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    Lsm2 LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated [ Rattus norvegicus (Norway rat) ]

    Gene ID: 684148, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Lsm2provided by RGD
    Official Full Name
    LSM2 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by RGD
    Primary source
    RGD:1598536
    See related
    Ensembl:ENSRNOG00000048725 AllianceGenome:RGD:1598536
    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
    G7b
    Summary
    Predicted to enable protein kinase binding activity and small GTPase binding activity. Predicted to contribute to RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to act upstream of or within mRNA catabolic process and spliceosomal tri-snRNP complex assembly. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be part of Lsm1-7-Pat1 complex; Lsm2-8 complex; and nucleus. Predicted to be active in P-body. Orthologous to human LSM2 (LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 59.7), Testes (RPKM 57.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Lsm2 in Genome Data Viewer
    Location:
    20p12
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (3848120..3853298, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (3843467..3847217, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (4966817..4970567)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108349032 Neighboring gene ribosomal protein L13, pseudogene 1 Neighboring gene heat shock protein family A (Hsp70) member 1 like Neighboring gene heat shock protein family A (Hsp70) member 1A Neighboring gene heat shock protein family A (Hsp70) member 1B

    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. Identification of a novel protein, DMAP, which interacts with the myotonic dystrophy protein kinase and shows strong homology to D1 snRNP. Fu YH. Genetica, 1996 Jan. PMID 8851885
    2. 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
    3. 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
    4. The deubiquitylase USP33 discriminates between RALB functions in autophagy and innate immune response. Simicek M, et al. Nat Cell Biol, 2013 Oct. PMID 24056301
    5. The spliceosome: design principles of a dynamic RNP machine. Wahl MC, et al. Cell, 2009 Feb 20. PMID 19239890

    See all (14) 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
    contributes_to RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables small GTPase binding 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
    		  
    acts_upstream_of_or_within spliceosomal tri-snRNP complex assembly ISO
    Inferred from Sequence Orthology
    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
    		  
    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
    		  
    part_of catalytic step 2 spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of catalytic step 2 spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of precatalytic spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    U6 snRNA-associated Sm-like protein LSm2
    Names
    LSM2 U6 small nuclear RNA and mRNA degradation associated
    LSM2 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_001004073.1 → NP_001004073.1  U6 snRNA-associated Sm-like protein LSm2 isoform 1

      See identical proteins and their annotated locations for NP_001004073.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      BX883045
      UniProtKB/TrEMBL
      A6KTP7, M0R7N1, Q6MG66
      Related
      ENSRNOP00000065463.1, ENSRNOT00000070846.3
      Conserved Domains (1) summary
      cd01725
      Location:38 → 126
      LSm2; Like-Sm protein 2

    2. NM_001165922.1 → NP_001159394.1  U6 snRNA-associated Sm-like protein LSm2 isoform 2

      See identical proteins and their annotated locations for NP_001159394.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate 5' exon compared to variant 1. The resulting protein (isoform 2) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      BX883045
      UniProtKB/TrEMBL
      A0A0G2K8Q7, A6KTP6
      Related
      ENSRNOP00000074699.1, ENSRNOT00000081265.2
      Conserved Domains (1) summary
      cd01725
      Location:2 → 90
      LSm2; Like-Sm protein 2

    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_086038.1 Reference GRCr8

      Range
      3848120..3853298 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063279506.1 → XP_063135576.1  U6 snRNA-associated Sm-like protein LSm2 isoform X1

    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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