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LSM1 (LSM1 homolog, mRNA degradation associated)

Identity

Alias_namesLSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)
LSM1, U6 small nuclear RNA associated
Alias_symbol (synonym)CASM
YJL124C
Other alias
HGNC (Hugo) LSM1
LocusID (NCBI) 27257
Atlas_Id 41208
Location 8p11.23  [Link to chromosome band 8p11]
Location_base_pair Starts at 38020839 and ends at 38034248 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
ADAM18 (8p11.22) / LSM1 (8p11.23)KIAA0556 (16p12.1) / LSM1 (8p11.23)LPP (3q28) / LSM1 (8p11.23)
LSM1 (8p11.23) / WHSC1L1 (8p11.23)PHB (17q21.33) / LSM1 (8p11.23)ADAM18 8p11.22 / LSM1 8p11.23
LSM1 8p11.23 / WHSC1L1 8p11.23PHB 17q21.33 / LSM1 8p11.23

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  Lung: Translocations in Squamous Cell Carcinoma


External links

Nomenclature
HGNC (Hugo)LSM1   20472
Cards
Entrez_Gene (NCBI)LSM1  27257  LSM1 homolog, mRNA degradation associated
AliasesCASM; YJL124C
GeneCards (Weizmann)LSM1
Ensembl hg19 (Hinxton)ENSG00000175324 [Gene_View]  chr8:38020839-38034248 [Contig_View]  LSM1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000175324 [Gene_View]  chr8:38020839-38034248 [Contig_View]  LSM1 [Vega]
ICGC DataPortalENSG00000175324
TCGA cBioPortalLSM1
AceView (NCBI)LSM1
Genatlas (Paris)LSM1
WikiGenes27257
SOURCE (Princeton)LSM1
Genetics Home Reference (NIH)LSM1
Genomic and cartography
GoldenPath hg19 (UCSC)LSM1  -     chr8:38020839-38034248 -  8p11.23   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)LSM1  -     8p11.23   [Description]    (hg38-Dec_2013)
EnsemblLSM1 - 8p11.23 [CytoView hg19]  LSM1 - 8p11.23 [CytoView hg38]
Mapping of homologs : NCBILSM1 [Mapview hg19]  LSM1 [Mapview hg38]
OMIM607281   
Gene and transcription
Genbank (Entrez)AF000177 AF147348 AJ238094 AK312159 BC001767
RefSeq transcript (Entrez)NM_014462
RefSeq genomic (Entrez)NC_000008 NC_018919 NT_167187 NW_004929337
Consensus coding sequences : CCDS (NCBI)LSM1
Cluster EST : UnigeneHs.425311 [ NCBI ]
CGAP (NCI)Hs.425311
Alternative Splicing GalleryENSG00000175324
Gene ExpressionLSM1 [ NCBI-GEO ]   LSM1 [ EBI - ARRAY_EXPRESS ]   LSM1 [ SEEK ]   LSM1 [ MEM ]
Gene Expression Viewer (FireBrowse)LSM1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)27257
GTEX Portal (Tissue expression)LSM1
Protein : pattern, domain, 3D structure
UniProt/SwissProtO15116   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO15116  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO15116
Splice isoforms : SwissVarO15116
PhosPhoSitePlusO15116
Domains : Interpro (EBI)LSM_dom    LSM_dom_euk/arc   
Domain families : Pfam (Sanger)LSM (PF01423)   
Domain families : Pfam (NCBI)pfam01423   
Domain families : Smart (EMBL)Sm (SM00651)  
Conserved Domain (NCBI)LSM1
DMDM Disease mutations27257
Blocks (Seattle)LSM1
SuperfamilyO15116
Human Protein AtlasENSG00000175324
Peptide AtlasO15116
HPRD06281
IPIIPI00004436   IPI00795354   IPI00794259   
Protein Interaction databases
DIP (DOE-UCLA)O15116
IntAct (EBI)O15116
FunCoupENSG00000175324
BioGRIDLSM1
STRING (EMBL)LSM1
ZODIACLSM1
Ontologies - Pathways
QuickGOO15116
