U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 78651, updated on 11-Apr-2024

    Summary

    Go to the top of the page Help
    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
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    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

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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 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
    		  
    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
    		  
    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
    		  
    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
    		  
    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
    		  
    part_of ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of sno(s)RNA-containing ribonucleoprotein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    U6 snRNA-associated Sm-like protein LSm6
    Names
    LSM6 homolog, U6 small nuclear RNA associated

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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_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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous