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    Lsm7 LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated [ Rattus norvegicus (Norway rat) ]

    Gene ID: 362829, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Lsm7provided by RGD
    Official Full Name
    LSM7 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by RGD
    Primary source
    RGD:1305354
    See related
    AllianceGenome:RGD:1305354
    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 contribute to RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be located in nucleus. Predicted to be part of several cellular components, including Lsm1-7-Pat1 complex; spliceosomal complex; and spliceosomal snRNP complex. Orthologous to human LSM7 (LSM7 homolog, U6 small nuclear RNA and mRNA degradation associated). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 136.8), Spleen (RPKM 122.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Lsm7 in Genome Data Viewer
    Location:
    7q11
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 7 NC_086025.1 (9507373..9509787)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 7 NC_051342.1 (8856698..8859113)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 7 NC_005106.4 (11724932..11732020)

    Chromosome 7 - NC_086025.1Genomic Context describing neighboring genes Neighboring gene transmembrane serine protease 9 Neighboring gene uncharacterized LOC120093773 Neighboring gene signal peptide peptidase-like 2B Neighboring gene leucine rich repeat and Ig domain containing 3 Neighboring gene ornithine decarboxylase antizyme 1

    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. 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
    2. The spliceosome: design principles of a dynamic RNP machine. Wahl MC, et al. Cell, 2009 Feb 20. PMID 19239890
    3. Molecular architecture of the human U4/U6.U5 tri-snRNP. Agafonov DE, et al. Science, 2016 Mar 25. PMID 26912367
    4. 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
    5. Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. Bertram K, et al. Cell, 2017 Aug 10. PMID 28781166

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    contributes_to RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in nuclear-transcribed mRNA catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of Lsm1-7-Pat1 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Lsm2-8 complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U12-type spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type precatalytic spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U2-type prespliceosome 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
    		  
    part_of catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of spliceosomal tri-snRNP 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 LSm7
    Names
    LSM7 U6 small nuclear RNA and mRNA degradation associated
    LSM7 homolog, U6 small nuclear RNA associated

    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_001108732.2 → NP_001102202.1  U6 snRNA-associated Sm-like protein LSm7 isoform 1

      See identical proteins and their annotated locations for NP_001102202.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      UniProtKB/TrEMBL
      A6K8E6, D4A2D8
      Conserved Domains (1) summary
      cd01729
      Location:9 → 97
      LSm7; Like-Sm protein 7

    2. NM_001401075.1 → NP_001388004.1  U6 snRNA-associated Sm-like protein LSm7 isoform 2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007

    3. NM_001401076.1 → NP_001388005.1  U6 snRNA-associated Sm-like protein LSm7 isoform 3

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000007
      Conserved Domains (1) summary
      cd01729
      Location:17 → 103
      LSm7; Like-Sm protein 7

    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_086025.1 Reference GRCr8

      Range
      9507373..9509787
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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