Ontology : AmiGOdeadenylation-dependent decapping of nuclear-transcribed mRNA  RNA cap binding  RNA splicing, via transesterification reactions  cytoplasmic mRNA processing body  mRNA binding  protein binding  nucleus  cytoplasm  cytosol  mRNA processing  RNA splicing  stem cell population maintenance  axon  dendrite  pre-mRNA binding  neuronal cell body  exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay  poly(A) RNA binding  negative regulation of neuron differentiation  histone mRNA catabolic process  messenger ribonucleoprotein complex  
Ontology : EGO-EBIdeadenylation-dependent decapping of nuclear-transcribed mRNA  RNA cap binding  RNA splicing, via transesterification reactions  cytoplasmic mRNA processing body  mRNA binding  protein binding  nucleus  cytoplasm  cytosol  mRNA processing  RNA splicing  stem cell population maintenance  axon  dendrite  pre-mRNA binding  neuronal cell body  exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay  poly(A) RNA binding  negative regulation of neuron differentiation  histone mRNA catabolic process  messenger ribonucleoprotein complex  
Pathways : KEGGRNA degradation   
NDEx NetworkLSM1
Atlas of Cancer Signalling NetworkLSM1
Wikipedia pathwaysLSM1
Orthology - Evolution
OrthoDB27257
GeneTree (enSembl)ENSG00000175324
Phylogenetic Trees/Animal Genes : TreeFamLSM1
HOVERGENO15116
HOGENOMO15116
Homologs : HomoloGeneLSM1
Homology/Alignments : Family Browser (UCSC)LSM1
Gene fusions - Rearrangements
Fusion : MitelmanADAM18/LSM1 [8p11.22/8p11.23]  [t(8;8)(p11;p11)]  
Fusion : MitelmanKIAA0556/LSM1 [16p12.1/8p11.23]  [t(8;16)(p11;p12)]  
Fusion : MitelmanLSM1/WHSC1L1 [8p11.23/8p11.23]  [t(8;8)(p11;p12)]  
Fusion : MitelmanPHB/LSM1 [17q21.33/8p11.23]  [t(8;17)(p11;q21)]  
Fusion: TCGAADAM18 8p11.22 LSM1 8p11.23 BRCA
Fusion: TCGALSM1 8p11.23 WHSC1L1 8p11.23 LUSC
Fusion: TCGAPHB 17q21.33 LSM1 8p11.23 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLSM1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LSM1
dbVarLSM1
ClinVarLSM1
1000_GenomesLSM1 
Exome Variant ServerLSM1
ExAC (Exome Aggregation Consortium)LSM1 (select the gene name)
Genetic variants : HAPMAP27257
Genomic Variants (DGV)LSM1 [DGVbeta]
DECIPHER (Syndromes)8:38020839-38034248  ENSG00000175324
CONAN: Copy Number AnalysisLSM1 
Mutations
ICGC Data PortalLSM1 
TCGA Data PortalLSM1 
Broad Tumor PortalLSM1
OASIS PortalLSM1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLSM1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDLSM1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch LSM1
DgiDB (Drug Gene Interaction Database)LSM1
DoCM (Curated mutations)LSM1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LSM1 (select a term)
intoGenLSM1
Cancer3DLSM1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM607281   
Orphanet
MedgenLSM1
Genetic Testing Registry LSM1
NextProtO15116 [Medical]
TSGene27257
GENETestsLSM1
Huge Navigator LSM1 [HugePedia]
snp3D : Map Gene to Disease27257
BioCentury BCIQLSM1
ClinGenLSM1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD27257
Chemical/Pharm GKB GenePA134864226
Clinical trialLSM1
Miscellaneous
canSAR (ICR)LSM1 (select the gene name)
Probes
Litterature
PubMed36 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLSM1
EVEXLSM1
GoPubMedLSM1
iHOPLSM1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Mar 14 13:13:52 CET 2017

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