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

Gene ID: 25804, updated on 5-Mar-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
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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. [Phase Separation of Purified Human LSM4 Protein].
    Title: [Phase Separation of Purified Human LSM4 Protein].
  2. 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.
  3. 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.
  4. 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.
  5. Observational study of gene-disease association. (HuGE Navigator)
    Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
  6. 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.
  7. 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.
  8. 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.
  9. 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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