Atlas of Genetics and Cytogenetics in Oncology and Haematology

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UPF2 (UPF2 regulator of nonsense mediated mRNA decay)

Identity

Alias (NCBI)HUPF2
RENT2
smg-3
HGNC (Hugo) UPF2
HGNC Alias symbRENT2
DKFZP434D222
KIAA1408
smg-3
HGNC Alias namesmg-3 homolog, nonsense mediated mRNA decay factor (C. elegans)
LocusID (NCBI) 26019
Atlas_Id 75496
Location 10p14  [Link to chromosome band 10p14]
Location_base_pair Starts at 11920022 and ends at 12043170 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)
CLASP1 (2q14.2) / UPF2 (10p14)ENY2 (8q23.1) / UPF2 (10p14)MIR100HG (11q24.1) / UPF2 (10p14)
PPP2R5C (14q32.31) / UPF2 (10p14)UPF2 (10p14) / GLUD1 (10q23.2)UPF2 (10p14) / LUM (12q21.33)
UPF2 (10p14) / MTAP (9p21.3)USP32 (17q23.1) / UPF2 (10p14)USP6NL (10p14) / UPF2 (10p14)

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

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(10;14)(p14;q32) PPP2R5C/UPF2

External links

Nomenclature
HGNC (Hugo)UPF2   17854
Cards
Entrez_Gene (NCBI)UPF2    UPF2 regulator of nonsense mediated mRNA decay
AliasesHUPF2; RENT2; smg-3
GeneCards (Weizmann)UPF2
Ensembl hg19 (Hinxton)ENSG00000151461 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000151461 [Gene_View]  ENSG00000151461 [Sequence]  chr10:11920022-12043170 [Contig_View]  UPF2 [Vega]
ICGC DataPortalENSG00000151461
TCGA cBioPortalUPF2
AceView (NCBI)UPF2
Genatlas (Paris)UPF2
SOURCE (Princeton)UPF2
Genetics Home Reference (NIH)UPF2
Genomic and cartography
GoldenPath hg38 (UCSC)UPF2  -     chr10:11920022-12043170 -  10p14   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)UPF2  -     10p14   [Description]    (hg19-Feb_2009)
GoldenPathUPF2 - 10p14 [CytoView hg19]  UPF2 - 10p14 [CytoView hg38]
ImmunoBaseENSG00000151461
genome Data Viewer NCBIUPF2 [Mapview hg19]  
OMIM605529   
Gene and transcription
Genbank (Entrez)AB037829 AF301013 AF318574 AK000764 AK074375
RefSeq transcript (Entrez)NM_015542 NM_080599
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)UPF2
Alternative Splicing GalleryENSG00000151461
Gene ExpressionUPF2 [ NCBI-GEO ]   UPF2 [ EBI - ARRAY_EXPRESS ]   UPF2 [ SEEK ]   UPF2 [ MEM ]
Gene Expression Viewer (FireBrowse)UPF2 [ Firebrowse - Broad ]
GenevisibleExpression of UPF2 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)26019
GTEX Portal (Tissue expression)UPF2
Human Protein AtlasENSG00000151461-UPF2 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9HAU5   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9HAU5  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9HAU5
Splice isoforms : SwissVarQ9HAU5
PhosPhoSitePlusQ9HAU5
Domains : Interpro (EBI)ARM-type_fold    MIF4-like_sf    MIF4G-like_typ-3    Nmd2/UPF2    Upf2/Nmd2_C   
Domain families : Pfam (Sanger)MIF4G (PF02854)    Upf2 (PF04050)   
Domain families : Pfam (NCBI)pfam02854    pfam04050   
Domain families : Smart (EMBL)MIF4G (SM00543)  
Conserved Domain (NCBI)UPF2
Blocks (Seattle)UPF2
PDB (RSDB)1UW4    2WJV    4CEK    4CEM   
PDB Europe1UW4    2WJV    4CEK    4CEM   
PDB (PDBSum)1UW4    2WJV    4CEK    4CEM   
PDB (IMB)1UW4    2WJV    4CEK    4CEM   
Structural Biology KnowledgeBase1UW4    2WJV    4CEK    4CEM   
SCOP (Structural Classification of Proteins)1UW4    2WJV    4CEK    4CEM   
