Free for academic non-profit institutions. Other users need a Commercial license

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-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. Among its related pathways are Gene Expression and Deadenylation-dependent mRNA decay. Gene Ontology (GO) annotations related to this gene include RNA cap binding.

UniProtKB/Swiss-Prot for LSM1 Gene

  • Plays a role in the degradation of histone mRNAs, the only eukaryotic mRNAs that are not polyadenylated (PubMed:18172165). Probably also part of an LSm subunits-containing complex involved in the general process of mRNA degradation (By similarity).

Gene Wiki entry for LSM1 Gene

Additional gene information for LSM1 Gene

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

Genomics for LSM1 Gene

GeneHancer (GH) Regulatory Elements for LSM1 Gene

Promoters and enhancers for LSM1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08I038175 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 550.8 -0.8 -767 4.9 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B E2F8 ZNF207 BAG4 LSM1 DDHD2 LETM2 ADGRA2 LOC102723716 ERLIN2 FGFR1 NSD3 GC08M038027
GH08I038170 Enhancer 1 ENCODE dbSUPER 0.8 +3.9 3884 3.8 HDAC1 HDGF RAD21 ZNF366 ZNF143 KLF7 EGR2 SMARCA5 ZNF654 ZNF362 DDHD2 LETM2 BAG4 LSM1 GC08M038168 RNU6-323P GC08M038027
GH08I038165 Enhancer 1.1 ENCODE dbSUPER 0.4 +9.9 9876 2.3 FOXA2 ARID4B DMAP1 YY1 ZNF121 RXRA MXD4 MIER2 PPARG ZNF592 GC08M038168 RNU6-323P DDHD2 BAG4 LSM1 GC08M038027
GH08I038181 Enhancer 0.8 Ensembl ENCODE 0.4 -5.2 -5171 0.6 BCOR ZNF680 ZNF121 NFIC ZNF766 ZNF341 ZNF580 ZBTB33 ZNF600 ZNF18 DDHD2 LETM2 FGFR1 BAG4 LSM1 GC08M038027
GH08I038184 Enhancer 0.8 ENCODE 0.4 -7.9 -7878 0.2 PKNOX1 FOXA2 ARID4B SIN3A ZNF2 RAD21 CHAMP1 ZSCAN5C SCRT2 ZNF143 LETM2 DDHD2 ENSG00000254898 LOC102723716 RAB11FIP1 BAG4 LSM1 GC08M038027
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around LSM1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LSM1 gene promoter:

Genomic Locations for LSM1 Gene

Genomic Locations for LSM1 Gene
chr8:38,163,321-38,176,730
(GRCh38/hg38)
Size:
13,410 bases
Orientation:
Minus strand
chr8:38,020,839-38,034,248
(GRCh37/hg19)

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 (PubMed:18172165). LSm subunits form a heteromer with a donut shape (By similarity).

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

Gene Families for LSM1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

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

Function for LSM1 Gene

Molecular function for LSM1 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in the degradation of histone mRNAs, the only eukaryotic mRNAs that are not polyadenylated (PubMed:18172165). Probably also part of an LSm subunits-containing complex involved in the general process of mRNA degradation (By similarity).

Phenotypes From GWAS Catalog for LSM1 Gene

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 HDA,IEA 22658674
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

Clone 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

Cytoplasm. Cytoplasm, P-body.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LSM1 gene
Compartment Confidence
nucleus 5
cytosol 5

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Vesicles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LSM1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000932 P-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:0000290 deadenylation-dependent decapping of nuclear-transcribed mRNA IBA --
GO:0000375 RNA splicing, via transesterification reactions TAS 10369684
GO:0000956 nuclear-transcribed mRNA catabolic process IEA --
GO:0006397 mRNA processing TAS,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:

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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

Evidence on tissue expression from TISSUES for LSM1 Gene

  • Lymph node(4.3)
  • Nervous system(4.3)
  • Eye(4.2)
  • Liver(2)
  • Muscle(2)
genes like me logo Genes that share expression patterns with LSM1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 33 34
  • 99.5 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia LSM1 34
  • 97 (a)
OneToOne
cow
(Bos Taurus)
Mammalia LSM1 33 34
  • 94.24 (n)
dog
(Canis familiaris)
Mammalia LSM1 33 34
  • 93.73 (n)
rat
(Rattus norvegicus)
Mammalia Lsm1 33
  • 90.48 (n)
mouse
(Mus musculus)
Mammalia Lsm1 33 16 34
  • 90.23 (n)
oppossum
(Monodelphis domestica)
Mammalia LSM1 34
  • 80 (a)
OneToOne
chicken
(Gallus gallus)
Aves LSM1 33 34
  • 75.19 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia lsm1 33
  • 78.95 (n)
Str.15407 33
zebrafish
(Danio rerio)
Actinopterygii lsm1 33 34
  • 75.44 (n)
Dr.14834 33
fruit fly
(Drosophila melanogaster)
Insecta CG4279 35
  • 63 (a)
LSm1 33 34
  • 62.37 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001686 33
  • 59.6 (n)
worm
(Caenorhabditis elegans)
Secernentea lsm-1 33 34
  • 58.61 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes LSM1 33 34 36
  • 61.32 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E15159g 33
  • 56.43 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFL212C 33
  • 54.78 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G14080 33
  • 53.67 (n)
rice
(Oryza sativa)
Liliopsida Os04g0445800 33
  • 56.09 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes lsm1 33
  • 54.24 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.10250 33
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 Variation AA Info Type
rs1000000268 -- 38,176,068(-) T/A intron_variant
rs1000096517 -- 38,171,438(-) G/A intron_variant
rs1000254934 -- 38,177,093(-) C/T upstream_transcript_variant
rs1000392532 -- 38,175,889(-) T/G intron_variant
rs1000449486 -- 38,176,224(-) G/A intron_variant

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)

Additional Variant Information for LSM1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LSM1

SNP Genotyping and Copy Number Assay Products

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

Disorders for LSM1 Gene

Additional Disease Information for LSM1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for LSM1 Gene.

No data available for MalaCards , 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 (Nature genetics 2011) 3 44 58
  2. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  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 TE … Marzluff WF (Genes & development 2008) 3 4 58
  4. CaSm (LSm-1) overexpression in lung cancer and mesothelioma is required for transformed phenotypes. (PMID: 18218995) Watson PM … Boylan AM (American journal of respiratory cell and molecular biology 2008) 3 22 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for LSM1 Gene

Sources for LSM1 Gene

Content
Loading form....