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SMG6 (SMG6, nonsense mediated mRNA decay factor)

Identity

Alias_namesC17orf31
chromosome 17 open reading frame 31
smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)
SMG6 nonsense mediated mRNA decay factor
Alias_symbol (synonym)KIAA0732
SMG-6
EST1A
Other aliashSMG5/7a
HGNC (Hugo) SMG6
LocusID (NCBI) 23293
Atlas_Id 56420
Location 17p13.3  [Link to chromosome band 17p13]
Location_base_pair Starts at 2059839 and ends at 2266199 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
AD_1 () / SMG6 (17p13.3)CDK12 (17q12) / SMG6 (17p13.3)ETV1 (7p21.2) / SMG6 (17p13.3)
NPIPB7 (16q23.1) / SMG6 (17p13.3)SETD2 (3p21.31) / SMG6 (17p13.3)SLC43A2 (17p13.3) / SMG6 (17p13.3)
SMG6 (17p13.3) / C10orf11 (10q22.2)SMG6 (17p13.3) / DHX33 (17p13.2)SMG6 (17p13.3) / DSG2 (18q12.1)
SMG6 (17p13.3) / ERG (21q22.2)SMG6 (17p13.3) / ITFG2 (12p13.33)SMG6 (17p13.3) / NXN (17p13.3)
SMG6 (17p13.3) / TNRC6A (16p12.1)SMG6 (17p13.3) / WDR20 (14q32.31)ZFP36L1 (14q24.1) / SMG6 (17p13.3)

