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

    Gene ID: 302953, updated on 13-Apr-2024

    Summary

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    Official Symbol
    Slx4provided by RGD
    Official Full Name
    SLX4 structure-specific endonuclease subunitprovided by RGD
    Primary source
    RGD:1566009
    See related
    Ensembl:ENSRNOG00000024445 AllianceGenome:RGD:1566009
    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
    Also known as
    Btbd12; RGD1566009
    Summary
    Predicted to enable enzyme activator activity and enzyme binding activity. Predicted to contribute to 3'-flap endonuclease activity; 5'-flap endonuclease activity; and crossover junction endodeoxyribonuclease activity. Predicted to be involved in DNA metabolic process and regulation of telomere maintenance. Predicted to act upstream of or within response to intra-S DNA damage checkpoint signaling. Predicted to be located in cell junction; cytosol; and nucleoplasm. Predicted to be part of Slx1-Slx4 complex. Predicted to colocalize with chromatin and chromosome, telomeric region. Human ortholog(s) of this gene implicated in Fanconi anemia complementation group P. Orthologous to human SLX4 (SLX4 structure-specific endonuclease subunit). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Adrenal (RPKM 79.8), Thymus (RPKM 68.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Slx4 in Genome Data Viewer
    Location:
    10q12
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (12032131..12055685)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (11526623..11549313)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (11787756..11808326)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene CREB binding protein Neighboring gene TNF receptor-associated protein 1 Neighboring gene deoxyribonuclease 1 Neighboring gene NLR family, CARD domain containing 3 Neighboring gene clusterin associated protein 1 Neighboring gene similar to human chromosome 16 open reading frame 90 Neighboring gene N(alpha)-acetyltransferase 60, NatF 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
    • 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. SLX4 assembles a telomere maintenance toolkit by bridging multiple endonucleases with telomeres. Wan B, et al. Cell Rep, 2013 Sep 12. PMID 24012755, Free PMC Article
    2. RTEL1 dismantles T loops and counteracts telomeric G4-DNA to maintain telomere integrity. Vannier JB, et al. Cell, 2012 May 11. PMID 22579284
    3. Drosophila MUS312 and the vertebrate ortholog BTBD12 interact with DNA structure-specific endonucleases in DNA repair and recombination. Andersen SL, et al. Mol Cell, 2009 Jul 10. PMID 19595722, Free PMC Article
    4. FBH1 co-operates with MUS81 in inducing DNA double-strand breaks and cell death following replication stress. Fugger K, et al. Nat Commun, 2013. PMID 23361013
    5. Coordination of structure-specific nucleases by human SLX4/BTBD12 is required for DNA repair. Muñoz IM, et al. Mol Cell, 2009 Jul 10. PMID 19595721

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables enzyme activator activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA double-strand break processing involved in repair via single-strand annealing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in DNA replication IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in double-strand break repair via homologous recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of telomere maintenance via telomere lengthening ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nucleotide-excision repair ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of t-circle formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of telomere maintenance ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in resolution of meiotic recombination intermediates IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within response to intra-S DNA damage checkpoint signaling ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in t-circle formation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in telomeric D-loop disassembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of ERCC4-ERCC1 complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of Holliday junction resolvase complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of Slx1-Slx4 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Slx1-Slx4 complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromosome, telomeric region ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol 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
    		  

    General protein information

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

    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_001398651.1 → NP_001385580.1  structure-specific endonuclease subunit SLX4

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      F1LU18
      Related
      ENSRNOP00000031220.6, ENSRNOT00000033919.7
      Conserved Domains (2) summary
      cl38908
      Location:599 → 713
      BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
      pfam09494
      Location:1640 → 1697
      Slx4; Slx4 endonuclease

    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_086028.1 Reference GRCr8

      Range
      12032131..12055685
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063268905.1 → XP_063124975.1  structure-specific endonuclease subunit SLX4 isoform X1

      UniProtKB/TrEMBL
      F1LU18

    2. XM_063268904.1 → XP_063124974.1  structure-specific endonuclease subunit SLX4 isoform X1

      UniProtKB/TrEMBL
      F1LU18

    3. XM_063268903.1 → XP_063124973.1  structure-specific endonuclease subunit SLX4 isoform X1

      UniProtKB/TrEMBL
      F1LU18

    4. XM_063268908.1 → XP_063124978.1  structure-specific endonuclease subunit SLX4 isoform X2

    5. XM_063268907.1 → XP_063124977.1  structure-specific endonuclease subunit SLX4 isoform X1

      UniProtKB/TrEMBL
      F1LU18

    6. XM_063268906.1 → XP_063124976.1  structure-specific endonuclease subunit SLX4 isoform X1

      UniProtKB/TrEMBL
      F1LU18

    7. XM_039087052.2 → XP_038942980.1  structure-specific endonuclease subunit SLX4 isoform X3

      Conserved Domains (3) summary
      PTZ00449
      Location:713 → 1027
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      cl38908
      Location:239 → 353
      BTB_POZ; BTB (Broad-Complex, Tramtrack and Bric a brac)/POZ (poxvirus and zinc finger) domain superfamily
      pfam09494
      Location:1280 → 1337
      Slx4; Slx4 endonuclease

    8. XM_039087053.2 → XP_038942981.1  structure-specific endonuclease subunit SLX4 isoform X4

      Conserved Domains (2) summary
      PTZ00449
      Location:386 → 700
      PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
      pfam09494
      Location:953 → 1010
      Slx4; Slx4 endonuclease
    Nucleotide Protein Strain
    Heading Accession and Version

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