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    Spidr scaffold protein involved in DNA repair [ Rattus norvegicus (Norway rat) ]

    Gene ID: 498119, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Spidrprovided by RGD
    Official Full Name
    scaffold protein involved in DNA repairprovided by RGD
    Primary source
    RGD:1566036
    See related
    EnsemblRapid:ENSRNOG00000037851 AllianceGenome:RGD:1566036
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1566036
    Summary
    Predicted to be involved in several processes, including cellular response to camptothecin; cellular response to hydroxyurea; and regulation of double-strand break repair. Predicted to be active in nuclear chromosome and nucleoplasm. Human ortholog(s) of this gene implicated in 46 XX gonadal dysgenesis. Orthologous to human SPIDR (scaffold protein involved in DNA repair). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Liver (RPKM 95.9), Lung (RPKM 84.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Spidr in Genome Data Viewer
    Location:
    11q23
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 11 NC_086029.1 (98270779..98511760, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 11 NC_051346.1 (84766593..85007597, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 11 NC_005110.4 (89009931..89260361, complement)

    Chromosome 11 - NC_086029.1Genomic Context describing neighboring genes Neighboring gene plakophilin 2 Neighboring gene Fcf1 rRNA-processing protein, pseudogene 7 Neighboring gene CCAAT/enhancer binding protein delta Neighboring gene uncharacterized LOC134481106 Neighboring gene translation machinery-associated protein 16 pseudogene Neighboring gene mitotic spindle organizing protein 2B Neighboring gene protein kinase, DNA-activated, catalytic subunit

    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. Scaffolding protein SPIDR/KIAA0146 connects the Bloom syndrome helicase with homologous recombination repair. Wan L, et al. Proc Natl Acad Sci U S A, 2013 Jun 25. PMID 23509288, Free PMC Article
    2. FIGNL1-containing protein complex is required for efficient homologous recombination repair. Yuan J, et al. Proc Natl Acad Sci U S A, 2013 Jun 25. PMID 23754376, Free PMC Article
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC156776

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in DNA damage response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cellular response to camptothecin ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cellular response to hydroxyurea ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in cellular response to ionizing radiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in double-strand break repair via homologous recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in double-strand break repair via homologous recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of double-strand break repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of protein-containing complex assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of double-strand break repair via homologous recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of establishment of protein localization to chromosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of establishment of protein localization to chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nuclear chromosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nuclear chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    DNA repair-scaffolding protein
    Names
    scaffolding protein involved in DNA repair

    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_001100988.2 → NP_001094458.1  DNA repair-scaffolding protein

      See identical proteins and their annotated locations for NP_001094458.1

      Status: PROVISIONAL

      Source sequence(s)
      JAXUCZ010000011
      UniProtKB/TrEMBL
      A0A0G2K1R3, A2VD15, E9PSZ4
      Related
      ENSRNOP00000054310.3, ENSRNOT00000057502.6
      Conserved Domains (2) summary
      pfam14950
      Location:11 → 335
      DUF4502; Domain of unknown function (DUF4502)
      pfam14951
      Location:485 → 864
      DUF4503; Domain of unknown function (DUF4503)

    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_086029.1 Reference GRCr8

      Range
      98270779..98511760 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063270716.1 → XP_063126786.1  DNA repair-scaffolding protein isoform X7

      Related
      ENSRNOP00000101694.1, ENSRNOT00000173455.1

    2. XM_008768898.4 → XP_008767120.1  DNA repair-scaffolding protein isoform X4

      UniProtKB/TrEMBL
      A0A0G2K1R3, A0A8I5Y2H8
      Related
      ENSRNOP00000071950.3, ENSRNOT00000089517.3
      Conserved Domains (2) summary
      pfam14950
      Location:11 → 392
      DUF4502; Domain of unknown function (DUF4502)
      pfam14951
      Location:542 → 921
      DUF4503; Domain of unknown function (DUF4503)

