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    Lsm6 LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated [ Rattus norvegicus (Norway rat) ]

    Gene ID: 498934, updated on 9-Dec-2024

    Summary

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    Symbol
    Lsm6provided by RGD
    Full Name
    LSM6 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by RGD
    Primary source
    RGD:1561937
    See related
    EnsemblRapid:ENSRNOG00000086773 AllianceGenome:RGD:1561937
    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
    RGD1561937
    Summary
    Predicted to enable RNA binding activity and protein heterodimerization activity. Predicted to be involved in mRNA splicing, via spliceosome and maturation of SSU-rRNA. Predicted to act upstream of or within mRNA catabolic process. Predicted to be located in cytoplasm and nucleus. Predicted to be part of several cellular components, including Lsm2-8 complex; U2-type precatalytic spliceosome; and spliceosomal snRNP complex. Predicted to be active in P-body and nucleolus. Orthologous to human LSM6 (LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 66.1), Spleen (RPKM 46.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Lsm6 in Genome Data Viewer
    Location:
    19q11
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 19 NC_086037.1 (46002592..46017152)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 19 NC_051354.1 (29098254..29112858)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 19 NC_005118.4 (32770640..32785215)

    Chromosome 19 - NC_086037.1Genomic Context describing neighboring genes Neighboring gene zinc finger protein 827 Neighboring gene uncharacterized LOC120098577 Neighboring gene uncharacterized LOC134483636 Neighboring gene U4 spliceosomal RNA Neighboring gene reeler domain containing 1 Neighboring gene solute carrier family 10, member 7 Neighboring gene large ribosomal subunit protein eL28-like

    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. The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci. Ingelfinger D, et al. RNA, 2002 Dec. PMID 12515382, Free PMC Article
    2. A doughnut-shaped heteromer of human Sm-like proteins binds to the 3'-end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro. Achsel T, et al. EMBO J, 1999 Oct 15. PMID 10523320, Free PMC Article
    3. The spliceosome: design principles of a dynamic RNP machine. Wahl MC, et al. Cell, 2009 Feb 20. PMID 19239890
    4. Molecular architecture of the human U4/U6.U5 tri-snRNP. Agafonov DE, et al. Science, 2016 Mar 25. PMID 26912367
    5. Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors. Chen YI, et al. Nucleic Acids Res, 2007. PMID 17537823, Free PMC Article

    See all (9) 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 RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein heterodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    acts_upstream_of_or_within mRNA catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in maturation of SSU-rRNA IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of Lsm2-8 complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type precatalytic spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U4/U6 x U5 tri-snRNP complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U4/U6 x U5 tri-snRNP complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U6 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of sno(s)RNA-containing ribonucleoprotein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    U6 snRNA-associated Sm-like protein LSm6
    Names
    LSM6 U6 small nuclear RNA and mRNA degradation associated
    LSM6 homolog, U6 small nuclear RNA associated
    Sm protein F
    rCG63582-like

    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_001126085.1 → NP_001119557.1  U6 snRNA-associated Sm-like protein LSm6

      See identical proteins and their annotated locations for NP_001119557.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473972
      UniProtKB/TrEMBL
      A6IBZ0, A6IYJ3, D3ZG07
      Related
      ENSRNOP00000111687.1, ENSRNOT00000159801.1
      Conserved Domains (1) summary
      cd01726
      Location:7 → 74
      LSm6; Like-Sm protein 6

    2. NM_001434588.1 → NP_001421517.1  U6 snRNA-associated Sm-like protein LSm6

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019
      UniProtKB/TrEMBL
      A6IBZ0, A6IYJ3, D3ZG07

    RNA

    1. NR_197949.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000019

    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_086037.1 Reference GRCr8

      Range
      46002592..46017152
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006255408.4 → XP_006255470.1  U6 snRNA-associated Sm-like protein LSm6 isoform X1

      Conserved Domains (1) summary
      cd01726
      Location:7 → 74
      LSm6; Like-Sm protein 6
    Nucleotide Protein Strain
    Heading Accession and Version

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