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LSM4 LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated [ Homo sapiens (human) ]

Gene ID: 25804, updated on 12-Oct-2019

Summary

Official Symbol
LSM4provided by HGNC
Official Full Name
LSM4 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by HGNC
Primary source
HGNC:HGNC:17259
See related
Ensembl:ENSG00000130520 MIM:607284
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
GRP; YER112W
Summary
This gene encodes a member of the LSm family of RNA-binding proteins. LSm proteins form stable heteromers that bind specifically to the 3'-terminal oligo(U) tract of U6 snRNA and may play a role in pre-mRNA splicing by mediating U4/U6 snRNP formation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]
Expression
Ubiquitous expression in testis (RPKM 22.8), colon (RPKM 19.7) and 25 other tissues See more
Orthologs

Genomic context

See LSM4 in Genome Data Viewer
Location:
19p13.11
Exon count:
5
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (18306236..18323076, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (18417040..18434001, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene microRNA 3188 Neighboring gene ribosomal protein L39 pseudogene 38 Neighboring gene Sharpr-MPRA regulatory region 14103 Neighboring gene uncharacterized LOC105372300 Neighboring gene RNA, 7SL, cytoplasmic 513, pseudogene Neighboring gene pyroglutamyl-peptidase I Neighboring gene Sharpr-MPRA regulatory region 798

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

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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
PH domain binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U6 snRNA 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 
cytoplasmic mRNA processing body assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS
Traceable Author Statement
more info
 
mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
spliceosomal snRNP assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IDA
Inferred from Direct Assay
more info
PubMed 
U6 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
neuron projection IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
U6 snRNA-associated Sm-like protein LSm4
Names
LSM4 U6 small nuclear RNA and mRNA degradation associated
LSM4 homolog, U6 small nuclear RNA associated
glycine-rich protein

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_001252129.2NP_001239058.1  U6 snRNA-associated Sm-like protein LSm4 isoform 2

    See identical proteins and their annotated locations for NP_001239058.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' coding region but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AA722246, BQ069184, BU539495, BX096089, CF147062, DB493307
    Consensus CDS
    CCDS62601.1
    UniProtKB/TrEMBL
    U3KQK1
    Related
    ENSP00000475950.1, ENST00000252816.10
    Conserved Domains (1) summary
    cd01723
    Location:163
    LSm4; Like-Sm protein 4
  2. NM_012321.5NP_036453.1  U6 snRNA-associated Sm-like protein LSm4 isoform 1

    See identical proteins and their annotated locations for NP_036453.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AA722246, BC000387, BU539495, BX096089, CF147062, DB493307
    Consensus CDS
    CCDS12374.1
    UniProtKB/Swiss-Prot
    Q9Y4Z0
    Related
    ENSP00000469468.1, ENST00000593829.5
    Conserved Domains (1) summary
    cd01723
    Location:277
    LSm4; Like-Sm protein 4

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_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    18306236..18323076 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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