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Aliases for LSM1 Gene

Aliases for LSM1 Gene

  • LSM1 Homolog, MRNA Degradation Associated 2 3
  • LSM1, U6 Small Nuclear RNA Associated 2 3
  • Small Nuclear Ribonuclear CaSm 3 4
  • Cancer-Associated Sm Protein 2 3
  • CASM 3 4
  • LSM1 Homolog, U6 Small Nuclear RNA Associated (S. Cerevisiae) 2
  • LSM1 Homolog, U6 Small Nuclear RNA Associated 3
  • Cancer‐Associated Sm Protein 3
  • Cancer-Associated Sm-Like Protein 3
  • LSM1 MRNA Degradation Associated 3
  • Cancer-Associated Sm-Like 4
  • YJL124C 3

External Ids for LSM1 Gene

Previous GeneCards Identifiers for LSM1 Gene

  • GC08M037561
  • GC08M038149
  • GC08M037761
  • GC08M038038
  • GC08M036555
  • GC08M038020

Summaries for LSM1 Gene

Entrez Gene Summary for LSM1 Gene

  • 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]

GeneCards Summary for LSM1 Gene

LSM1 (LSM1 Homolog, MRNA Degradation Associated) is a Protein Coding gene. Diseases associated with LSM1 include mesothelioma. Among its related pathways are Gene Expression and Deadenylation-dependent mRNA decay. GO annotations related to this gene include poly(A) RNA binding and RNA cap binding.

UniProtKB/Swiss-Prot for LSM1 Gene

  • Plays a role in replication-dependent histone mRNA degradation. Binds specifically to the 3-terminal U-tract of U6 snRNA.

Gene Wiki entry for LSM1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LSM1 Gene

Genomics for LSM1 Gene

Regulatory Elements for LSM1 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for LSM1 Gene

Chromosome:
8
Start:
38,163,321 bp from pter
End:
38,176,730 bp from pter
Size:
13,410 bases
Orientation:
Minus strand

Genomic View for LSM1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for LSM1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LSM1 Gene

Proteins for LSM1 Gene

  • Protein details for LSM1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O15116-LSM1_HUMAN
    Recommended name:
    U6 snRNA-associated Sm-like protein LSm1
    Protein Accession:
    O15116
    Secondary Accessions:
    • B2R5E6

    Protein attributes for LSM1 Gene

    Size:
    133 amino acids
    Molecular mass:
    15179 Da
    Quaternary structure:
    • Interacts with SLBP. Interaction with SLBP occurs when histone mRNA is being rapidly degraded during the S phase. LSm subunits form a heteromer with a doughnut shape.

neXtProt entry for LSM1 Gene

Proteomics data for LSM1 Gene at MOPED

Post-translational modifications for LSM1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for LSM1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for LSM1 Gene

Domains & Families for LSM1 Gene

Suggested Antigen Peptide Sequences for LSM1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

O15116

UniProtKB/Swiss-Prot:

LSM1_HUMAN :
  • Belongs to the snRNP Sm proteins family.
Family:
  • Belongs to the snRNP Sm proteins family.
genes like me logo Genes that share domains with LSM1: view

No data available for Gene Families for LSM1 Gene

Function for LSM1 Gene

Molecular function for LSM1 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in replication-dependent histone mRNA degradation. Binds specifically to the 3-terminal U-tract of U6 snRNA.

Gene Ontology (GO) - Molecular Function for LSM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000339 RNA cap binding IBA --
GO:0005515 protein binding IPI 15231747
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with LSM1: view

Phenotypes for LSM1 Gene

GenomeRNAi human phenotypes for LSM1:
genes like me logo Genes that share phenotypes with LSM1: view

Animal Model Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for LSM1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for LSM1 Gene

Localization for LSM1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LSM1 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for LSM1 Gene COMPARTMENTS Subcellular localization image for LSM1 gene
Compartment Confidence
nucleus 5
cytosol 4

Gene Ontology (GO) - Cellular Components for LSM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 cytoplasmic mRNA processing body IBA --
GO:0005634 nucleus IDA 18559850
GO:0005737 cytoplasm IDA 18559850
GO:0005829 cytosol TAS --
GO:0005845 mRNA cap binding complex IBA --
genes like me logo Genes that share ontologies with LSM1: view

Pathways & Interactions for LSM1 Gene

genes like me logo Genes that share pathways with LSM1: view

Pathways by source for LSM1 Gene

1 KEGG pathway for LSM1 Gene

Gene Ontology (GO) - Biological Process for LSM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay TAS --
GO:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA IBA --
GO:0000375 RNA splicing, via transesterification reactions TAS 10369684
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing TAS 10369684
genes like me logo Genes that share ontologies with LSM1: view

No data available for SIGNOR curated interactions for LSM1 Gene

Drugs & Compounds for LSM1 Gene

No Compound Related Data Available

Transcripts for LSM1 Gene

Unigene Clusters for LSM1 Gene

LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae):
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for LSM1

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for LSM1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d
SP1:
SP2: - -
SP3: -
SP4: - -

Relevant External Links for LSM1 Gene

GeneLoc Exon Structure for
LSM1
ECgene alternative splicing isoforms for
LSM1

Expression for LSM1 Gene

mRNA expression in normal human tissues for LSM1 Gene

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for LSM1 Gene



SOURCE GeneReport for Unigene cluster for LSM1 Gene Hs.425311

mRNA Expression by UniProt/SwissProt for LSM1 Gene

O15116-LSM1_HUMAN
Tissue specificity: Has elevated expression in pancreatic cancer and in several cancer-derived cell lines
genes like me logo Genes that share expression patterns with LSM1: view

