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Lsm5 LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated [ Mus musculus (house mouse) ]

Gene ID: 66373, updated on 11-Apr-2024

Summary

Official Symbol
Lsm5provided by MGI
Official Full Name
LSM5 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by MGI
Primary source
MGI:MGI:1913623
See related
Ensembl:ENSMUSG00000091625 AllianceGenome:MGI:1913623
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
2010208O10Rik; 2310034K10Rik
Summary
Predicted to enable protein heterodimerization activity. Predicted to contribute to RNA binding activity. Acts upstream of or within response to bacterium. Predicted to be located in cytoplasm and nucleus. Predicted to be part of several cellular components, including Lsm1-7-Pat1 complex; Lsm2-8 complex; and spliceosomal snRNP complex. Is expressed in esophagus; midbrain ventricular layer; renal cortex; telencephalon ventricular layer; and thymus primordium. Orthologous to human LSM5 (LSM5 homolog, U6 small nuclear RNA and mRNA degradation associated). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in liver E14 (RPKM 29.2), CNS E11.5 (RPKM 27.3) and 11 other tissues See more
Orthologs
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Genomic context

See Lsm5 in Genome Data Viewer
Location:
6 B3; 6 27.72 cM
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (56678048..56681684, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (56701063..56704699, complement)

Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene phosphodiesterase 1C Neighboring gene STARR-seq mESC enhancer starr_15989 Neighboring gene predicted gene, 24709 Neighboring gene predicted gene, 22493 Neighboring gene CapStarr-seq enhancer MGSCv37_chr6:56654682-56654884 Neighboring gene STARR-seq mESC enhancer starr_15990 Neighboring gene STARR-positive B cell enhancer ABC_E679 Neighboring gene STARR-seq mESC enhancer starr_15991 Neighboring gene AVL9 cell migration associated Neighboring gene predicted gene 10209 Neighboring gene kelch repeat and BTB (POZ) domain containing 2

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

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 ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within mRNA catabolic process ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
 
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in mRNA splicing, via spliceosome ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within response to bacterium IEP
Inferred from Expression Pattern
more info
PubMed 
Component Evidence Code Pubs
part_of Lsm1-7-Pat1 complex IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of Lsm2-8 complex ISO
Inferred from Sequence Orthology
more info
 
part_of U2-type precatalytic spliceosome ISO
Inferred from Sequence Orthology
more info
 
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 ISO
Inferred from Sequence Orthology
more info
 
part_of U6 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
part_of ribonucleoprotein complex IEA
Inferred from Electronic Annotation
more info
 
part_of spliceosomal complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
U6 snRNA-associated Sm-like protein LSm5
Names
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_025520.3NP_079796.1  U6 snRNA-associated Sm-like protein LSm5

    See identical proteins and their annotated locations for NP_079796.1

    Status: VALIDATED

    Source sequence(s)
    BC061085, BC132626, CB204385
    Consensus CDS
    CCDS51788.1
    UniProtKB/Swiss-Prot
    A2RTT1, P62322
    Related
    ENSMUSP00000126565.3, ENSMUST00000170382.5
    Conserved Domains (1) summary
    cd01732
    Location:1186
    LSm5; Like-Sm protein 5

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000072.7 Reference GRCm39 C57BL/6J

    Range
    56678048..56681684 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)