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UPF1 (UPF1, RNA helicase and ATPase)

Identity

Alias_namesRENT1
regulator of nonsense transcripts 1
UPF1 regulator of nonsense transcripts homolog (yeast)
Alias_symbol (synonym)HUPF1
KIAA0221
NORF1
pNORF1
smg-2
Other alias
HGNC (Hugo) UPF1
LocusID (NCBI) 5976
Atlas_Id 50179
Location 19p13.11  [Link to chromosome band 19p13]
Location_base_pair Starts at 18942744 and ends at 18979041 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
AKT2 (19q13.2) / UPF1 (19p13.11)PDLIM7 (5q35.3) / UPF1 (19p13.11)UPF1 (19p13.11) / EIF3M (11p13)
UPF1 (19p13.11) / UPF1 (19p13.11)AKT2 19q13.2 / UPF1 19p13.11UPF1 19p13.11 / EIF3M 11p13

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)UPF1   9962
Cards
Entrez_Gene (NCBI)UPF1  5976  UPF1, RNA helicase and ATPase
AliasesHUPF1; NORF1; RENT1; pNORF1; 
smg-2
GeneCards (Weizmann)UPF1
Ensembl hg19 (Hinxton)ENSG00000005007 [Gene_View]  chr19:18942744-18979041 [Contig_View]  UPF1 [Vega]
Ensembl hg38 (Hinxton)ENSG00000005007 [Gene_View]  chr19:18942744-18979041 [Contig_View]  UPF1 [Vega]
ICGC DataPortalENSG00000005007
TCGA cBioPortalUPF1
AceView (NCBI)UPF1
Genatlas (Paris)UPF1
WikiGenes5976
SOURCE (Princeton)UPF1
Genetics Home Reference (NIH)UPF1
Genomic and cartography
GoldenPath hg19 (UCSC)UPF1  -     chr19:18942744-18979041 +  19p13.11   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)UPF1  -     19p13.11   [Description]    (hg38-Dec_2013)
EnsemblUPF1 - 19p13.11 [CytoView hg19]  UPF1 - 19p13.11 [CytoView hg38]
Mapping of homologs : NCBIUPF1 [Mapview hg19]  UPF1 [Mapview hg38]
OMIM601430   
Gene and transcription
Genbank (Entrez)AF074016 AK125797 AK128727 BC034291 BC039817
RefSeq transcript (Entrez)NM_001297549 NM_002911
RefSeq genomic (Entrez)NC_000019 NC_018930 NT_011295 NW_004929414
Consensus coding sequences : CCDS (NCBI)UPF1
Cluster EST : UnigeneHs.515266 [ NCBI ]
CGAP (NCI)Hs.515266
Alternative Splicing GalleryENSG00000005007
Gene ExpressionUPF1 [ NCBI-GEO ]   UPF1 [ EBI - ARRAY_EXPRESS ]   UPF1 [ SEEK ]   UPF1 [ MEM ]
Gene Expression Viewer (FireBrowse)UPF1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5976
GTEX Portal (Tissue expression)UPF1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ92900   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ92900  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ92900
Splice isoforms : SwissVarQ92900
Catalytic activity : Enzyme3.6.4.- [ Enzyme-Expasy ]   3.6.4.-3.6.4.- [ IntEnz-EBI ]   3.6.4.- [ BRENDA ]   3.6.4.- [ KEGG ]   
PhosPhoSitePlusQ92900
Domains : Interpro (EBI)P-loop_NTPase    RNA-helicase_UPF1_UPF2-interct   
Domain families : Pfam (Sanger)UPF1_Zn_bind (PF09416)   
Domain families : Pfam (NCBI)pfam09416   
Conserved Domain (NCBI)UPF1
DMDM Disease mutations5976
Blocks (Seattle)UPF1
PDB (SRS)2GJK    2GK6    2GK7    2IYK    2WJV    2WJY    2XZO    2XZP   
PDB (PDBSum)2GJK    2GK6    2GK7    2IYK    2WJV    2WJY    2XZO    2XZP   
PDB (IMB)2GJK    2GK6    2GK7    2IYK    2WJV    2WJY    2XZO    2XZP   
PDB (RSDB)2GJK    2GK6    2GK7    2IYK    2WJV    2WJY    2XZO    2XZP   
Structural Biology KnowledgeBase2GJK    2GK6    2GK7    2IYK    2WJV    2WJY    2XZO    2XZP   
SCOP (Structural Classification of Proteins)2GJK    2GK6    2GK7    2IYK    2WJV    2WJY    2XZO    2XZP   
CATH (Classification of proteins structures)2GJK    2GK6    2GK7    2IYK    2WJV    2WJY    2XZO    2XZP   
SuperfamilyQ92900
Human Protein AtlasENSG00000005007
Peptide AtlasQ92900
HPRD03254
IPIIPI00034049   IPI00399170   IPI00445531   
Protein Interaction databases
DIP (DOE-UCLA)Q92900
IntAct (EBI)Q92900
FunCoupENSG00000005007
BioGRIDUPF1
STRING (EMBL)UPF1
ZODIACUPF1
Ontologies - Pathways
QuickGOQ92900
