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Lsm2 LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated [ Rattus norvegicus (Norway rat) ]

Gene ID: 684148, updated on 17-Aug-2024

Summary

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Official Symbol
Lsm2provided by RGD
Official Full Name
LSM2 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by RGD
Primary source
RGD:1598536
See related
EnsemblRapid:ENSRNOG00000048725 AllianceGenome:RGD:1598536
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as
G7b
Summary
Predicted to enable protein kinase binding activity and small GTPase binding activity. Predicted to contribute to RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to act upstream of or within mRNA catabolic process and spliceosomal tri-snRNP complex assembly. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be part of Lsm1-7-Pat1 complex; Lsm2-8 complex; and nucleus. Predicted to be active in P-body. Orthologous to human LSM2 (LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Thymus (RPKM 59.7), Testes (RPKM 57.0) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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Location:
20p12
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (3848120..3853298, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (3843467..3847217, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (4966817..4970567)

Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108349032 Neighboring gene ribosomal protein L13, pseudogene 1 Neighboring gene heat shock protein family A (Hsp70) member 1 like Neighboring gene heat shock protein family A (Hsp70) member 1A Neighboring gene heat shock protein family A (Hsp70) member 1B

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Identification of a novel protein, DMAP, which interacts with the myotonic dystrophy protein kinase and shows strong homology to D1 snRNP. Fu YH. Genetica, 1996 Jan. PMID 8851885
  2. 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
  3. 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
  4. The deubiquitylase USP33 discriminates between RALB functions in autophagy and innate immune response. Simicek M, et al. Nat Cell Biol, 2013 Oct. PMID 24056301
  5. The spliceosome: design principles of a dynamic RNP machine. Wahl MC, et al. Cell, 2009 Feb 20. PMID 19239890

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
contributes_to RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein kinase binding ISO
Inferred from Sequence Orthology
more info
  
enables small GTPase binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
acts_upstream_of_or_within mRNA catabolic process ISO
Inferred from Sequence Orthology
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 spliceosomal tri-snRNP complex assembly ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
more info
  
is_active_in P-body IBA
Inferred from Biological aspect of Ancestor
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
  
part_of catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of catalytic step 2 spliceosome ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
part_of precatalytic spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
U6 snRNA-associated Sm-like protein LSm2
Names
LSM2 U6 small nuclear RNA and mRNA degradation associated
LSM2 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_001004073.1 → NP_001004073.1  U6 snRNA-associated Sm-like protein LSm2 isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    BX883045
    UniProtKB/TrEMBL
    A6KTP7, M0R7N1, Q6MG66
    Related
    ENSRNOP00000065463.1, ENSRNOT00000070846.5
    Conserved Domains (1) summary
    cd01725
    Location:38 → 126
    LSm2; Like-Sm protein 2

  2. NM_001165922.1 → NP_001159394.1  U6 snRNA-associated Sm-like protein LSm2 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate 5' exon compared to variant 1. The resulting protein (isoform 2) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    BX883045
    UniProtKB/TrEMBL
    A0A0G2K8Q7, A6KTP6
    Conserved Domains (1) summary
    cd01725
    Location:2 → 90
    LSm2; Like-Sm protein 2

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086038.1 Reference GRCr8

    Range
    3848120..3853298 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063279506.1 → XP_063135576.1  U6 snRNA-associated Sm-like protein LSm2 isoform X1

Nucleotide Protein Strain
Heading Accession and Version

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