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

Summary

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

Location:: 19p13.11

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (18306236..18323076, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (18440354..18457193, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (18417046..18433886, complement)

Chromosome 19 - NC_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
[Phase Separation of Purified Human LSM4 Protein].
Title: [Phase Separation of Purified Human LSM4 Protein].
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.
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.
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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
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.
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.
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.
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.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH64873 (e-PCR)
- UniSTS:13586

G29334 (e-PCR)
- UniSTS:14960

LSM4 (e-PCR)
- UniSTS:505728

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 more info	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)

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
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