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Lsm4 LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated [ Mus musculus (house mouse) ]

Gene ID: 50783, updated on 5-Mar-2024

Summary

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Official Symbol
Lsm4provided by MGI
Official Full Name
LSM4 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by MGI
Primary source
MGI:MGI:1354692
See related
Ensembl:ENSMUSG00000031848 AllianceGenome:MGI:1354692
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
Summary
Predicted to enable PH domain binding activity and U6 snRNA binding activity. Predicted to be involved in P-body assembly and spliceosomal snRNP assembly. Predicted to act upstream of or within RNA splicing and mRNA processing. Predicted to be located in several cellular components, including cytosol; neuron projection; and nucleoplasm. Predicted to be part of Lsm2-8 complex; U2-type precatalytic spliceosome; and spliceosomal snRNP complex. Predicted to be active in P-body. Is expressed in branchial arch; central nervous system; limb; maxillary process; and sensory organ. Orthologous to human LSM4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in liver E14.5 (RPKM 70.2), CNS E11.5 (RPKM 67.3) and 28 other tissues See more
Orthologs
human all
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Genomic context

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Location:
8 B3.3; 8 34.15 cM
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (71124663..71131402)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (70673231..70678752)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_21778 Neighboring gene predicted gene, 34154 Neighboring gene STARR-seq mESC enhancer starr_21782 Neighboring gene pyroglutamyl-peptidase I Neighboring gene STARR-positive B cell enhancer ABC_E10505 Neighboring gene STARR-positive B cell enhancer ABC_E6646 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:73197019-73197273 Neighboring gene predicted gene, 39191 Neighboring gene STARR-positive B cell enhancer ABC_E6647 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:73219441-73219628 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:73222195-73222304 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:73222558-73222745 Neighboring gene STARR-positive B cell enhancer ABC_E6648 Neighboring gene jun D proto-oncogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

Bibliography

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Related articles in PubMed

  1. Peri-implantation lethality in mice lacking the Sm motif-containing protein Lsm4. Hirsch E, et al. Mol Cell Biol, 2000 Feb. PMID 10629062, Free PMC Article
  2. Role for LSM genes in the regulation of circadian rhythms. Perez-Santángelo S, et al. Proc Natl Acad Sci U S A, 2014 Oct 21. PMID 25288739, Free PMC Article
  3. Comparative analysis of human 19p12-13 region in Fugu and mouse. Clarke D, et al. Mamm Genome, 2001 Jun. PMID 11353399
  4. GW182 is critical for the stability of GW bodies expressed during the cell cycle and cell proliferation. Yang Z, et al. J Cell Sci, 2004 Nov 1. PMID 15494374
  5. USP15 Deubiquitinates TUT1 Associated with RNA Metabolism and Maintains Cerebellar Homeostasis. Kim J, et al. Mol Cell Biol, 2020 Oct 13. PMID 32839293, Free PMC Article

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Gene trapped (1)  1 citation
  • Endonuclease-mediated (2) 

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

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables PH domain binding ISO
Inferred from Sequence Orthology
more info
  
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables U6 snRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in P-body assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in RNA processing IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA splicing, via spliceosome ISO
Inferred from Sequence Orthology
more info
  
involved_in nuclear-transcribed mRNA catabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in spliceosomal snRNP assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
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 ISO
Inferred from Sequence Orthology
more info
  
part_of U6 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
located_in membrane ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
part_of protein-containing complex ISO
Inferred from Sequence Orthology
more info
  
part_of ribonucleoprotein complex IEA
Inferred from Electronic Annotation
more info
  
part_of spliceosomal complex ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
part_of spliceosomal tri-snRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
U6 snRNA-associated Sm-like protein LSm4
Names
LSM4 homolog, U6 small nuclear RNA associated
U6 snRNA-associated SM-like protein 4

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_001359042.1 → NP_001345971.1  U6 snRNA-associated Sm-like protein LSm4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC162446, AC166931, CD776868
    UniProtKB/TrEMBL
    Q9D181
    Related
    ENSMUSP00000147320.2, ENSMUST00000210071.2
    Conserved Domains (1) summary
    cd01723
    Location:1 → 63
    LSm4; Like-Sm protein 4

  2. NM_015816.4 → NP_056631.2  U6 snRNA-associated Sm-like protein LSm4 isoform 1

    See identical proteins and their annotated locations for NP_056631.2

    Status: VALIDATED

    Source sequence(s)
    AJ249439, AK010910, CA322716
    Consensus CDS
    CCDS40374.1
    UniProtKB/TrEMBL
    Q9CY46, Q9D181
    Related
    ENSMUSP00000034311.9, ENSMUST00000034311.15
    Conserved Domains (1) summary
    cd01723
    Location:2 → 77
    LSm4; Like-Sm protein 4

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_000074.7 Reference GRCm39 C57BL/6J

    Range
    71124663..71131402
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030243665.2 → XP_030099525.1  U6 snRNA-associated Sm-like protein LSm4 isoform X1

    UniProtKB/TrEMBL
    Q9CY46, Q9D181
    Conserved Domains (1) summary
    cd01723
    Location:2 → 77
    LSm4; Like-Sm protein 4
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9QXA5.1 GenPept UniProtKB/Swiss-Prot:Q9QXA5

Gene LinkOut

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