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Lsm6 LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated [ Mus musculus (house mouse) ]

Gene ID: 78651, updated on 26-Sep-2022

Summary

Official Symbol
Lsm6provided by MGI
Official Full Name
LSM6 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by MGI
Primary source
MGI:MGI:1925901
See related
Ensembl:ENSMUSG00000031683 AllianceGenome:MGI:1925901
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
1500031N17Rik; 2410088K19Rik
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. Is expressed in brain and pancreas epithelium. Orthologous to human LSM6 (LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in CNS E11.5 (RPKM 14.6), CNS E14 (RPKM 9.0) and 26 other tissues See more
Orthologs
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Genomic context

See Lsm6 in Genome Data Viewer
Location:
8; 8 C1
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (79531497..79547781, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (78804868..78821152, complement)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene reeler domain containing 1 pseudogene Neighboring gene cytochrome c oxidase subunit NDUFA4 pseudogene Neighboring gene Rpl21 pseudogene Neighboring gene calponin 2 pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC117708

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables protein heterodimerization activity ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within mRNA catabolic process ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
 
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
acts_upstream_of_or_within rRNA processing IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within 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
PubMed 
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
PubMed 
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
PubMed 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
part_of spliceosomal complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
U6 snRNA-associated Sm-like protein LSm6
Names
LSM6 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_001191004.1NP_001177933.1  U6 snRNA-associated Sm-like protein LSm6

    See identical proteins and their annotated locations for NP_001177933.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC167022, AK141884, DV648841
    Consensus CDS
    CCDS40396.1
    UniProtKB/Swiss-Prot
    P62313
    UniProtKB/TrEMBL
    A0A6P5Q2F6, A0A8C6IFM5, Q542U7
    Related
    ENSMUSP00000119841.2, ENSMUST00000130325.8
    Conserved Domains (1) summary
    cd01726
    Location:774
    LSm6; Like-Sm protein 6
  2. NM_030145.3NP_084421.1  U6 snRNA-associated Sm-like protein LSm6

    See identical proteins and their annotated locations for NP_084421.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AC167022, AK158236, DV648841
    Consensus CDS
    CCDS40396.1
    UniProtKB/Swiss-Prot
    P62313
    UniProtKB/TrEMBL
    A0A6P5Q2F6, A0A8C6IFM5, Q542U7
    Related
    ENSMUSP00000049722.7, ENSMUST00000051867.7
    Conserved Domains (1) summary
    cd01726
    Location:774
    LSm6; Like-Sm protein 6

RefSeqs of Annotated Genomes: Mus musculus 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 GRCm39 C57BL/6J

Genomic

  1. NC_000074.7 Reference GRCm39 C57BL/6J

    Range
    79531497..79547781 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030243855.1XP_030099715.1  U6 snRNA-associated Sm-like protein LSm6 isoform X1

    UniProtKB/TrEMBL
    A0A6P5Q2F6, A0A8C6IFM5, Q542U7
    Conserved Domains (1) summary
    cd01726
    Location:774
    LSm6; Like-Sm protein 6
  2. XM_036154383.1XP_036010276.1  U6 snRNA-associated Sm-like protein LSm6 isoform X1

    UniProtKB/TrEMBL
    A0A6P5Q2F6, A0A8C6IFM5, Q542U7
    Related
    ENSMUSP00000148221.2, ENSMUST00000146824.2
    Conserved Domains (1) summary
    cd01726
    Location:774
    LSm6; Like-Sm protein 6