LSM2 LSM2 homolog, U6 small nuclear RNA and mRNA degradation associated [Homo sapiens (human)] - Gene

Summary

Official Symbol: LSM2provided by HGNC
Official Full Name: LSM2 homolog, U6 small nuclear RNA and mRNA degradation associatedprovided by HGNC
Primary source: HGNC:HGNC:13940
See related: Ensembl:ENSG00000204392 MIM:607282; AllianceGenome:HGNC:13940
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: G7B; snRNP; C6orf28; YBL026W
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. Pseudogenes of this gene are located on the short arm of chromosomes 6 and 19. [provided by RefSeq, Nov 2011]
Expression: Ubiquitous expression in lymph node (RPKM 15.9), appendix (RPKM 13.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.33

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (31797396..31806966, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (31650444..31660015, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (31765173..31774743, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The mechanism of LSM2 in the progression of live hepatocellular carcinoma was analyzed based on bioinformatics.
Title: The mechanism of LSM2 in the progression of live hepatocellular carcinoma was analyzed based on bioinformatics.
LSM2 is associated with a poor prognosis and promotes cell proliferation, migration, and invasion in skin cutaneous melanoma.
Title: LSM2 is associated with a poor prognosis and promotes cell proliferation, migration, and invasion in skin cutaneous melanoma.
SNRPN is a key player in pancreatic adenocarcinoma cell growth; depletion of SNRPN led to S phase cell cycle arrest and apoptosis
Title: Small nuclear ribonucleoprotein associated polypeptide N accelerates cell proliferation in pancreatic adenocarcinoma.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of gene-disease association. (HuGE Navigator)
Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Use of expression data and the CGEMS genome-wide breast cancer association study to identify genes that may modify risk in BRCA1/2 mutation carriers.
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

RH102480 (e-PCR)
- UniSTS:96814

STS-AA035265 (e-PCR)
- UniSTS:40895

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
contributes_to RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables U6 snRNA binding	NAS Non-traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables small GTPase binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within mRNA catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	IC Inferred by Curator 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
acts_upstream_of_or_within spliceosomal tri-snRNP complex assembly	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of Lsm1-7-Pat1 complex	IBA Inferred from Biological aspect of Ancestor more info
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	IBA Inferred from Biological aspect of Ancestor more info
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
part_of catalytic step 2 spliceosome	IBA Inferred from Biological aspect of Ancestor more info
part_of catalytic step 2 spliceosome	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
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 precatalytic spliceosome	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: U6 snRNA-associated Sm-like protein LSm2

Names: LSM2 U6 small nuclear RNA and mRNA degradation associated; LSM2 homolog, U6 small nuclear RNA associated; protein G7b; small nuclear ribonuclear protein D homolog; snRNP core Sm-like protein Sm-x5

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.