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

    Gene ID: 25804, updated on 6-May-2024

    Summary

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    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; AllianceGenome:HGNC:17259
    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
    mouse all
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    Genomic context

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    Location:
    19p13.11
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (18306236..18323076, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (18440354..18457193, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (18417046..18433886, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904652 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18398502-18399345 Neighboring gene CRISPRi-validated cis-regulatory element chr19.2871 Neighboring gene ribosomal protein L39 pseudogene 38 Neighboring gene uncharacterized LOC124904653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10385 Neighboring gene CRISPRi-validated cis-regulatory element chr19.2872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18404637-18405276 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:18405513-18405695 Neighboring gene CRISPRi-validated cis-regulatory element chr19.2873 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18415779-18416284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18417751-18418708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18425352-18425852 Neighboring gene uncharacterized LOC105372300 Neighboring gene Sharpr-MPRA regulatory region 14103 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:18429424-18430170 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10389 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14313 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:18434425-18435027 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14314 Neighboring gene uncharacterized LOC124904654 Neighboring gene RNA, 7SL, cytoplasmic 513, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:18451278-18451965 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:18454745-18455584 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr19:18455585-18456422 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr19:18456925-18457507 Neighboring gene pyroglutamyl-peptidase I Neighboring gene ReSE screen-validated silencer GRCh37_chr19:18460464-18460672 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:18472794-18473579 Neighboring gene Sharpr-MPRA regulatory region 798

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. [Phase Separation of Purified Human LSM4 Protein]. Li H, et al. Mol Biol (Mosk), 2023 Jan-Feb. PMID 36976747
    2. LSm4 associates with the plasma membrane and acts as a co-factor in cell volume regulation. Gandini R, et al. Cell Physiol Biochem, 2008. PMID 19088440
    3. Circ_0025033 promotes the progression of ovarian cancer by activating the expression of LSM4 via targeting miR-184. Hou W, et al. Pathol Res Pract, 2021 Jan. PMID 33285422
    4. The C-terminal extension of Lsm4 interacts directly with the 3' end of the histone mRNP and is required for efficient histone mRNA degradation. Lyons SM, et al. RNA, 2014 Jan. PMID 24255165, Free PMC Article
    5. Multiple interacting oncogenes on the 8p11-p12 amplicon in human breast cancer. Yang ZQ, et al. Cancer Res, 2006 Dec 15. PMID 17178857

    See all (83) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. METTL3-mediated the m6A modification of SF3B4 facilitates the development of non-small cell lung cancer by enhancing LSM4 expression.
      Title: METTL3-mediated the m6A modification of SF3B4 facilitates the development of non-small cell lung cancer by enhancing LSM4 expression.
    2. [Phase Separation of Purified Human LSM4 Protein].
      Title: [Phase Separation of Purified Human LSM4 Protein].
    3. Circ_0025033 promotes the progression of ovarian cancer by activating the expression of LSM4 via targeting miR-184.
      Title: Circ_0025033 promotes the progression of ovarian cancer by activating the expression of LSM4 via targeting miR-184.
    4. Results show that the RGG domain of human Lsm4 stimulates processing bodies formation. Also, a novel interaction of the Lsm4 RGG domain with HAT1 and RBBP7 was discovered, leading to the possibility of a posttranslational modifications network involved in mRNP regulation.
      Title: The C-Terminal RGG Domain of Human Lsm4 Promotes Processing Body Formation Stimulated by Arginine Dimethylation.
    5. C-terminal extension of Lsm4 interacts directly with the histone mRNP, contacting both SLBP and 3'hExo.
      Title: The C-terminal extension of Lsm4 interacts directly with the 3' end of the histone mRNP and is required for efficient histone mRNA degradation.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
    7. LSm4 not only acts in RNA processing, but also as a co-factor in cell volume regulation.
      Title: LSm4 associates with the plasma membrane and acts as a co-factor in cell volume regulation.
    8. Data show that ICln159, a truncated ICln mutant, belongs to the pleckstrin homology (PH) domain family of proteins and interacts with LSm4, a protein involved in splicing and mRNA degradation.
      Title: ICln159 folds into a pleckstrin homology domain-like structure. Interaction with kinases and the splicing factor LSm4.
    9. Gene induces transformed phenotype when overexpressed in a cancer breast cell line.
      Title: Multiple interacting oncogenes on the 8p11-p12 amplicon in human breast cancer.
    10. LSm1-7 proteins colocalize with DCP1,DCP2 and Xrn1 in cytoplasmic foci
      Title: The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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 GOA

    Function Evidence Code Pubs
    enables PH domain binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA binding HDA PubMed 
    enables U6 snRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in P-body assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in RNA splicing TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of U2-type precatalytic spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U4/U6 x U5 tri-snRNP complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of U4/U6 x U5 tri-snRNP complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of U6 snRNP IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    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 U6 small nuclear RNA and mRNA degradation associated
    LSM4 homolog, U6 small nuclear RNA associated
    glycine-rich protein

    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_001252129.2 → NP_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:1 → 63
      LSm4; Like-Sm protein 4

    2. NM_012321.5 → NP_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
      ENSP00000469468.2, ENST00000593829.6
      Conserved Domains (1) summary
      cd01723
      Location:2 → 77
      LSm4; Like-Sm protein 4

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      18440354..18457193 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y4Z0.1 GenPept UniProtKB/Swiss-Prot:Q9Y4Z0

    Gene LinkOut

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

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