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

Gene ID: 27257, updated on 5-Aug-2018

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; Vega:OTTHUMG00000164051
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

Genomic context

See LSM1 in Genome Data Viewer
Location:
8p11.23
Exon count:
4
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 8 NC_000008.11 (38163321..38176730, complement)
105 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 STAR 5' regulatory region Neighboring gene uncharacterized LOC105379382 Neighboring gene steroidogenic acute regulatory protein Neighboring gene RNA, U6 small nuclear 323, pseudogene Neighboring gene BCL2 associated athanogene 4 Neighboring gene DDHD domain containing 2 Neighboring gene phospholipid phosphatase 5 Neighboring gene nuclear receptor binding SET domain protein 3 Neighboring gene NUP98-NSD3 recombination region

Genomic regions, transcripts, and products

Expression

  • Project title: 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Deadenylation-dependent mRNA decay, organism-specific biosystem (from REACTOME)
    Deadenylation-dependent mRNA decay, organism-specific biosystemAfter undergoing rounds of translation, mRNA is normally destroyed by the deadenylation-dependent pathway. Though the trigger is unclear, deadenylation likely proceeds in two steps: one catalyzed by...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Lsm 1-7 complex, organism-specific biosystem (from KEGG)
    Lsm 1-7 complex, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Lsm 1-7 complex, conserved biosystem (from KEGG)
    Lsm 1-7 complex, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • RNA degradation, organism-specific biosystem (from KEGG)
    RNA degradation, organism-specific biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
  • RNA degradation, conserved biosystem (from KEGG)
    RNA degradation, conserved biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
  • mRNA decay by 5' to 3' exoribonuclease, organism-specific biosystem (from REACTOME)
    mRNA decay by 5' to 3' exoribonuclease, organism-specific biosystemDegradation of mRNA from 5' to 3' occurs in three steps. First, the mRNA is bound at its 3' end by the Lsm1-7 complex. The bound Lsm1-7 may prevent nucleases from accessing the 3' end. Second, the 7-...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA cap binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA binding IEA
Inferred from Electronic Annotation
more info
 
pre-mRNA binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA splicing TAS
Traceable Author Statement
more info
PubMed 
RNA splicing, via transesterification reactions TAS
Traceable Author Statement
more info
PubMed 
deadenylation-dependent decapping of nuclear-transcribed mRNA IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS
Traceable Author Statement
more info
 
histone mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
mRNA processing IEA
Inferred from Electronic Annotation
more info
 
negative regulation of neuron differentiation IEA
Inferred from Electronic Annotation
more info
 
stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Lsm1-7-Pat1 complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
P-body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
axon IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
dendrite IEA
Inferred from Electronic Annotation
more info
 
mRNA cap binding complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
messenger ribonucleoprotein complex IEA
Inferred from Electronic Annotation
more info
 
neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

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)

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_014462.2NP_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, BE670269, BP376421, BU941962
    Consensus CDS
    CCDS6103.1
    UniProtKB/Swiss-Prot
    O15116
    UniProtKB/TrEMBL
    A0A0S2Z590
    Related
    ENSP00000310596.4, OTTHUMP00000225703, ENST00000311351.8, OTTHUMT00000376965
    Conserved Domains (2) summary
    cd01728
    Location:477
    LSm1; Like-Sm protein 1
    cl26124
    Location:64131
    Rotamase_2; PPIC-type PPIASE domain

RNA

  1. NR_045492.1 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, BP376421, BU521199, BU941962
    Related
    ENST00000520755.5, OTTHUMT00000376966
  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: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p12 Primary Assembly

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