CATH (Classification of proteins structures)1UW4    2WJV    4CEK    4CEM   
SuperfamilyQ9HAU5
Human Protein Atlas [tissue]ENSG00000151461-UPF2 [tissue]
Peptide AtlasQ9HAU5
HPRD10405
IPIIPI00300504   IPI00472081   IPI00556093   IPI00152670   
Protein Interaction databases
DIP (DOE-UCLA)Q9HAU5
IntAct (EBI)Q9HAU5
BioGRIDUPF2
STRING (EMBL)UPF2
ZODIACUPF2
Ontologies - Pathways
QuickGOQ9HAU5
Ontology : AmiGOnuclear-transcribed mRNA catabolic process, nonsense-mediated decay  nuclear-transcribed mRNA catabolic process, nonsense-mediated decay  nuclear-transcribed mRNA catabolic process, nonsense-mediated decay  liver development  RNA binding  protein binding  nucleus  cytoplasm  cytoplasm  cytosol  cytosol  polysome  mRNA export from nucleus  animal organ regeneration  exon-exon junction complex  exon-exon junction complex  cytoplasmic ribonucleoprotein granule  telomeric DNA binding  perinuclear region of cytoplasm  
Ontology : EGO-EBInuclear-transcribed mRNA catabolic process, nonsense-mediated decay  nuclear-transcribed mRNA catabolic process, nonsense-mediated decay  nuclear-transcribed mRNA catabolic process, nonsense-mediated decay  liver development  RNA binding  protein binding  nucleus  cytoplasm  cytoplasm  cytosol  cytosol  polysome  mRNA export from nucleus  animal organ regeneration  exon-exon junction complex  exon-exon junction complex  cytoplasmic ribonucleoprotein granule  telomeric DNA binding  perinuclear region of cytoplasm  
NDEx NetworkUPF2
Atlas of Cancer Signalling NetworkUPF2
Wikipedia pathwaysUPF2
Orthology - Evolution
OrthoDB26019
GeneTree (enSembl)ENSG00000151461
Phylogenetic Trees/Animal Genes : TreeFamUPF2
HOGENOMQ9HAU5
Homologs : HomoloGeneUPF2
Homology/Alignments : Family Browser (UCSC)UPF2
Gene fusions - Rearrangements
Fusion : QuiverUPF2
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerUPF2 [hg38]
dbVarUPF2
ClinVarUPF2
MonarchUPF2
1000_GenomesUPF2 
Exome Variant ServerUPF2
GNOMAD BrowserENSG00000151461
Varsome BrowserUPF2
Genomic Variants (DGV)UPF2 [DGVbeta]
DECIPHERUPF2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisUPF2 
Mutations
ICGC Data PortalUPF2 
TCGA Data PortalUPF2 
Broad Tumor PortalUPF2
OASIS PortalUPF2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICUPF2  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DUPF2
Mutations and Diseases : HGMDUPF2
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 UPF2
DgiDB (Drug Gene Interaction Database)UPF2
DoCM (Curated mutations)UPF2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)UPF2 (select a term)
intoGenUPF2
Cancer3DUPF2(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM605529   
Orphanet
DisGeNETUPF2
MedgenUPF2
Genetic Testing Registry UPF2
NextProtQ9HAU5 [Medical]
GENETestsUPF2
Target ValidationUPF2
Huge Navigator UPF2 [HugePedia]
ClinGenUPF2
Clinical trials, drugs, therapy
MyCancerGenomeUPF2
Protein Interactions : CTD
Pharm GKB GenePA134945630
Clinical trialUPF2
Miscellaneous
canSAR (ICR)UPF2 (select the gene name)
HarmonizomeUPF2
DataMed IndexUPF2
Probes
Litterature
PubMed75 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineUPF2
EVEXUPF2
GoPubMedUPF2
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Sat Dec 5 17:34:13 CET 2020
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