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

    Gene ID: 298074, updated on 30-Mar-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
    Ensembl: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
    • 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. Noise Stress Induces an Epidermal Growth Factor Receptor/Xeroderma Pigmentosum-A Response in the Auditory Nerve. Guthrie OW. J Histochem Cytochem, 2017 Mar. PMID 28056182, Free PMC Article
    2. 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
    3. Nucleotide excision repair by mutant xeroderma pigmentosum group A (XPA) proteins with deficiency in interaction with RPA. Saijo M, et al. J Biol Chem, 2011 Feb 18. PMID 21148310, Free PMC Article
    4. Real-time quantification of Xeroderma pigmentosum mRNA from the mammalian cochlea. Guthrie OW, et al. Ear Hear, 2010 Oct. PMID 20539233, Free PMC Article
    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, ENSRNOT00000064685.2
      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
      ENSRNOP00000080582.1, ENSRNOT00000108242.1
      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

      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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