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SMG7 (SMG7, nonsense mediated mRNA decay factor)

Identity

Alias_namesC1orf16
chromosome 1 open reading frame 16
smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)
Alias_symbol (synonym)KIAA0250
EST1C
SGA56M
SMG-7
Other alias
HGNC (Hugo) SMG7
LocusID (NCBI) 9887
Atlas_Id 73556
Location 1q25.3  [Link to chromosome band 1q25]
Location_base_pair Starts at 183472371 and ends at 183554193 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)
CDK13 (7p14.1) / SMG7 (1q25.3)SMG7 (1q25.3) / FBXL20 (17q12)SMG7 (1q25.3) / HNRNPF (10q11.21)
SMG7 (1q25.3) / SMG7 (1q25.3)

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)SMG7   16792
Cards
Entrez_Gene (NCBI)SMG7  9887  SMG7, nonsense mediated mRNA decay factor
AliasesC1orf16; EST1C; SGA56M
GeneCards (Weizmann)SMG7
Ensembl hg19 (Hinxton)ENSG00000116698 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000116698 [Gene_View]  chr1:183472371-183554193 [Contig_View]  SMG7 [Vega]
ICGC DataPortalENSG00000116698
TCGA cBioPortalSMG7
AceView (NCBI)SMG7
Genatlas (Paris)SMG7
WikiGenes9887
SOURCE (Princeton)SMG7
Genetics Home Reference (NIH)SMG7
Genomic and cartography
GoldenPath hg38 (UCSC)SMG7  -     chr1:183472371-183554193 +  1q25.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SMG7  -     1q25.3   [Description]    (hg19-Feb_2009)
EnsemblSMG7 - 1q25.3 [CytoView hg19]  SMG7 - 1q25.3 [CytoView hg38]
Mapping of homologs : NCBISMG7 [Mapview hg19]  SMG7 [Mapview hg38]
OMIM610964   
Gene and transcription
Genbank (Entrez)AB085674 AK056035 AK074297 AK091477 AK297207
RefSeq transcript (Entrez)NM_001174061 NM_001331007 NM_001350219 NM_001350220 NM_001350221 NM_001350222 NM_014837 NM_173156 NM_201568 NM_201569
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SMG7
Cluster EST : UnigeneHs.591463 [ NCBI ]
CGAP (NCI)Hs.591463
Alternative Splicing GalleryENSG00000116698
Gene ExpressionSMG7 [ NCBI-GEO ]   SMG7 [ EBI - ARRAY_EXPRESS ]   SMG7 [ SEEK ]   SMG7 [ MEM ]
Gene Expression Viewer (FireBrowse)SMG7 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)9887
GTEX Portal (Tissue expression)SMG7
Human Protein AtlasENSG00000116698-SMG7 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ92540   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ92540  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ92540
Splice isoforms : SwissVarQ92540
PhosPhoSitePlusQ92540
Domains : Interpro (EBI)DNA/RNA-bd_Est1-type    EST1    TPR-like_helical_dom   
Domain families : Pfam (Sanger)EST1 (PF10374)    EST1_DNA_bind (PF10373)   
Domain families : Pfam (NCBI)pfam10374    pfam10373   
Conserved Domain (NCBI)SMG7
DMDM Disease mutations9887
Blocks (Seattle)SMG7
PDB (SRS)1YA0   
PDB (PDBSum)1YA0   
PDB (IMB)1YA0   
PDB (RSDB)1YA0   
Structural Biology KnowledgeBase1YA0   
SCOP (Structural Classification of Proteins)1YA0   
CATH (Classification of proteins structures)1YA0   
SuperfamilyQ92540
Human Protein Atlas [tissue]ENSG00000116698-SMG7 [tissue]
Peptide AtlasQ92540
HPRD10723
IPIIPI00217494   IPI00448672   IPI00657821   IPI00968194   IPI00973089   IPI00968033   IPI01008861   IPI00908426   IPI00968142   IPI00966868   IPI00645240   
Protein Interaction databases
DIP (DOE-UCLA)Q92540
IntAct (EBI)Q92540
FunCoupENSG00000116698
BioGRIDSMG7
STRING (EMBL)SMG7
ZODIACSMG7
Ontologies - Pathways
QuickGOQ92540
Ontology : AmiGOnuclear-transcribed mRNA catabolic process, nonsense-mediated decay  ribonuclease activity  protein binding  nucleus  telomerase holoenzyme complex  cytoplasm  cytosol  cytosol  mRNA export from nucleus  telomere maintenance via telomerase  regulation of dephosphorylation  telomeric DNA binding  ribonucleoprotein complex binding  regulation of RNA stability  intermediate filament cytoskeleton  protein phosphatase 2A binding  telomerase RNA binding  RNA phosphodiester bond hydrolysis  
Ontology : EGO-EBInuclear-transcribed mRNA catabolic process, nonsense-mediated decay  ribonuclease activity  protein binding  nucleus  telomerase holoenzyme complex  cytoplasm  cytosol  cytosol  mRNA export from nucleus  telomere maintenance via telomerase  regulation of dephosphorylation  telomeric DNA binding  ribonucleoprotein complex binding  regulation of RNA stability  intermediate filament cytoskeleton  protein phosphatase 2A binding  telomerase RNA binding  RNA phosphodiester bond hydrolysis  
Pathways : KEGGmRNA surveillance pathway   
NDEx NetworkSMG7
Atlas of Cancer Signalling NetworkSMG7
Wikipedia pathwaysSMG7
Orthology - Evolution
OrthoDB9887
GeneTree (enSembl)ENSG00000116698
Phylogenetic Trees/Animal Genes : TreeFamSMG7
HOVERGENQ92540
HOGENOMQ92540
Homologs : HomoloGeneSMG7
Homology/Alignments : Family Browser (UCSC)SMG7
Gene fusions - Rearrangements
Tumor Fusion PortalSMG7
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMG7 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMG7
dbVarSMG7
ClinVarSMG7
1000_GenomesSMG7 
Exome Variant ServerSMG7
ExAC (Exome Aggregation Consortium)ENSG00000116698
GNOMAD BrowserENSG00000116698
Genetic variants : HAPMAP9887
Genomic Variants (DGV)SMG7 [DGVbeta]
DECIPHERSMG7 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSMG7 
Mutations
ICGC Data PortalSMG7 
TCGA Data PortalSMG7 
Broad Tumor PortalSMG7
OASIS PortalSMG7 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMG7  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSMG7
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 SMG7
DgiDB (Drug Gene Interaction Database)SMG7
DoCM (Curated mutations)SMG7 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMG7 (select a term)
intoGenSMG7
Cancer3DSMG7(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM610964   
Orphanet
DisGeNETSMG7
MedgenSMG7
Genetic Testing Registry SMG7
NextProtQ92540 [Medical]
TSGene9887
GENETestsSMG7
Target ValidationSMG7
Huge Navigator SMG7 [HugePedia]
snp3D : Map Gene to Disease9887
BioCentury BCIQSMG7
ClinGenSMG7
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD9887
Chemical/Pharm GKB GenePA25605
Clinical trialSMG7
Miscellaneous
canSAR (ICR)SMG7 (select the gene name)
Probes
Litterature
PubMed34 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMG7
EVEXSMG7
GoPubMedSMG7
iHOPSMG7
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Nov 20 20:13:07 CET 2017

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