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LSM6 (LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated)

Identity

Alias_namesLSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae)
Alias_symbol (synonym)YDR378C
Other alias
HGNC (Hugo) LSM6
LocusID (NCBI) 11157
Atlas_Id 68689
Location 4q31.22  [Link to chromosome band 4q31]
Location_base_pair Starts at 146175683 and ends at 146190061 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
SEMA6A (5q23.1) / LSM6 (4q31.22)

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)LSM6   17017
Cards
Entrez_Gene (NCBI)LSM6  11157  LSM6 homolog, U6 small nuclear RNA and mRNA degradation associated
AliasesYDR378C
GeneCards (Weizmann)LSM6
Ensembl hg19 (Hinxton)ENSG00000164167 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000164167 [Gene_View]  chr4:146175683-146190061 [Contig_View]  LSM6 [Vega]
ICGC DataPortalENSG00000164167
TCGA cBioPortalLSM6
AceView (NCBI)LSM6
Genatlas (Paris)LSM6
WikiGenes11157
SOURCE (Princeton)LSM6
Genetics Home Reference (NIH)LSM6
Genomic and cartography
GoldenPath hg38 (UCSC)LSM6  -     chr4:146175683-146190061 +  4q31.22   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LSM6  -     4q31.22   [Description]    (hg19-Feb_2009)
EnsemblLSM6 - 4q31.22 [CytoView hg19]  LSM6 - 4q31.22 [CytoView hg38]
Mapping of homologs : NCBILSM6 [Mapview hg19]  LSM6 [Mapview hg38]
OMIM607286   
Gene and transcription
Genbank (Entrez)AF182292 AI351504 AJ238098 AK312126 BC016026
RefSeq transcript (Entrez)NM_007080
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)LSM6
Cluster EST : UnigeneHs.190520 [ NCBI ]
CGAP (NCI)Hs.190520
Alternative Splicing GalleryENSG00000164167
Gene ExpressionLSM6 [ NCBI-GEO ]   LSM6 [ EBI - ARRAY_EXPRESS ]   LSM6 [ SEEK ]   LSM6 [ MEM ]
Gene Expression Viewer (FireBrowse)LSM6 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)11157
GTEX Portal (Tissue expression)LSM6
Protein : pattern, domain, 3D structure
UniProt/SwissProtP62312   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP62312  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP62312
Splice isoforms : SwissVarP62312
PhosPhoSitePlusP62312
Domains : Interpro (EBI)Lsm6/sSmF    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)LSM6
DMDM Disease mutations11157
Blocks (Seattle)LSM6
PDB (SRS)3JCR   
PDB (PDBSum)3JCR   
PDB (IMB)3JCR   
PDB (RSDB)3JCR   
Structural Biology KnowledgeBase3JCR   
SCOP (Structural Classification of Proteins)3JCR   
CATH (Classification of proteins structures)3JCR   
SuperfamilyP62312
Human Protein AtlasENSG00000164167
Peptide AtlasP62312
HPRD06286
IPIIPI00001146   
Protein Interaction databases
DIP (DOE-UCLA)P62312
IntAct (EBI)P62312
FunCoupENSG00000164167
BioGRIDLSM6
STRING (EMBL)LSM6
ZODIACLSM6
Ontologies - Pathways
QuickGOP62312
Ontology : AmiGOmRNA splicing, via spliceosome  RNA binding  protein binding  nucleoplasm  spliceosomal complex  small nucleolar ribonucleoprotein complex  cytosol  rRNA processing  tRNA processing  RNA splicing  small nuclear ribonucleoprotein complex  exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay  extracellular exosome  
Ontology : EGO-EBImRNA splicing, via spliceosome  RNA binding  protein binding  nucleoplasm  spliceosomal complex  small nucleolar ribonucleoprotein complex  cytosol  rRNA processing  tRNA processing  RNA splicing  small nuclear ribonucleoprotein complex  exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay  extracellular exosome  
Pathways : KEGGRNA degradation    Spliceosome   
NDEx NetworkLSM6
Atlas of Cancer Signalling NetworkLSM6
Wikipedia pathwaysLSM6
Orthology - Evolution
OrthoDB11157
GeneTree (enSembl)ENSG00000164167
Phylogenetic Trees/Animal Genes : TreeFamLSM6
HOVERGENP62312
HOGENOMP62312
Homologs : HomoloGeneLSM6
Homology/Alignments : Family Browser (UCSC)LSM6
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLSM6 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LSM6
dbVarLSM6
ClinVarLSM6
1000_GenomesLSM6 
Exome Variant ServerLSM6
ExAC (Exome Aggregation Consortium)LSM6 (select the gene name)
Genetic variants : HAPMAP11157
Genomic Variants (DGV)LSM6 [DGVbeta]
DECIPHERLSM6 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisLSM6 
Mutations
ICGC Data PortalLSM6 
TCGA Data PortalLSM6 
Broad Tumor PortalLSM6
OASIS PortalLSM6 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLSM6  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDLSM6
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch LSM6
DgiDB (Drug Gene Interaction Database)LSM6
DoCM (Curated mutations)LSM6 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LSM6 (select a term)
intoGenLSM6
Cancer3DLSM6(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM607286   
Orphanet
MedgenLSM6
Genetic Testing Registry LSM6
NextProtP62312 [Medical]
TSGene11157
GENETestsLSM6
Target ValidationLSM6
Huge Navigator LSM6 [HugePedia]
snp3D : Map Gene to Disease11157
BioCentury BCIQLSM6
ClinGenLSM6
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD11157
Chemical/Pharm GKB GenePA128394584
Clinical trialLSM6
Miscellaneous
canSAR (ICR)LSM6 (select the gene name)
Probes
Litterature
PubMed19 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLSM6
EVEXLSM6
GoPubMedLSM6
iHOPLSM6
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed May 31 15:25:08 CEST 2017

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