Protein tissue co-expression partners for LSM1 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Protein differential expression in normal tissues for LSM1 Gene

Orthologs for LSM1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for LSM1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia LSM1 35
  • 94.24 (n)
  • 99.25 (a)
LSM1 36
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia LSM1 35
  • 93.73 (n)
  • 100 (a)
LSM1 36
  • 100 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lsm1 35
  • 90.23 (n)
  • 97.74 (a)
Lsm1 16
Lsm1 36
  • 98 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia LSM1 35
  • 99.5 (n)
  • 100 (a)
LSM1 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lsm1 35
  • 90.48 (n)
  • 97.74 (a)
oppossum
(Monodelphis domestica)
Mammalia LSM1 36
  • 80 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LSM1 36
  • 97 (a)
OneToOne
chicken
(Gallus gallus)
Aves LSM1 35
  • 75.19 (n)
  • 93.23 (a)
LSM1 36
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia lsm1 35
  • 78.95 (n)
  • 95.49 (a)
Str.15407 35
zebrafish
(Danio rerio)
Actinopterygii Dr.14834 35
lsm1 35
  • 75.44 (n)
  • 85.71 (a)
lsm1 36
  • 86 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG4279 37
  • 63 (a)
LSm1 35
  • 62.37 (n)
  • 63.71 (a)
LSm1 36
  • 58 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001686 35
  • 59.6 (n)
  • 58.33 (a)
worm
(Caenorhabditis elegans)
Secernentea lsm-1 35
  • 58.61 (n)
  • 59.34 (a)
lsm-1 36
  • 49 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFL212C 35
  • 54.78 (n)
  • 49.57 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E15159g 35
  • 56.43 (n)
  • 47.37 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LSM1 35
  • 61.32 (n)
  • 56.79 (a)
LSM1 36
  • 29 (a)
OneToOne
LSM1 38
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G14080 35
  • 53.67 (n)
  • 54 (a)
rice
(Oryza sativa)
Liliopsida Os04g0445800 35
  • 56.09 (n)
  • 50 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.10250 35
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes lsm1 35
  • 54.24 (n)
  • 48.31 (a)
Species with no ortholog for LSM1:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for LSM1 Gene

ENSEMBL:
Gene Tree for LSM1 (if available)
TreeFam:
Gene Tree for LSM1 (if available)

Paralogs for LSM1 Gene

(1) SIMAP similar genes for LSM1 Gene using alignment to 3 proteins:

Pseudogenes.org Pseudogenes for LSM1 Gene

genes like me logo Genes that share paralogs with LSM1: view

No data available for Paralogs for LSM1 Gene

Variants for LSM1 Gene

Sequence variations from dbSNP and Humsavar for LSM1 Gene

SNP ID Clin Chr 08 pos Sequence Context AA Info Type MAF
rs2720051 -- 38,174,530(+) AGAGG(A/G)CCAAA intron-variant
rs2843738 -- 38,172,190(-) ATCCG(C/G)GTTGC intron-variant
rs2843739 -- 38,171,208(-) CTTCA(A/G)AGCAG intron-variant
rs2843744 -- 38,167,657(-) GAAAA(A/C/G)ACTTA intron-variant
rs2843745 -- 38,167,105(-) GAAAC(A/T)TGGTT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for LSM1 Gene

Variant ID Type Subtype PubMed ID
nsv397579 CNV Loss 16902084

Variation tolerance for LSM1 Gene

Residual Variation Intolerance Score: 46.79% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.13; 2.93% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for LSM1 Gene

HapMap Linkage Disequilibrium report
LSM1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LSM1 Gene

Disorders for LSM1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for LSM1 Gene - From: GeneCards

Disorder Aliases PubMed IDs
mesothelioma
- elite association
Search LSM1 in MalaCards View complete list of genes associated with diseases

Relevant External Links for LSM1

Genetic Association Database (GAD)
LSM1
Human Genome Epidemiology (HuGE) Navigator
LSM1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
LSM1
genes like me logo Genes that share disorders with LSM1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LSM1 Gene

Publications for LSM1 Gene

  1. CaSm (LSm-1) overexpression in lung cancer and mesothelioma is required for transformed phenotypes. (PMID: 18218995) Watson P.M. … Boylan A.M. (Am. J. Respir. Cell Mol. Biol. 2008) 23 67
  2. Bystander effect contributes to the antitumor efficacy of CaSm antisense gene therapy in a preclinical model of advanced pancreatic cancer. (PMID: 16226492) Yan Y. … Cole D.J. (Mol. Ther. 2006) 23 67
  3. Establishing a murine pancreatic cancer CaSm model: up-regulation of CaSm is required for the transformed phenotype of murine pancreatic adenocarcinoma. (PMID: 15727932) Yan Y. … Cole D.J. (Mol. Ther. 2005) 23 67
  4. CaSm antisense gene therapy: a novel approach for the treatment of pancreatic cancer. (PMID: 12894573) Kelley J.R. … Cole D.J. (Anticancer Res. 2003) 23 67
  5. Down-regulation of Lsm1 is involved in human prostate cancer progression. (PMID: 11953827) Takahashi S. … Shirai T. (Br. J. Cancer 2002) 2 67

Products for LSM1 Gene

Sources for LSM1 Gene

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