LSM1 LSM1 homolog, mRNA degradation associated [Homo sapiens (human)] - Gene

Summary

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Official Symbol: LSM1provided by HGNC
Official Full Name: LSM1 homolog, mRNA degradation associatedprovided by HGNC
Primary source: HGNC:HGNC:20472
See related: Ensembl:ENSG00000175324 MIM:607281; AllianceGenome:HGNC:20472
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: CASM; YJL124C
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. Increased expression of this gene may play a role in cellular transformation and the progression of several malignancies including lung cancer, mesothelioma and breast cancer. Alternatively spliced transcript variants have been observed for this gene, and a pseudogene of this gene is located on the short arm of chromosome 9. [provided by RefSeq, Nov 2011]
Expression: Ubiquitous expression in heart (RPKM 16.1), placenta (RPKM 14.6) and 25 other tissues See more
Orthologs: mouse all
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Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (38163321..38176730, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (38440300..38453709, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (38020839..38034248, complement)

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?

The role of LSM1 in breast cancer: Shaping metabolism and tumor-associated macrophage infiltration.
Title: The role of LSM1 in breast cancer: Shaping metabolism and tumor-associated macrophage infiltration.
Integrated analysis of pivotal biomarker of LSM1, immune cell infiltration and therapeutic drugs in breast cancer.
Title: Integrated analysis of pivotal biomarker of LSM1, immune cell infiltration and therapeutic drugs in breast cancer.
DIS3L2 and LSm proteins are involved in the surveillance of Sm ring-deficient snRNAs.
Title: DIS3L2 and LSm proteins are involved in the surveillance of Sm ring-deficient snRNAs.
These results provide evidence that LSm1 binding to the DENV RNA 3' UTR positively regulates DENV RNA replication.
Title: LSm1 binds to the Dengue virus RNA 3' UTR and is a positive regulator of Dengue virus replication.
The results of this study provided further support for previous genetic findings reporting the association of an intronic SNP (rs16887244) in LSM1 and schizophrenia in a Chinese sample
Title: Further evidence for the association between the LSM1 gene and schizophrenia.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Results suggest that LSm-1/CaSm functions as an oncogene in the promotion of cellular transformation and cancer progression.
Title: CaSm (LSm-1) overexpression in lung cancer and mesothelioma is required for transformed phenotypes.
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.
LSM1 is a breast cancer oncogene from the 8p11-12 amplicon.
Title: Transforming function of the LSM1 oncogene in human breast cancers with the 8p11-12 amplicon.
Lsm1 is deeply involved in prostate cancer progression through its down-regulation, independent of any gene mutation.
Title: Down-regulation of Lsm1 is involved in human prostate cancer progression.

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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

EBI GWAS Catalog

Description
Common variants on 8p12 and 1q24.2 confer risk of schizophrenia. EBI GWAS Catalog EBI GWAS CatalogPubMed

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

RH46977 (e-PCR)
- UniSTS:48335

STS-T10665 (e-PCR)
- UniSTS:30168

D8S2102 (e-PCR)
- UniSTS:57084

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables pre-mRNA binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA splicing	TAS Traceable Author Statement more info	PubMed
involved_in RNA splicing, via transesterification reactions	TAS Traceable Author Statement more info	PubMed
involved_in deadenylation-dependent decapping of nuclear-transcribed mRNA	IBA Inferred from Biological aspect of Ancestor more info
involved_in histone mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in neuron differentiation	IEA Inferred from Electronic Annotation more info
involved_in stem cell population maintenance	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of Lsm1-7-Pat1 complex	IBA Inferred from Biological aspect of Ancestor more info
is_active_in P-body	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in dendrite	IEA Inferred from Electronic Annotation more info
located_in neuronal cell body	IEA Inferred from Electronic Annotation more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of ribonucleoprotein complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: U6 snRNA-associated Sm-like protein LSm1

Names: LSM1 homolog, U6 small nuclear RNA associated; LSM1 mRNA degradation associated; LSM1, U6 small nuclear RNA associated; LSM1-like protein U6 small nuclear RNA associated; cancer-associated Sm protein; cancer-associated Sm-like protein; small nuclear ribonuclear CaSm

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_014462.3 → NP_055277.1 U6 snRNA-associated Sm-like protein LSm1

See identical proteins and their annotated locations for NP_055277.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and is protein-coding.

Source sequence(s)

AJ238094, BP376421

Consensus CDS

CCDS6103.1

UniProtKB/Swiss-Prot

B2R5E6, O15116

UniProtKB/TrEMBL

A0A0S2Z590

Related

ENSP00000310596.4, ENST00000311351.9

Conserved Domains (2) summary

PRK10788
Location:64 → 131

PRK10788; periplasmic folding chaperone; Provisional

cd01728
Location:4 → 77

LSm1; Like-Sm protein 1

RNA

NR_045492.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1.

Source sequence(s)

BE670269, BU521199

Related

ENST00000520755.5
NR_045493.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the 5' region, compared to variant 1. This variant is represented as non-coding because it lacks an in-frame coding region, compared to variant 1.

Source sequence(s)

AF147348, BE670269, BU941962

Related

ENST00000520286.5