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    Slx4 SLX4 structure-specific endonuclease subunit [ Rattus norvegicus (Norway rat) ]

    Gene ID: 302953, updated on 9-Sep-2018

    Summary

    Official Symbol
    Slx4provided by RGD
    Official Full Name
    SLX4 structure-specific endonuclease subunitprovided by RGD
    Primary source
    RGD:1566009
    See related
    Ensembl:ENSRNOG00000024445
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Btbd12; RGD1566009
    Annotation information
    Annotation category: partial on reference assembly
    Expression
    Biased expression in Adrenal (RPKM 79.8), Thymus (RPKM 68.8) and 9 other tissues See more
    Orthologs

    Genomic context

    See Slx4 in Genome Data Viewer
    Location:
    10q12
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (11787756..11808326)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 10 NC_005109.3 (10542217..10563267)

    Chromosome 10 - NC_005109.4Genomic Context describing neighboring genes Neighboring gene CREB binding protein Neighboring gene TNF receptor-associated protein 1 Neighboring gene deoxyribonuclease 1 Neighboring gene uncharacterized LOC108352058 Neighboring gene NLR family, CARD domain containing 3 Neighboring gene clusterin associated protein 1 Neighboring gene RGD1561796

    Genomic regions, transcripts, and products

    Expression

    • 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

    Pathways from BioSystems

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    contributes_to 3'-flap endonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    contributes_to 3'-flap endonuclease activity ISO
    Inferred from Sequence Orthology
    more info
     
    contributes_to 5'-flap endonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    contributes_to 5'-flap endonuclease activity ISO
    Inferred from Sequence Orthology
    more info
     
    contributes_to crossover junction endodeoxyribonuclease activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    contributes_to crossover junction endodeoxyribonuclease activity ISO
    Inferred from Sequence Orthology
    more info
     
    enzyme activator activity IEA
    Inferred from Electronic Annotation
    more info
     
    enzyme activator activity ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    DNA double-strand break processing involved in repair via single-strand annealing IEA
    Inferred from Electronic Annotation
    more info
     
    DNA double-strand break processing involved in repair via single-strand annealing ISO
    Inferred from Sequence Orthology
    more info
     
    DNA repair ISO
    Inferred from Sequence Orthology
    more info
     
    DNA replication IEA
    Inferred from Electronic Annotation
    more info
     
    double-strand break repair via homologous recombination IEA
    Inferred from Electronic Annotation
    more info
     
    double-strand break repair via homologous recombination ISO
    Inferred from Sequence Orthology
    more info
     
    interstrand cross-link repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    meiotic DNA double-strand break processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    negative regulation of telomere maintenance via telomere lengthening IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of telomere maintenance via telomere lengthening ISO
    Inferred from Sequence Orthology
    more info
     
    nucleotide-excision repair IEA
    Inferred from Electronic Annotation
    more info
     
    nucleotide-excision repair ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of catalytic activity IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of t-circle formation ISO
    Inferred from Sequence Orthology
    more info
     
    resolution of meiotic recombination intermediates IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    response to intra-S DNA damage checkpoint signaling IEA
    Inferred from Electronic Annotation
    more info
     
    response to intra-S DNA damage checkpoint signaling ISO
    Inferred from Sequence Orthology
    more info
     
    t-circle formation IEA
    Inferred from Electronic Annotation
    more info
     
    t-circle formation ISO
    Inferred from Sequence Orthology
    more info
     
    telomeric D-loop disassembly IEA
    Inferred from Electronic Annotation
    more info
     
    telomeric D-loop disassembly ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    ERCC4-ERCC1 complex IEA
    Inferred from Electronic Annotation
    more info
     
    colocalizes_with ERCC4-ERCC1 complex ISO
    Inferred from Sequence Orthology
    more info
     
    Holliday junction resolvase complex IEA
    Inferred from Electronic Annotation
    more info
     
    colocalizes_with Holliday junction resolvase complex ISO
    Inferred from Sequence Orthology
    more info
     
    Slx1-Slx4 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Slx1-Slx4 complex ISO
    Inferred from Sequence Orthology
    more info
     
    cell junction IEA
    Inferred from Electronic Annotation
    more info
     
    cell junction ISO
    Inferred from Sequence Orthology
    more info
     
    chromosome, telomeric region ISO
    Inferred from Sequence Orthology
    more info
     
    cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    nuclear chromatin IEA
    Inferred from Electronic Annotation
    more info
     
    colocalizes_with nuclear chromatin ISO
    Inferred from Sequence Orthology
    more info
     
    nuclear chromosome, telomeric region IEA
    Inferred from Electronic Annotation
    more info
     
    colocalizes_with nuclear chromosome, telomeric region ISO
    Inferred from Sequence Orthology
    more info
     
    nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     

    General protein information

    Preferred Names
    structure-specific endonuclease subunit SLX4
    Names
    BTB (POZ) domain containing 12
    SLX4 structure-specific endonuclease subunit homolog

    NCBI Reference Sequences (RefSeq)

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

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

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005109.4 Reference Rnor_6.0 Primary Assembly

      Range
      11787756..11808326
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006245835.3XP_006245897.2  structure-specific endonuclease subunit SLX4

      See identical proteins and their annotated locations for XP_006245897.2

      Related
      ENSRNOP00000031220.6, ENSRNOT00000033919.6
      Conserved Domains (3) summary
      smart00225
      Location:627723
      BTB; Broad-Complex, Tramtrack and Bric a brac
      pfam00651
      Location:616723
      BTB; BTB/POZ domain
      pfam09494
      Location:16501706
      Slx4; Slx4 endonuclease

    Alternate Rn_Celera

    Genomic

    1. AC_000078.1 Alternate Rn_Celera

      Range
      10485070..10505983
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006220566.3XP_006220628.2  structure-specific endonuclease subunit SLX4

      See identical proteins and their annotated locations for XP_006220628.2

      Conserved Domains (3) summary
      smart00225
      Location:627723
      BTB; Broad-Complex, Tramtrack and Bric a brac
      pfam00651
      Location:616723
      BTB; BTB/POZ domain
      pfam09494
      Location:16501706
      Slx4; Slx4 endonuclease
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