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Aliases for LSM1 Gene

Aliases for LSM1 Gene

  • LSM1 Homolog, MRNA Degradation Associated 2 3 5
  • 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-Like Protein U6 Small Nuclear RNA Associated 3
  • LSM1 Homolog, U6 Small Nuclear RNA Associated 3
  • U6 SnRNA-Associated Sm-Like Protein LSm1 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 Pancreatic Cancer. Among its related pathways are Deadenylation-dependent mRNA decay and Gene Expression. 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

Enhancers for LSM1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH08F038175 1.5 FANTOM5 Ensembl ENCODE 0.8 -0.8 -803 4.9 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 FOS ENSG00000254306 DDHD2 LETM2 LOC102723716 FGFR1 BAG4 NSD3 LSM1 GC08M038027
GH08F038181 0.9 Ensembl ENCODE 0.4 -5.4 -5371 1.0 BCOR KLF1 ZNF680 ZBTB7A ZNF121 ZNF341 ZNF580 ZBTB33 ZNF600 SPI1 DDHD2 LETM2 FGFR1 LSM1 GC08M038027
GH08F038184 0.8 Ensembl ENCODE 0.4 -7.9 -7871 0.4 DRAP1 CTCF MXI1 PKNOX1 SAP130 ARID4B CEBPG ZNF2 RAD21 CHAMP1 LETM2 DDHD2 ENSG00000254898 LOC102723716 RAB11FIP1 LSM1 GC08M038027
GH08F038195 0.2 ENCODE 0.3 -19.0 -19018 0.2 MTA2 ZBED1 JUNB TBX21 EP300 IKZF1 TCF7 ZBTB33 RNU6-323P LETM2 GC08M038027 LSM1
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around LSM1 on UCSC Golden Path with GeneCards custom track

Promoters for LSM1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001390109 -270 4001 HDGF PKNOX1 CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 FOS

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

Genes around LSM1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LSM1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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

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:0003723 RNA binding IEA --
GO:0003729 mRNA binding IEA --
GO:0005515 protein binding IPI 15231747
GO:0036002 pre-mRNA binding IEA --
genes like me logo Genes that share ontologies with LSM1: view
genes like me logo Genes that share phenotypes with LSM1: view

Animal Models for LSM1 Gene

MGI Knock Outs for LSM1:
  • Lsm1 tm1b(EUCOMM)Hmgu

Animal Model Products

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , 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
cytosol 5
nucleus 5

Gene Ontology (GO) - Cellular Components for LSM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 cytoplasmic mRNA processing body IEA,IBA --
GO:0005634 nucleus IEA,IDA 18559850
GO:0005737 cytoplasm IDA 18559850
GO:0005829 cytosol TAS --
GO:0030424 axon IEA --
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: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 IEA,TAS 10369684
GO:0019827 stem cell population maintenance IEA --
genes like me logo Genes that share ontologies with LSM1: view

No data available for SIGNOR curated interactions for LSM1 Gene

Transcripts for LSM1 Gene

Unigene Clusters for LSM1 Gene

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

Inhibitory RNA Products

Clone Products

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, MaxQB, and MOPED for LSM1 Gene



Protein tissue co-expression partners for LSM1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LSM1 Gene:

LSM1

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

Primer 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
chimpanzee
(Pan troglodytes)
Mammalia LSM1 34 35
  • 99.5 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LSM1 35
  • 97 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LSM1 34 35
  • 94.24 (n)
dog
(Canis familiaris)
Mammalia LSM1 34 35
  • 93.73 (n)
rat
(Rattus norvegicus)
Mammalia Lsm1 34
  • 90.48 (n)
mouse
(Mus musculus)
Mammalia Lsm1 34 16 35
  • 90.23 (n)
oppossum
(Monodelphis domestica)
Mammalia LSM1 35
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves LSM1 34 35
  • 75.19 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia lsm1 34
  • 78.95 (n)
Str.15407 34
zebrafish
(Danio rerio)
Actinopterygii lsm1 34 35
  • 75.44 (n)
Dr.14834 34
fruit fly
(Drosophila melanogaster)
Insecta CG4279 36
  • 63 (a)
LSm1 34 35
  • 62.37 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001686 34
  • 59.6 (n)
worm
(Caenorhabditis elegans)
Secernentea lsm-1 34 35
  • 58.61 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LSM1 34 35 37
  • 61.32 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E15159g 34
  • 56.43 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFL212C 34
  • 54.78 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G14080 34
  • 53.67 (n)
rice
(Oryza sativa)
Liliopsida Os04g0445800 34
  • 56.09 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes lsm1 34
  • 54.24 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.10250 34
Species where no ortholog for LSM1 was found in the sources mined by GeneCards:
  • 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
rs10095098 -- 38,170,510(+) AAAAA(A/C)CCATA intron-variant
rs10099971 -- 38,175,958(+) GAAGC(A/C)CCCCC intron-variant, upstream-variant-2KB
rs10683003 -- 38,162,840(+) TTTTT(-/TTTT)GAGAC intron-variant, downstream-variant-500B
rs111528122 -- 38,172,513(+) GATGG(C/T)GTATC intron-variant
rs112053141 -- 38,163,067(+) TACCC(A/G)CCTCG intron-variant, downstream-variant-500B

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

Variant ID Type Subtype PubMed ID
dgv7162n100 CNV gain 25217958
nsv397579 CNV deletion 16902084

Variation tolerance for LSM1 Gene

Residual Variation Intolerance Score: 46.8% 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

SNPedia medical, phenotypic, and genealogical associations of SNPs for
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: DISEASES and GeneCards

Disorder Aliases PubMed IDs
pancreatic cancer
  • pancreatic carcinoma, somatic
- elite association - COSMIC cancer census association via MalaCards
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. Common variants on 8p12 and 1q24.2 confer risk of schizophrenia. (PMID: 22037555) Shi Y. … He L. (Nat. Genet. 2011) 3 46 64
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  3. Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'. (PMID: 18172165) Mullen T.E. … Marzluff W.F. (Genes Dev. 2008) 3 4 64
  4. 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) 3 22 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for LSM1 Gene

Sources for LSM1 Gene

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