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    Shld1 shieldin complex subunit 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 681292, updated on 6-Jun-2024

    Summary

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    Official Symbol
    Shld1provided by RGD
    Official Full Name
    shieldin complex subunit 1provided by RGD
    Primary source
    RGD:1597982
    See related
    Ensembl:ENSRNOG00000021268 AllianceGenome:RGD:1597982
    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 be involved in negative regulation of double-strand break repair via homologous recombination; positive regulation of double-strand break repair via nonhomologous end joining; and positive regulation of isotype switching. Predicted to be located in chromosome. Predicted to be active in site of double-strand break. Orthologous to human SHLD1 (shieldin complex subunit 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Spleen (RPKM 18.7), Lung (RPKM 16.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Shld1 in Genome Data Viewer
    Location:
    3q36
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (140391611..140462273)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (119938695..120011068)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (125318682..125396705)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC120101670 Neighboring gene glycerophosphocholine phosphodiesterase 1 Neighboring gene uncharacterized LOC102552951 Neighboring gene U6 spliceosomal RNA Neighboring gene chromogranin B Neighboring gene tRNA methyltransferase 6 non-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. DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of NHEJ and PARP Inhibitor Sensitivity. Gupta R, et al. Cell, 2018 May 3. PMID 29656893, Free PMC Article
    2. 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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    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in negative regulation of double-strand break repair via homologous recombination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of double-strand break repair via homologous recombination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of double-strand break repair via nonhomologous end joining IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of double-strand break repair via nonhomologous end joining ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of isotype switching IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of isotype switching ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in chromosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in site of double-strand break IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in site of double-strand break ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    shieldin complex subunit 1
    Names
    uncharacterized protein C20orf196 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_001399552.1 → NP_001386481.1  shieldin complex subunit 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      A0A8I6A0G4, A0A8I6AUR4, A6HQH1
      Related
      ENSRNOP00000084844.1, ENSRNOT00000102243.1

    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_086021.1 Reference GRCr8

      Range
      140391611..140462273
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039106576.2 → XP_038962504.1  shieldin complex subunit 1 isoform X3

      UniProtKB/TrEMBL
      A0A8I6AUR4
      Conserved Domains (1) summary
      pfam15021
      Location:4 → 226
      DUF4521; Protein of unknown function (DUF4521)

    2. XM_008762239.4 → XP_008760461.1  shieldin complex subunit 1 isoform X4

      See identical proteins and their annotated locations for XP_008760461.1

      UniProtKB/TrEMBL
      A0A8I6AUR4, D3ZVK4
      Related
      ENSRNOP00000028891.5
      Conserved Domains (1) summary
      pfam15021
      Location:5 → 205
      DUF4521; Protein of unknown function (DUF4521)

    3. XM_063284550.1 → XP_063140620.1  shieldin complex subunit 1 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AUR4

    4. XM_063284549.1 → XP_063140619.1  shieldin complex subunit 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZYL2

    5. XM_063284551.1 → XP_063140621.1  shieldin complex subunit 1 isoform X5

    Nucleotide Protein Strain
    Heading Accession and Version

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