domains (3) summary
    TIGR00598
    Location:124 → 292
    rad14; DNA repair protein
    pfam01286
    Location:123 → 152
    XPA_N; XPA protein N-terminal
    pfam05181
    Location:154 → 205
    XPA_C; XPA protein C-terminus

  5. XM_039109457.2 → XP_038965385.1  DNA repair protein complementing XP-A cells isoform X4

    Conserved Domains (1) summary
    cd21076
    Location:120 → 226
    DBD_XPA; DNA-binding domain found in DNA repair protein complementing XP-A cells (XPA) and similar proteins

  6. XM_017593241.2 → XP_017448730.1  DNA repair protein complementing XP-A cells isoform X2

  7. XM_008763697.3 → XP_008761919.1  DNA repair protein complementing XP-A cells isoform X5

    Conserved Domains (2) summary
    pfam01286
    Location:123 → 152
    XPA_N; XPA protein N-terminal
    pfam05181
    Location:154 → 205
    XPA_C; XPA protein C-terminus

RNA

  1. XR_010066351.1 RNA Sequence

  2. XR_010066350.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version

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