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    LSM1 LSM1 homolog, mRNA degradation associated [ Homo sapiens (human) ]

    Gene ID: 27257, updated on 2-Nov-2024

    Summary

    Official Symbol
    LSM1provided by HGNC
    Official Full Name
    LSM1 homolog, mRNA degradation associatedprovided by HGNC
    Primary source
    HGNC:HGNC:20472
    See related
    Ensembl:ENSG00000175324 MIM:607281; AllianceGenome:HGNC:20472
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CASM; YJL124C
    Summary
    This gene encodes a member of the LSm family of RNA-binding proteins. LSm proteins form stable heteromers that bind specifically to the 3'-terminal oligo(U) tract of U6 snRNA and may play a role in pre-mRNA splicing by mediating U4/U6 snRNP formation. Increased expression of this gene may play a role in cellular transformation and the progression of several malignancies including lung cancer, mesothelioma and breast cancer. Alternatively spliced transcript variants have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Nov 2011]
    Expression
    Ubiquitous expression in heart (RPKM 16.1), placenta (RPKM 14.6) and 25 other tissues See more
    Orthologs
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    Genomic context

    See LSM1 in Genome Data Viewer
    Location:
    8p11.23
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (38163321..38176730, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (38440300..38453709, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (38020839..38034248, complement)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ASH2 like, histone lysine methyltransferase complex subunit Neighboring gene RNA, U6 small nuclear 988, pseudogene Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:37990733-37991476 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr8:37991477-37992222 Neighboring gene Sharpr-MPRA regulatory region 4493 Neighboring gene STAR 5' regulatory region Neighboring gene uncharacterized LOC105379382 Neighboring gene steroidogenic acute regulatory protein Neighboring gene RNA, U6 small nuclear 323, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:38032979-38033836 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38033837-38034694 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27245 Neighboring gene BAG cochaperone 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27246 Neighboring gene Sharpr-MPRA regulatory region 4585 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19117 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:38089405-38089904 Neighboring gene DDHD domain containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19119 Neighboring gene phospholipid phosphatase 5

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables pre-mRNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in RNA splicing, via transesterification reactions TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in deadenylation-dependent decapping of nuclear-transcribed mRNA IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in histone mRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuron differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in stem cell population maintenance 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
     
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in axon IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in dendrite IEA
    Inferred from Electronic Annotation
    more info
     
    located_in neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    U6 snRNA-associated Sm-like protein LSm1
    Names
    LSM1 homolog, U6 small nuclear RNA associated
    LSM1 mRNA degradation associated
    LSM1, U6 small nuclear RNA associated
    LSM1-like protein U6 small nuclear RNA associated
    cancer-associated Sm protein
    cancer-associated Sm-like protein
    small nuclear ribonuclear CaSm

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_014462.3NP_055277.1  U6 snRNA-associated Sm-like protein LSm1

      See identical proteins and their annotated locations for NP_055277.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and is protein-coding.
      Source sequence(s)
      AJ238094, BP376421
      Consensus CDS
      CCDS6103.1
      UniProtKB/Swiss-Prot
      B2R5E6, O15116
      UniProtKB/TrEMBL
      A0A0S2Z590
      Related
      ENSP00000310596.4, ENST00000311351.9
      Conserved Domains (2) summary
      PRK10788
      Location:64131
      PRK10788; periplasmic folding chaperone; Provisional
      cd01728
      Location:477
      LSm1; Like-Sm protein 1

    RNA

    1. NR_045492.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1.
      Source sequence(s)
      BE670269, BU521199
      Related
      ENST00000520755.5
    2. NR_045493.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' region, compared to variant 1. This variant is represented as non-coding because it lacks an in-frame coding region, compared to variant 1.
      Source sequence(s)
      AF147348, BE670269, BU941962
      Related
      ENST00000520286.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      38163321..38176730 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      38440300..38453709 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)