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

    Gene ID: 50783, updated on 9-May-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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    See Lsm4 in Genome Data Viewer
    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)
    • Endonuclease-mediated (2) 
    • Gene trapped (1)  1 citation

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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