    3. XM_039088589.2 → XP_038944517.1  DNA repair-scaffolding protein isoform X1

      UniProtKB/TrEMBL
      A0A0G2K1R3
      Conserved Domains (2) summary
      pfam14950
      Location:11 → 392
      DUF4502; Domain of unknown function (DUF4502)
      pfam14951
      Location:542 → 927
      DUF4503; Domain of unknown function (DUF4503)

    4. XM_039088595.2 → XP_038944523.1  DNA repair-scaffolding protein isoform X11

      UniProtKB/TrEMBL
      A0A0G2K1R3
      Conserved Domains (2) summary
      pfam14950
      Location:11 → 335
      DUF4502; Domain of unknown function (DUF4502)
      pfam14951
      Location:485 → 870
      DUF4503; Domain of unknown function (DUF4503)

    5. XM_039088594.2 → XP_038944522.1  DNA repair-scaffolding protein isoform X10

      UniProtKB/TrEMBL
      A0A0G2K1R3
      Related
      ENSRNOP00000078167.2, ENSRNOT00000111413.2
      Conserved Domains (2) summary
      pfam14950
      Location:11 → 392
      DUF4502; Domain of unknown function (DUF4502)
      pfam14951
      Location:537 → 874
      DUF4503; Domain of unknown function (DUF4503)

    6. XM_039088593.2 → XP_038944521.1  DNA repair-scaffolding protein isoform X9

      UniProtKB/TrEMBL
      A0A0G2K1R3
      Conserved Domains (2) summary
      pfam14950
      Location:11 → 392
      DUF4502; Domain of unknown function (DUF4502)
      pfam14951
      Location:537 → 875
      DUF4503; Domain of unknown function (DUF4503)

    7. XM_039088590.2 → XP_038944518.1  DNA repair-scaffolding protein isoform X3

      UniProtKB/TrEMBL
      A0A0G2K1R3
      Conserved Domains (2) summary
      pfam14950
      Location:11 → 392
      DUF4502; Domain of unknown function (DUF4502)
      pfam14951
      Location:542 → 922
      DUF4503; Domain of unknown function (DUF4503)

    8. XM_063270715.1 → XP_063126785.1  DNA repair-scaffolding protein isoform X6

    9. XM_017598050.3 → XP_017453539.1  DNA repair-scaffolding protein isoform X2

      UniProtKB/TrEMBL
      A0A0G2K1R3

    10. XM_039088591.2 → XP_038944519.1  DNA repair-scaffolding protein isoform X5

      UniProtKB/TrEMBL
      A0A0G2K1R3
      Conserved Domains (2) summary
      pfam14950
      Location:11 → 392
      DUF4502; Domain of unknown function (DUF4502)
      pfam14951
      Location:542 → 909
      DUF4503; Domain of unknown function (DUF4503)

    11. XM_039088592.2 → XP_038944520.1  DNA repair-scaffolding protein isoform X8

      UniProtKB/TrEMBL
      A0A0G2K1R3
      Conserved Domains (2) summary
      pfam14950
      Location:11 → 392
      DUF4502; Domain of unknown function (DUF4502)
      pfam14951
      Location:542 → 890
      DUF4503; Domain of unknown function (DUF4503)

    12. XM_063270718.1 → XP_063126788.1  DNA repair-scaffolding protein isoform X12

    13. XM_063270717.1 → XP_063126787.1  DNA repair-scaffolding protein isoform X12

    14. XM_063270720.1 → XP_063126790.1  DNA repair-scaffolding protein isoform X13

    15. XM_063270719.1 → XP_063126789.1  DNA repair-scaffolding protein isoform X12

    16. XM_039088598.2 → XP_038944526.1  DNA repair-scaffolding protein isoform X15

      Conserved Domains (1) summary
      pfam14951
      Location:81 → 466
      DUF4503; Domain of unknown function (DUF4503)

    17. XM_039088597.2 → XP_038944525.1  DNA repair-scaffolding protein isoform X14

      Conserved Domains (1) summary
      pfam14950
      Location:11 → 392
      DUF4502; Domain of unknown function (DUF4502)
    Nucleotide Protein Strain
    Heading Accession and Version

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