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

Gene ID: 11157, updated on 5-Mar-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
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Genomic context

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Location:
4q31.22
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (146175718..146191535)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (149491695..149507512)
105.20220307 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. 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
  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. 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

See all (53) 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)

Genotypes

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_2023_10

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

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