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    LSM5 LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated [ Homo sapiens (human) ]

    Gene ID: 23658, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LSM5provided by HGNC
    Official Full Name
    LSM5 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by HGNC
    Primary source
    HGNC:HGNC:17162
    See related
    Ensembl:ENSG00000106355 MIM:607285; AllianceGenome:HGNC:17162
    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
    YER146W
    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 thyroid (RPKM 6.1), colon (RPKM 6.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LSM5 in Genome Data Viewer
    Location:
    7p14.3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (32485338..32495283, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (32624513..32634448, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (32524950..32534895, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene phosphoribosyl pyrophosphate synthetase 2 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:32503825-32504417 Neighboring gene solute carrier family 25 member 5 pseudogene 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25825 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25826 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:32534898-32535696 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:32535697-32536495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25827 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:32552756-32553330 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:32553885-32554509 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25828 Neighboring gene AVL9 cell migration associated Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:32630869-32631369 Neighboring gene DPY19L1 pseudogene 1 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr7:32643581-32644106 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:32647796-32648296 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25829 Neighboring gene MPRA-validated peak6470 silencer Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:32720210-32720968 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:32727464-32728054 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:32742322-32742822 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:32742823-32743323 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:32747389-32747892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25830 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18079 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18080 Neighboring gene zinc and ring finger 2 pseudogene 1

    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 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. Autoantibody to hLSm4 and the heptameric LSm complex in anti-Sm sera. Eystathioy T, et al. Arthritis Rheum, 2002 Mar. PMID 11920408
    2. 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
    3. The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci. Ingelfinger D, et al. RNA, 2002 Dec. PMID 12515382, Free PMC Article
    4. A doughnut-shaped heteromer of human Sm-like proteins binds to the 3'-end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro. Achsel T, et al. EMBO J, 1999 Oct 15. PMID 10523320, Free PMC Article
    5. Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin. Salgado-Garrido J, et al. EMBO J, 1999 Jun 15. PMID 10369684, Free PMC Article

    See all (49) 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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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study identifies novel loci associated with concentrations of four plasma phospholipid fatty acids in the de novo lipogenesis pathway: results from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortiu
    EBI GWAS Catalog
    Genome-wide association study of primary dentition pit-and-fissure and smooth surface caries.
    EBI GWAS Catalog

    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

    Clone Names

    • FLJ12710

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to 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
    acts_upstream_of_or_within mRNA catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mRNA processing TAS
    Traceable Author Statement
    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 response to bacterium IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of Lsm1-7-Pat1 complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of Lsm2-8 complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    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
    		  
    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 

    General protein information

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    Preferred Names
    U6 snRNA-associated Sm-like protein LSm5
    Names
    LSM5 U6 small nuclear RNA and mRNA degradation associated
    LSM5 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_001130710.2 → NP_001124182.1  U6 snRNA-associated Sm-like protein LSm5 isoform b

      See identical proteins and their annotated locations for NP_001124182.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, lacks a segment of the 5' coding region, and uses a downstream translation initiation codon, compared to variant 1. The resulting isoform (b) is shorter at the N-terminus, compared to isoform a. Both variants 2 and 3 encode the same isoform.
      Source sequence(s)
      AC018641, AF182291, BF700164, BM786181, CX782029
      Consensus CDS
      CCDS47571.1
      UniProtKB/Swiss-Prot
      Q9Y4Y9
      Related
      ENSP00000386363.3, ENST00000409909.7
      Conserved Domains (1) summary
      cd01732
      Location:1 → 57
      LSm5; Like-Sm protein 5

    2. NM_001139499.2 → NP_001132971.1  U6 snRNA-associated Sm-like protein LSm5 isoform b

      See identical proteins and their annotated locations for NP_001132971.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, lacks a segment of the 5' coding region, and uses a downstream translation initiation codon, compared to variant 1. The resulting isoform (b) is shorter at the N-terminus, compared to isoform a. Both variants 2 and 3 encode the same isoform.
      Source sequence(s)
      AC018641, BF700164, CX782029, DA736378
      Consensus CDS
      CCDS47571.1
      UniProtKB/Swiss-Prot
      Q9Y4Y9
      Related
      ENSP00000387126.3, ENST00000409952.3
      Conserved Domains (1) summary
      cd01732
      Location:1 → 57
      LSm5; Like-Sm protein 5

    3. NM_012322.3 → NP_036454.1  U6 snRNA-associated Sm-like protein LSm5 isoform a

      See identical proteins and their annotated locations for NP_036454.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant encodes the longer isoform (a).
      Source sequence(s)
      AC018641, AF182291, BC040717, BF667238, BM786181, CX782029
      Consensus CDS
      CCDS5438.1
      UniProtKB/Swiss-Prot
      Q9Y4Y9
      UniProtKB/TrEMBL
      A0A090N8Y5
      Related
      ENSP00000410758.2, ENST00000450169.7
      Conserved Domains (1) summary
      cd01732
      Location:11 → 86
      LSm5; Like-Sm protein 5

    RNA

    1. NR_024466.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an alternate 5' exon, compared to variant 1. This variant is represented as non-coding because translation from the start codon used by variant 1 would result in nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC018641, BC040717, CX782029

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      32485338..32495283 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420100.1 → XP_047276056.1  U6 snRNA-associated Sm-like protein LSm5 isoform X1

      Related
      ENSP00000386707.1, ENST00000410044.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      32624513..32634448 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054357732.1 → XP_054213707.1  U6 snRNA-associated Sm-like protein LSm5 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y4Y9.3 GenPept UniProtKB/Swiss-Prot:Q9Y4Y9

    Gene LinkOut

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

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