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LSM4 (LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated)

Identity

Alias_namesLSM4 homolog
Alias_symbol (synonym)YER112W
Other aliasGRP
HGNC (Hugo) LSM4
LocusID (NCBI) 25804
Atlas_Id 46135
Location 19p13.11  [Link to chromosome band 19p13]
Location_base_pair Starts at 18306230 and ends at 18323191 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
KPNB1 (17q21.32) / LSM4 (19p13.11)LSM4 (19p13.11) / ATP11A (13q34)LSM4 (19p13.11) / ELL (19p13.11)
LSM4 (19p13.11) / LSM4 (19p13.11)

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)LSM4   17259
Cards
Entrez_Gene (NCBI)LSM4  25804  LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated
AliasesGRP; YER112W
GeneCards (Weizmann)LSM4
Ensembl hg19 (Hinxton)ENSG00000130520 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000130520 [Gene_View]  chr19:18306230-18323191 [Contig_View]  LSM4 [Vega]
ICGC DataPortalENSG00000130520
TCGA cBioPortalLSM4
AceView (NCBI)LSM4
Genatlas (Paris)LSM4
WikiGenes25804
SOURCE (Princeton)LSM4
Genetics Home Reference (NIH)LSM4
Genomic and cartography
GoldenPath hg38 (UCSC)LSM4  -     chr19:18306230-18323191 -  19p13.11   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LSM4  -     19p13.11   [Description]    (hg19-Feb_2009)
EnsemblLSM4 - 19p13.11 [CytoView hg19]  LSM4 - 19p13.11 [CytoView hg38]
Mapping of homologs : NCBILSM4 [Mapview hg19]  LSM4 [Mapview hg38]
OMIM607284   
Gene and transcription
Genbank (Entrez)AA722246 AF117235 AF182290 AF251218 AJ238096
RefSeq transcript (Entrez)NM_001252129 NM_012321
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)LSM4
Cluster EST : UnigeneHs.515255 [ NCBI ]
CGAP (NCI)Hs.515255
Alternative Splicing GalleryENSG00000130520
Gene ExpressionLSM4 [ NCBI-GEO ]   LSM4 [ EBI - ARRAY_EXPRESS ]   LSM4 [ SEEK ]   LSM4 [ MEM ]
Gene Expression Viewer (FireBrowse)LSM4 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)25804
GTEX Portal (Tissue expression)LSM4
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9Y4Z0   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9Y4Z0  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9Y4Z0
Splice isoforms : SwissVarQ9Y4Z0
PhosPhoSitePlusQ9Y4Z0
Domains : Interpro (EBI)Lsm4    LSm4/Sm_D1/D3    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)LSM4
DMDM Disease mutations25804
Blocks (Seattle)LSM4
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   
SuperfamilyQ9Y4Z0
Human Protein AtlasENSG00000130520
Peptide AtlasQ9Y4Z0
HPRD06284
IPIIPI00294955   
Protein Interaction databases
DIP (DOE-UCLA)Q9Y4Z0
IntAct (EBI)Q9Y4Z0
FunCoupENSG00000130520
BioGRIDLSM4
STRING (EMBL)LSM4
ZODIACLSM4
Ontologies - Pathways
QuickGOQ9Y4Z0
Ontology : AmiGOspliceosomal complex assembly  spliceosomal snRNP assembly  mRNA splicing, via spliceosome  P-body  nuclear-transcribed mRNA catabolic process  RNA binding  protein binding  nucleoplasm  spliceosomal complex  U6 snRNP  cytosol  cytosol  RNA splicing  membrane  U6 snRNA binding  cytoplasmic mRNA processing body assembly  PH domain binding  neuron projection  protein complex  exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay  spliceosomal tri-snRNP complex  
Ontology : EGO-EBIspliceosomal complex assembly  spliceosomal snRNP assembly  mRNA splicing, via spliceosome  P-body  nuclear-transcribed mRNA catabolic process  RNA binding  protein binding  nucleoplasm  spliceosomal complex  U6 snRNP  cytosol  cytosol  RNA splicing  membrane  U6 snRNA binding  cytoplasmic mRNA processing body assembly  PH domain binding  neuron projection  protein complex  exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay  spliceosomal tri-snRNP complex  
Pathways : KEGGRNA degradation    Spliceosome   
NDEx NetworkLSM4
Atlas of Cancer Signalling NetworkLSM4
Wikipedia pathwaysLSM4
Orthology - Evolution
OrthoDB25804
GeneTree (enSembl)ENSG00000130520
Phylogenetic Trees/Animal Genes : TreeFamLSM4
HOVERGENQ9Y4Z0
HOGENOMQ9Y4Z0
Homologs : HomoloGeneLSM4
Homology/Alignments : Family Browser (UCSC)LSM4
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLSM4 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LSM4
dbVarLSM4
ClinVarLSM4
1000_GenomesLSM4 
Exome Variant ServerLSM4
ExAC (Exome Aggregation Consortium)LSM4 (select the gene name)
Genetic variants : HAPMAP25804
Genomic Variants (DGV)LSM4 [DGVbeta]
DECIPHERLSM4 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisLSM4 
Mutations
ICGC Data PortalLSM4 
TCGA Data PortalLSM4 
Broad Tumor PortalLSM4
OASIS PortalLSM4 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLSM4  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDLSM4
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 LSM4
DgiDB (Drug Gene Interaction Database)LSM4
DoCM (Curated mutations)LSM4 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LSM4 (select a term)
intoGenLSM4
Cancer3DLSM4(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM607284   
Orphanet
MedgenLSM4
Genetic Testing Registry LSM4
NextProtQ9Y4Z0 [Medical]
TSGene25804
GENETestsLSM4
Target ValidationLSM4
Huge Navigator LSM4 [HugePedia]
snp3D : Map Gene to Disease25804
BioCentury BCIQLSM4
ClinGenLSM4
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD25804
Chemical/Pharm GKB GenePA134906569
Clinical trialLSM4
Miscellaneous
canSAR (ICR)LSM4 (select the gene name)
Probes
Litterature
PubMed35 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLSM4
EVEXLSM4
GoPubMedLSM4
iHOPLSM4
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 25 19:16:35 CEST 2017

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