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LSM3 (LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated)

Identity

Alias_namesLSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae)
Alias_symbol (synonym)YLR438C
SMX4
USS2
Other alias
HGNC (Hugo) LSM3
LocusID (NCBI) 27258
Atlas_Id 68687
Location 3p25.1  [Link to chromosome band 3p25]
Location_base_pair Starts at 14178728 and ends at 14198369 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
ZACN (17q25.1) / LSM3 (3p25.1)

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

 


External links

Nomenclature
HGNC (Hugo)LSM3   17874
Cards
Entrez_Gene (NCBI)LSM3  27258  LSM3 homolog, U6 small nuclear RNA and mRNA degradation associated
AliasesSMX4; USS2; YLR438C
GeneCards (Weizmann)LSM3
Ensembl hg19 (Hinxton)ENSG00000170860 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000170860 [Gene_View]  ENSG00000170860 [Sequence]  chr3:14178728-14198369 [Contig_View]  LSM3 [Vega]
ICGC DataPortalENSG00000170860
TCGA cBioPortalLSM3
AceView (NCBI)LSM3
Genatlas (Paris)LSM3
WikiGenes27258
SOURCE (Princeton)LSM3
Genetics Home Reference (NIH)LSM3
Genomic and cartography
GoldenPath hg38 (UCSC)LSM3  -     chr3:14178728-14198369 +  3p25.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LSM3  -     3p25.1   [Description]    (hg19-Feb_2009)
GoldenPathLSM3 - 3p25.1 [CytoView hg19]  LSM3 - 3p25.1 [CytoView hg38]
ImmunoBaseENSG00000170860
Mapping of homologs : NCBILSM3 [Mapview hg19]  LSM3 [Mapview hg38]
OMIM607283   
Gene and transcription
Genbank (Entrez)AF182289 AF182418 AJ238095 AK312189 BC007055
RefSeq transcript (Entrez)NM_014463
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)LSM3
Cluster EST : UnigeneHs.111632 [ NCBI ]
CGAP (NCI)Hs.111632
Alternative Splicing GalleryENSG00000170860
Gene ExpressionLSM3 [ NCBI-GEO ]   LSM3 [ EBI - ARRAY_EXPRESS ]   LSM3 [ SEEK ]   LSM3 [ MEM ]
Gene Expression Viewer (FireBrowse)LSM3 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)27258
GTEX Portal (Tissue expression)LSM3
Human Protein AtlasENSG00000170860-LSM3 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP62310   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP62310  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP62310
Splice isoforms : SwissVarP62310
PhosPhoSitePlusP62310
Domains : Interpro (EBI)Lsm3    LSM_dom_euk/arc    LSM_dom_sf   
Domain families : Pfam (Sanger)LSM (PF01423)   
Domain families : Pfam (NCBI)pfam01423   
Domain families : Smart (EMBL)Sm (SM00651)  
Conserved Domain (NCBI)LSM3
DMDM Disease mutations27258
Blocks (Seattle)LSM3
PDB (RSDB)3JCR    5O9Z   
PDB Europe3JCR    5O9Z   
PDB (PDBSum)3JCR    5O9Z   
PDB (IMB)3JCR    5O9Z   
Structural Biology KnowledgeBase3JCR    5O9Z   
SCOP (Structural Classification of Proteins)3JCR    5O9Z   
CATH (Classification of proteins structures)3JCR    5O9Z   
SuperfamilyP62310
Human Protein Atlas [tissue]ENSG00000170860-LSM3 [tissue]
Peptide AtlasP62310
HPRD06283
IPIIPI00219229   
Protein Interaction databases
DIP (DOE-UCLA)P62310
IntAct (EBI)P62310
FunCoupENSG00000170860
BioGRIDLSM3
STRING (EMBL)LSM3
ZODIACLSM3
Ontologies - Pathways
QuickGOP62310
Ontology : AmiGOmRNA splicing, via spliceosome  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  P-body  RNA binding  RNA binding  protein binding  nucleus  nucleus  nucleoplasm  U6 snRNP  cytosol  mRNA processing  cytoplasmic mRNA processing body assembly  exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay  U4/U6 x U5 tri-snRNP complex  U4/U6 x U5 tri-snRNP complex  U2-type precatalytic spliceosome  catalytic step 2 spliceosome  catalytic step 2 spliceosome  Lsm2-8 complex  Lsm1-7-Pat1 complex  
Ontology : EGO-EBImRNA splicing, via spliceosome  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  mRNA splicing, via spliceosome  P-body  RNA binding  RNA binding  protein binding  nucleus  nucleus  nucleoplasm  U6 snRNP  cytosol  mRNA processing  cytoplasmic mRNA processing body assembly  exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay  U4/U6 x U5 tri-snRNP complex  U4/U6 x U5 tri-snRNP complex  U2-type precatalytic spliceosome  catalytic step 2 spliceosome  catalytic step 2 spliceosome  Lsm2-8 complex  Lsm1-7-Pat1 complex  
NDEx NetworkLSM3
Atlas of Cancer Signalling NetworkLSM3
Wikipedia pathwaysLSM3
Orthology - Evolution
OrthoDB27258
GeneTree (enSembl)ENSG00000170860
Phylogenetic Trees/Animal Genes : TreeFamLSM3
HOGENOMP62310
Homologs : HomoloGeneLSM3
Homology/Alignments : Family Browser (UCSC)LSM3
Gene fusions - Rearrangements
Fusion : QuiverLSM3
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLSM3 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LSM3
dbVarLSM3
ClinVarLSM3
1000_GenomesLSM3 
Exome Variant ServerLSM3
ExAC (Exome Aggregation Consortium)ENSG00000170860
GNOMAD BrowserENSG00000170860
Varsome BrowserLSM3
Genetic variants : HAPMAP27258
Genomic Variants (DGV)LSM3 [DGVbeta]
DECIPHERLSM3 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisLSM3 
Mutations
ICGC Data PortalLSM3 
TCGA Data PortalLSM3 
Broad Tumor PortalLSM3
OASIS PortalLSM3 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLSM3  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DLSM3
Mutations and Diseases : HGMDLSM3
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch LSM3
DgiDB (Drug Gene Interaction Database)LSM3
DoCM (Curated mutations)LSM3 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LSM3 (select a term)
intoGenLSM3
Cancer3DLSM3(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM607283   
Orphanet
DisGeNETLSM3
MedgenLSM3
Genetic Testing Registry LSM3
NextProtP62310 [Medical]
TSGene27258
GENETestsLSM3
Target ValidationLSM3
Huge Navigator LSM3 [HugePedia]
snp3D : Map Gene to Disease27258
BioCentury BCIQLSM3
ClinGenLSM3
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD27258
Chemical/Pharm GKB GenePA134881991
Clinical trialLSM3
Miscellaneous
canSAR (ICR)LSM3 (select the gene name)
DataMed IndexLSM3
Probes
Litterature
PubMed51 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLSM3
EVEXLSM3
GoPubMedLSM3
iHOPLSM3
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 Sep 3 15:51:19 CEST 2019

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