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

Gene ID: 11157, updated on 10-Oct-2019

Summary

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
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

Genomic context

See LSM6 in Genome Data Viewer
Location:
4q31.22
Exon count:
8
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (146175703..146204436)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (147096835..147111213)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377469 Neighboring gene uncharacterized LOC105377470 Neighboring gene long intergenic non-protein coding RNA 1095 Neighboring gene reeler domain containing 1 Neighboring gene solute carrier family 10 member 7 Neighboring gene uncharacterized LOC105377472

Genomic regions, transcripts, and products

Expression

  • 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

Pathways from BioSystems

  • Deadenylation-dependent mRNA decay, organism-specific biosystem (from REACTOME)
    Deadenylation-dependent mRNA decay, organism-specific biosystemAfter undergoing rounds of translation, mRNA is normally destroyed by the deadenylation-dependent pathway. Though the trigger is unclear, deadenylation likely proceeds in two steps: one catalyzed by...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Lsm 1-7 complex, organism-specific biosystem (from KEGG)
    Lsm 1-7 complex, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Lsm 1-7 complex, conserved biosystem (from KEGG)
    Lsm 1-7 complex, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • Lsm 2-8 complex, organism-specific biosystem (from KEGG)
    Lsm 2-8 complex, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Lsm 2-8 complex, conserved biosystem (from KEGG)
    Lsm 2-8 complex, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • RNA degradation, organism-specific biosystem (from KEGG)
    RNA degradation, organism-specific biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
  • RNA degradation, conserved biosystem (from KEGG)
    RNA degradation, conserved biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystem (from KEGG)
    Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mRNA decay by 5' to 3' exoribonuclease, organism-specific biosystem (from REACTOME)
    mRNA decay by 5' to 3' exoribonuclease, organism-specific biosystemDegradation of mRNA from 5' to 3' occurs in three steps. First, the mRNA is bound at its 3' end by the Lsm1-7 complex. The bound Lsm1-7 may prevent nucleases from accessing the 3' end. Second, the 7-...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA splicing TAS
Traceable Author Statement
more info
PubMed 
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS
Traceable Author Statement
more info
 
mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
maturation of SSU-rRNA IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
tRNA processing IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Lsm2-8 complex IDA
Inferred from Direct Assay
more info
PubMed 
P-body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
U4/U6 x U5 tri-snRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U4/U6 x U5 tri-snRNP complex IDA
Inferred from Direct Assay
more info
PubMed 
U6 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
small nuclear ribonucleoprotein complex TAS
Traceable Author Statement
more info
PubMed 
small nucleolar ribonucleoprotein complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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)

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_007080.3NP_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
    Related
    ENSP00000296581.5, ENST00000296581.11
    Conserved Domains (1) summary
    cd01726
    Location:774
    LSm6; Like-Sm protein 6

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    146175703..146204436
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/Swiss-Prot
    P62312
    Related
    ENSP00000497311.1, ENST00000649747.1
    Conserved Domains (1) summary
    cd01726
    Location:774
    LSm6; Like-Sm protein 6
  2. XM_017007673.1XP_016863162.1  U6 snRNA-associated Sm-like protein LSm6 isoform X1

    UniProtKB/Swiss-Prot
    P62312
    Related
    ENSP00000422392.1, ENST00000502781.5
    Conserved Domains (1) summary
    cd01726
    Location:774
    LSm6; Like-Sm protein 6

RNA

  1. XR_001741099.1 RNA Sequence

  2. XR_001741100.1 RNA Sequence

  3. XR_001741098.1 RNA Sequence

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