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    LSM6 LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated [ Homo sapiens (human) ]

    Gene ID: 11157, updated on 9-Dec-2024

    Summary

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    Official Symbol
    LSM6provided by HGNC
    Official Full Name
    LSM6 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by HGNC
    Primary source
    HGNC:HGNC:17017
    See related
    Ensembl:ENSG00000164167 MIM:607286; AllianceGenome:HGNC:17017
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    YDR378C
    Summary
    Sm-like proteins were identified in a variety of organisms based on sequence homology with the Sm protein family (see SNRPD2; MIM 601061). Sm-like proteins contain the Sm sequence motif, which consists of 2 regions separated by a linker of variable length that folds as a loop. The Sm-like proteins are thought to form a stable heteromer present in tri-snRNP particles, which are important for pre-mRNA splicing.[supplied by OMIM, Apr 2004]
    Expression
    Ubiquitous expression in fat (RPKM 5.0), lymph node (RPKM 4.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LSM6 in Genome Data Viewer
    Location:
    4q31.22
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (146175718..146191535)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (149491695..149507512)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (147096870..147112687)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377468 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:146975373-146976572 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21976 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21978 Neighboring gene uncharacterized LOC105377469 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21979 Neighboring gene long intergenic non-protein coding RNA 1095 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15739 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:147143236-147144435 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:147162227-147163143 Neighboring gene Sharpr-MPRA regulatory region 13307 Neighboring gene reeler domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21981 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21982 Neighboring gene solute carrier family 10 member 7 Neighboring gene uncharacterized LOC105377472

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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 Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Translation and replication of hepatitis C virus genomic RNA depends on ancient cellular proteins that control mRNA fates. Scheller N, et al. Proc Natl Acad Sci U S A, 2009 Aug 11. PMID 19628699, Free PMC Article
    2. Autoantibody to hLSm4 and the heptameric LSm complex in anti-Sm sera. Eystathioy T, et al. Arthritis Rheum, 2002 Mar. PMID 11920408
    3. Specific sequences of the Sm and Sm-like (Lsm) proteins mediate their interaction with the spinal muscular atrophy disease gene product (SMN). Friesen WJ, et al. J Biol Chem, 2000 Aug 25. PMID 10851237
    4. UBE2E ubiquitin-conjugating enzymes and ubiquitin isopeptidase Y regulate TDP-43 protein ubiquitination. Hans F, et al. J Biol Chem, 2014 Jul 4. PMID 24825905, Free PMC Article
    5. The C-Terminal RGG Domain of Human Lsm4 Promotes Processing Body Formation Stimulated by Arginine Dimethylation. Arribas-Layton M, et al. Mol Cell Biol, 2016 Sep 1. PMID 27247266, Free PMC Article

    See all (57) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LSm1-7 proteins colocalize with DCP1,DCP2 and Xrn1 in cytoplasmic foci
      Title: The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein heterodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within mRNA catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in maturation of SSU-rRNA IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in tRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of Lsm2-8 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type precatalytic spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U4/U6 x U5 tri-snRNP complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of U6 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of small nuclear ribonucleoprotein complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    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 U6 small nuclear RNA and mRNA degradation associated
    LSM6 homolog, U6 small nuclear RNA associated
    Sm protein F

    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_007080.3 → NP_009011.1  U6 snRNA-associated Sm-like protein LSm6

      See identical proteins and their annotated locations for NP_009011.1

      Status: VALIDATED

      Source sequence(s)
      AC097372, AI351504, BC016026, DB465201
      Consensus CDS
      CCDS3767.1
      UniProtKB/Swiss-Prot
      P62312, Q4W5J5, Q9Y4Y8
      Related
      ENSP00000296581.5, ENST00000296581.11
      Conserved Domains (1) summary
      cd01726
      Location:7 → 74
      LSm6; Like-Sm protein 6

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      146175718..146191535
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017007673.2 → XP_016863162.1  U6 snRNA-associated Sm-like protein LSm6 isoform X1

      UniProtKB/Swiss-Prot
      P62312, Q4W5J5, Q9Y4Y8
      Related
      ENSP00000422392.1, ENST00000502781.5
      Conserved Domains (1) summary
      cd01726
      Location:7 → 74
      LSm6; Like-Sm protein 6

    2. XM_017007672.2 → XP_016863161.1  U6 snRNA-associated Sm-like protein LSm6 isoform X1

      UniProtKB/Swiss-Prot
      P62312, Q4W5J5, Q9Y4Y8
      Related
      ENSP00000497311.1, ENST00000649747.1
      Conserved Domains (1) summary
      cd01726
      Location:7 → 74
      LSm6; Like-Sm protein 6

    RNA

    1. XR_001741098.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      149491695..149507512
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348836.1 → XP_054204811.1  U6 snRNA-associated Sm-like protein LSm6 isoform X1

      UniProtKB/Swiss-Prot
      P62312, Q4W5J5, Q9Y4Y8

    2. XM_054348835.1 → XP_054204810.1  U6 snRNA-associated Sm-like protein LSm6 isoform X1

      UniProtKB/Swiss-Prot
      P62312, Q4W5J5, Q9Y4Y8

    RNA

    1. XR_008486892.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P62312.1 GenPept UniProtKB/Swiss-Prot:P62312

    Gene LinkOut

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

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