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

Gene ID: 78651, updated on 27-Nov-2024

Summary

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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 central nervous system; pancreas epithelium; and sensory organ. Orthologous to human LSM6 (LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in CNS E11.5 (RPKM 14.6), CNS E14 (RPKM 9.0) and 26 other tissues See more
Orthologs
human all
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Genomic context

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See Lsm6 in Genome Data Viewer
Location:
8 C1; 8 37.22 cM
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_02 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 STARR-positive B cell enhancer ABC_E5021 Neighboring gene STARR-seq mESC enhancer starr_22000 Neighboring gene Rpl21 pseudogene Neighboring gene STARR-seq mESC enhancer starr_22001 Neighboring gene STARR-seq mESC enhancer starr_22002 Neighboring gene calponin 2 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

Bibliography

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Related articles in PubMed

  1. USP15 Deubiquitinates TUT1 Associated with RNA Metabolism and Maintains Cerebellar Homeostasis. Kim J, et al. Mol Cell Biol, 2020 Oct 13. PMID 32839293, Free PMC Article
  2. A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain. McKee AE, et al. BMC Dev Biol, 2005 Jul 20. PMID 16033648, Free PMC Article
  3. Cracking the egg: molecular dynamics and evolutionary aspects of the transition from the fully grown oocyte to embryo. Evsikov AV, et al. Genes Dev, 2006 Oct 1. PMID 17015433, Free PMC Article
  4. Identification of transcripts with enriched expression in the developing and adult pancreas. Hoffman BG, et al. Genome Biol, 2008. PMID 18554416, Free PMC Article
  5. BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain. Pourhaghighi R, et al. Cell Syst, 2020 Apr 22. PMID 32325033, Free PMC Article

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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
  
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables protein heterodimerization activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
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
  
involved_in mRNA splicing, via spliceosome ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in maturation of SSU-rRNA IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in rRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in 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
  
part_of Lsm2-8 complex ISS
Inferred from Sequence or Structural Similarity
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 U2-type precatalytic spliceosome ISS
Inferred from Sequence or Structural Similarity
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 U4/U6 x U5 tri-snRNP complex ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of U6 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of sno(s)RNA-containing ribonucleoprotein 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 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_001191004.1 → NP_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
    Q542U7
    Related
    ENSMUSP00000119841.2, ENSMUST00000130325.8
    Conserved Domains (1) summary
    cd01726
    Location:7 → 74
    LSm6; Like-Sm protein 6

  2. NM_030145.3 → NP_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
    Q542U7
    Related
    ENSMUSP00000049722.7, ENSMUST00000051867.7
    Conserved Domains (1) summary
    cd01726
    Location:7 → 74
    LSm6; Like-Sm protein 6

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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_030243855.1 → XP_030099715.1  U6 snRNA-associated Sm-like protein LSm6 isoform X1

    UniProtKB/Swiss-Prot
    P62313
    UniProtKB/TrEMBL
    Q542U7
    Conserved Domains (1) summary
    cd01726
    Location:7 → 74
    LSm6; Like-Sm protein 6

  2. XM_036154383.1 → XP_036010276.1  U6 snRNA-associated Sm-like protein LSm6 isoform X1

    UniProtKB/Swiss-Prot
    P62313
    UniProtKB/TrEMBL
    Q542U7
    Related
    ENSMUSP00000148221.2, ENSMUST00000146824.2
    Conserved Domains (1) summary
    cd01726
    Location:7 → 74
    LSm6; Like-Sm protein 6
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P62313.1 GenPept UniProtKB/Swiss-Prot:P62313

Gene LinkOut

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