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)SMG6   17809
Cards
Entrez_Gene (NCBI)SMG6  23293  SMG6, nonsense mediated mRNA decay factor
AliasesC17orf31; EST1A; SMG-6; hSMG5/7a
GeneCards (Weizmann)SMG6
Ensembl hg19 (Hinxton)ENSG00000070366 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000070366 [Gene_View]  chr17:2059839-2266199 [Contig_View]  SMG6 [Vega]
ICGC DataPortalENSG00000070366
TCGA cBioPortalSMG6
AceView (NCBI)SMG6
Genatlas (Paris)SMG6
WikiGenes23293
SOURCE (Princeton)SMG6
Genetics Home Reference (NIH)SMG6
Genomic and cartography
GoldenPath hg38 (UCSC)SMG6  -     chr17:2059839-2266199 -  17p13.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SMG6  -     17p13.3   [Description]    (hg19-Feb_2009)
EnsemblSMG6 - 17p13.3 [CytoView hg19]  SMG6 - 17p13.3 [CytoView hg38]
Mapping of homologs : NCBISMG6 [Mapview hg19]  SMG6 [Mapview hg38]
OMIM610963   
Gene and transcription
Genbank (Entrez)AB018275 AK024131 AK074270 AK093007 AK302964
RefSeq transcript (Entrez)NM_001170957 NM_001256827 NM_001256828 NM_001282326 NM_017575
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SMG6
Cluster EST : UnigeneHs.448342 [ NCBI ]
CGAP (NCI)Hs.448342
Alternative Splicing GalleryENSG00000070366
Gene ExpressionSMG6 [ NCBI-GEO ]   SMG6 [ EBI - ARRAY_EXPRESS ]   SMG6 [ SEEK ]   SMG6 [ MEM ]
Gene Expression Viewer (FireBrowse)SMG6 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23293
GTEX Portal (Tissue expression)SMG6
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ86US8   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ86US8  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ86US8
Splice isoforms : SwissVarQ86US8
Catalytic activity : Enzyme3.1.-.- [ Enzyme-Expasy ]   3.1.-.-3.1.-.- [ IntEnz-EBI ]   3.1.-.- [ BRENDA ]   3.1.-.- [ KEGG ]   
PhosPhoSitePlusQ86US8
Domains : Interpro (EBI)DNA/RNA-bd_Est1-type    EST1    PIN_dom    PIN_domain-like    TPR-like_helical_dom   
Domain families : Pfam (Sanger)EST1 (PF10374)    EST1_DNA_bind (PF10373)    PIN_4 (PF13638)   
Domain families : Pfam (NCBI)pfam10374    pfam10373    pfam13638   
Domain families : Smart (EMBL)PINc (SM00670)  
Conserved Domain (NCBI)SMG6
DMDM Disease mutations23293
Blocks (Seattle)SMG6
PDB (SRS)2DOK    2HWW    2HWX    4UM2   
PDB (PDBSum)2DOK    2HWW    2HWX    4UM2   
PDB (IMB)2DOK    2HWW    2HWX    4UM2   
PDB (RSDB)2DOK    2HWW    2HWX    4UM2   
Structural Biology KnowledgeBase2DOK    2HWW    2HWX    4UM2   
SCOP (Structural Classification of Proteins)2DOK    2HWW    2HWX    4UM2   
CATH (Classification of proteins structures)2DOK    2HWW    2HWX    4UM2   
SuperfamilyQ86US8
Human Protein AtlasENSG00000070366
Peptide AtlasQ86US8
HPRD06502
IPIIPI00015793   IPI01012883   IPI01012801   IPI00014252   
Protein Interaction databases
DIP (DOE-UCLA)Q86US8
IntAct (EBI)Q86US8
FunCoupENSG00000070366
BioGRIDSMG6
STRING (EMBL)SMG6
ZODIACSMG6
Ontologies - Pathways
QuickGOQ86US8
Ontology : AmiGOnuclear-transcribed mRNA catabolic process, nonsense-mediated decay  nuclear-transcribed mRNA catabolic process, nonsense-mediated decay  telomerase catalytic core complex  chromosome, telomeric region  endoribonuclease activity  endoribonuclease activity  endoribonuclease activity  protein binding  nucleus  telomerase holoenzyme complex  nucleolus  cytoplasm  cytosol  cytosol  mRNA export from nucleus  regulation of telomere maintenance  regulation of telomere maintenance via telomerase  regulation of telomere maintenance via telomerase  exon-exon junction complex  regulation of dephosphorylation  telomeric DNA binding  ribonucleoprotein complex binding  regulation of RNA stability  metal ion binding  regulation of telomerase activity  telomerase RNA binding  DNA polymerase binding  RNA phosphodiester bond hydrolysis, endonucleolytic  negative regulation of telomere capping  
Ontology : EGO-EBInuclear-transcribed mRNA catabolic process, nonsense-mediated decay  nuclear-transcribed mRNA catabolic process, nonsense-mediated decay  telomerase catalytic core complex  chromosome, telomeric region  endoribonuclease activity  endoribonuclease activity  endoribonuclease activity  protein binding  nucleus  telomerase holoenzyme complex  nucleolus  cytoplasm  cytosol  cytosol  mRNA export from nucleus  regulation of telomere maintenance  regulation of telomere maintenance via telomerase  regulation of telomere maintenance via telomerase  exon-exon junction complex  regulation of dephosphorylation  telomeric DNA binding  ribonucleoprotein complex binding  regulation of RNA stability  metal ion binding  regulation of telomerase activity  telomerase RNA binding  DNA polymerase binding  RNA phosphodiester bond hydrolysis, endonucleolytic  negative regulation of telomere capping  
Pathways : KEGGmRNA surveillance pathway   
NDEx NetworkSMG6
Atlas of Cancer Signalling NetworkSMG6
Wikipedia pathwaysSMG6
Orthology - Evolution
OrthoDB23293
GeneTree (enSembl)ENSG00000070366
Phylogenetic Trees/Animal Genes : TreeFamSMG6
HOVERGENQ86US8
HOGENOMQ86US8
Homologs : HomoloGeneSMG6
Homology/Alignments : Family Browser (UCSC)SMG6
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMG6 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMG6
dbVarSMG6
ClinVarSMG6
1000_GenomesSMG6 
Exome Variant ServerSMG6
ExAC (Exome Aggregation Consortium)SMG6 (select the gene name)
Genetic variants : HAPMAP23293
Genomic Variants (DGV)SMG6 [DGVbeta]
DECIPHERSMG6 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSMG6 
Mutations
ICGC Data PortalSMG6 
TCGA Data PortalSMG6 
Broad Tumor PortalSMG6
OASIS PortalSMG6 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMG6  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSMG6
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 SMG6
DgiDB (Drug Gene Interaction Database)SMG6
DoCM (Curated mutations)SMG6 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMG6 (select a term)
intoGenSMG6
Cancer3DSMG6(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM610963   
Orphanet
MedgenSMG6
Genetic Testing Registry SMG6
NextProtQ86US8 [Medical]
TSGene23293
GENETestsSMG6
Target ValidationSMG6
Huge Navigator SMG6 [HugePedia]
snp3D : Map Gene to Disease23293
BioCentury BCIQSMG6
ClinGenSMG6
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23293
Chemical/Pharm GKB GenePA25584
Clinical trialSMG6
Miscellaneous
canSAR (ICR)SMG6 (select the gene name)
Probes
Litterature
PubMed46 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMG6
EVEXSMG6
GoPubMedSMG6
iHOPSMG6
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Jun 7 12:56:33 CEST 2017

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