Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

SMG5 (SMG5, nonsense mediated mRNA decay factor)

Identity

Alias_namessmg-5 homolog
Alias_symbol (synonym)KIAA1089
LPTS-RP1
LPTSRP1
RP11-54H19.7
SMG-5
EST1B
Other alias
HGNC (Hugo) SMG5
LocusID (NCBI) 23381
Atlas_Id 54645
Location 1q22  [Link to chromosome band 1q22]
Location_base_pair Starts at 156249224 and ends at 156282890 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)
ARHGEF2 (1q22) / SMG5 (1q22)SMG5 (1q22) / CCT3 (1q22)SMG5 (1q22) / DIDO1 (20q13.33)
SMG5 (1q22) / OFD1 (Xp22.2)SMG5 (1q22) / PAQR6 (1q22)ARHGEF2 1q22 / SMG5 1q22

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)SMG5   24644
Cards
Entrez_Gene (NCBI)SMG5  23381  SMG5, nonsense mediated mRNA decay factor
AliasesEST1B; LPTS-RP1; LPTSRP1; SMG-5
GeneCards (Weizmann)SMG5
Ensembl hg19 (Hinxton)ENSG00000198952 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000198952 [Gene_View]  chr1:156249224-156282890 [Contig_View]  SMG5 [Vega]
ICGC DataPortalENSG00000198952
TCGA cBioPortalSMG5
AceView (NCBI)SMG5
Genatlas (Paris)SMG5
WikiGenes23381
SOURCE (Princeton)SMG5
Genetics Home Reference (NIH)SMG5
Genomic and cartography
GoldenPath hg38 (UCSC)SMG5  -     chr1:156249224-156282890 -  1q22   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SMG5  -     1q22   [Description]    (hg19-Feb_2009)
EnsemblSMG5 - 1q22 [CytoView hg19]  SMG5 - 1q22 [CytoView hg38]
Mapping of homologs : NCBISMG5 [Mapview hg19]  SMG5 [Mapview hg38]
OMIM610962   
Gene and transcription
Genbank (Entrez)AB029012 AB085691 AK025988 AK026395 AK027486
RefSeq transcript (Entrez)NM_001323614 NM_001323615 NM_001323616 NM_001323617 NM_015327
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SMG5
Cluster EST : UnigeneHs.516837 [ NCBI ]
CGAP (NCI)Hs.516837
Alternative Splicing GalleryENSG00000198952
Gene ExpressionSMG5 [ NCBI-GEO ]   SMG5 [ EBI - ARRAY_EXPRESS ]   SMG5 [ SEEK ]   SMG5 [ MEM ]
Gene Expression Viewer (FireBrowse)SMG5 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23381
GTEX Portal (Tissue expression)SMG5
Human Protein AtlasENSG00000198952-SMG5 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9UPR3   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9UPR3  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9UPR3
Splice isoforms : SwissVarQ9UPR3
PhosPhoSitePlusQ9UPR3
Domains : Interpro (EBI)DNA/RNA-bd_Est1-type    EST1    PIN_dom    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)SMG5
DMDM Disease mutations23381
Blocks (Seattle)SMG5
PDB (SRS)2HWY   
PDB (PDBSum)2HWY   
PDB (IMB)2HWY   
PDB (RSDB)2HWY   
Structural Biology KnowledgeBase2HWY   
SCOP (Structural Classification of Proteins)2HWY   
CATH (Classification of proteins structures)2HWY   
SuperfamilyQ9UPR3
Human Protein Atlas [tissue]ENSG00000198952-SMG5 [tissue]
Peptide AtlasQ9UPR3
HPRD16869
IPIIPI00167861   IPI00514879   IPI00640773   
Protein Interaction databases
DIP (DOE-UCLA)Q9UPR3
IntAct (EBI)Q9UPR3
FunCoupENSG00000198952
BioGRIDSMG5
STRING (EMBL)SMG5
ZODIACSMG5
Ontologies - Pathways
QuickGOQ9UPR3
Ontology : AmiGOnuclear-transcribed mRNA catabolic process, nonsense-mediated decay  P-body  ribonuclease activity  protein binding  nucleus  telomerase holoenzyme complex  cytoplasm  cytosol  mRNA export from nucleus  ubiquitin protein ligase binding  regulation of telomere maintenance  regulation of telomere maintenance via telomerase  regulation of dephosphorylation  telomeric DNA binding  histone deacetylase binding  ribonucleoprotein complex binding  regulation of RNA stability  protein phosphatase 2A binding  telomerase RNA binding  DNA polymerase binding  RNA phosphodiester bond hydrolysis  
Ontology : EGO-EBInuclear-transcribed mRNA catabolic process, nonsense-mediated decay  P-body  ribonuclease activity  protein binding  nucleus  telomerase holoenzyme complex  cytoplasm  cytosol  mRNA export from nucleus  ubiquitin protein ligase binding  regulation of telomere maintenance  regulation of telomere maintenance via telomerase  regulation of dephosphorylation  telomeric DNA binding  histone deacetylase binding  ribonucleoprotein complex binding  regulation of RNA stability  protein phosphatase 2A binding  telomerase RNA binding  DNA polymerase binding  RNA phosphodiester bond hydrolysis  
Pathways : KEGGmRNA surveillance pathway   
NDEx NetworkSMG5
Atlas of Cancer Signalling NetworkSMG5
Wikipedia pathwaysSMG5
Orthology - Evolution
OrthoDB23381
GeneTree (enSembl)ENSG00000198952
Phylogenetic Trees/Animal Genes : TreeFamSMG5
HOVERGENQ9UPR3
HOGENOMQ9UPR3
Homologs : HomoloGeneSMG5
Homology/Alignments : Family Browser (UCSC)SMG5
Gene fusions - Rearrangements
Fusion: TCGA_MDACCARHGEF2 1q22 SMG5 1q22 HNSC
Tumor Fusion PortalSMG5
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSMG5 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SMG5
dbVarSMG5
ClinVarSMG5
1000_GenomesSMG5 
Exome Variant ServerSMG5
ExAC (Exome Aggregation Consortium)ENSG00000198952
GNOMAD BrowserENSG00000198952
Genetic variants : HAPMAP23381
Genomic Variants (DGV)SMG5 [DGVbeta]
DECIPHERSMG5 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSMG5 
Mutations
ICGC Data PortalSMG5 
TCGA Data PortalSMG5 
Broad Tumor PortalSMG5
OASIS PortalSMG5 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSMG5  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSMG5
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 SMG5
DgiDB (Drug Gene Interaction Database)SMG5
DoCM (Curated mutations)SMG5 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SMG5 (select a term)
intoGenSMG5
Cancer3DSMG5(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM610962   
Orphanet
DisGeNETSMG5
MedgenSMG5
Genetic Testing Registry SMG5
NextProtQ9UPR3 [Medical]
TSGene23381
GENETestsSMG5
Target ValidationSMG5
Huge Navigator SMG5 [HugePedia]
snp3D : Map Gene to Disease23381
BioCentury BCIQSMG5
ClinGenSMG5
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23381
Chemical/Pharm GKB GenePA143485617
Clinical trialSMG5
Miscellaneous
canSAR (ICR)SMG5 (select the gene name)
Probes
Litterature
PubMed32 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSMG5
EVEXSMG5
GoPubMedSMG5
iHOPSMG5
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Mon Nov 20 20:59:54 CET 2017

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.