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

Gene ID: 23658, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (32485338..32495283, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (32624513..32634448, complement)
105.20220307 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
  • 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 (46) 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

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_2023_10

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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