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  nuclear-transcribed mRNA catabolic process, nonsense-mediated decay  nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay  telomere maintenance  nuclear chromosome, telomeric region  chromatin  cytoplasmic mRNA processing body  nuclear-transcribed mRNA catabolic process  chromatin binding  RNA binding  ATP-dependent RNA helicase activity  ATP-dependent RNA helicase activity  helicase activity  protein binding  ATP binding  nucleus  nucleoplasm  cytoplasm  cytosol  DNA replication  DNA repair  mRNA export from nucleus  regulation of translational termination  regulation of translational termination  zinc ion binding  dosage compensation by inactivation of X chromosome  telomere maintenance via semi-conservative replication  exon-exon junction complex  telomeric DNA binding  supraspliceosomal complex  poly(A) RNA binding  positive regulation of mRNA catabolic process  3'-UTR-mediated mRNA destabilization  histone mRNA catabolic process  cellular response to lipopolysaccharide  cellular response to interleukin-1  
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  nuclear-transcribed mRNA catabolic process, nonsense-mediated decay  nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay  telomere maintenance  nuclear chromosome, telomeric region  chromatin  cytoplasmic mRNA processing body  nuclear-transcribed mRNA catabolic process  chromatin binding  RNA binding  ATP-dependent RNA helicase activity  ATP-dependent RNA helicase activity  helicase activity  protein binding  ATP binding  nucleus  nucleoplasm  cytoplasm  cytosol  DNA replication  DNA repair  mRNA export from nucleus  regulation of translational termination  regulation of translational termination  zinc ion binding  dosage compensation by inactivation of X chromosome  telomere maintenance via semi-conservative replication  exon-exon junction complex  telomeric DNA binding  supraspliceosomal complex  poly(A) RNA binding  positive regulation of mRNA catabolic process  3'-UTR-mediated mRNA destabilization  histone mRNA catabolic process  cellular response to lipopolysaccharide  cellular response to interleukin-1  
Pathways : KEGGRNA transport    mRNA surveillance pathway   
NDEx NetworkUPF1
Atlas of Cancer Signalling NetworkUPF1
Wikipedia pathwaysUPF1
Orthology - Evolution
OrthoDB5976
GeneTree (enSembl)ENSG00000005007
Phylogenetic Trees/Animal Genes : TreeFamUPF1
HOVERGENQ92900
HOGENOMQ92900
Homologs : HomoloGeneUPF1
Homology/Alignments : Family Browser (UCSC)UPF1
Gene fusions - Rearrangements
Fusion : MitelmanAKT2/UPF1 [19q13.2/19p13.11]  [t(19;19)(p13;q13)]  
Fusion : MitelmanUPF1/EIF3M [19p13.11/11p13]  [t(11;19)(p13;p13)]  
Fusion: TCGAAKT2 19q13.2 UPF1 19p13.11 LGG
Fusion: TCGAUPF1 19p13.11 EIF3M 11p13 PRAD
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerUPF1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)UPF1
dbVarUPF1
ClinVarUPF1
1000_GenomesUPF1 
Exome Variant ServerUPF1
ExAC (Exome Aggregation Consortium)UPF1 (select the gene name)
Genetic variants : HAPMAP5976
Genomic Variants (DGV)UPF1 [DGVbeta]
DECIPHER (Syndromes)19:18942744-18979041  ENSG00000005007
CONAN: Copy Number AnalysisUPF1 
Mutations
ICGC Data PortalUPF1 
TCGA Data PortalUPF1 
Broad Tumor PortalUPF1
OASIS PortalUPF1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICUPF1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDUPF1
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 UPF1
DgiDB (Drug Gene Interaction Database)UPF1
DoCM (Curated mutations)UPF1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)UPF1 (select a term)
intoGenUPF1
Cancer3DUPF1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM601430   
Orphanet
MedgenUPF1
Genetic Testing Registry UPF1
NextProtQ92900 [Medical]
TSGene5976
GENETestsUPF1
Huge Navigator UPF1 [HugePedia]
snp3D : Map Gene to Disease5976
BioCentury BCIQUPF1
ClinGenUPF1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5976
Chemical/Pharm GKB GenePA34328
Clinical trialUPF1
Miscellaneous
canSAR (ICR)UPF1 (select the gene name)
Probes
Litterature
PubMed128 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineUPF1
EVEXUPF1
GoPubMedUPF1
iHOPUPF1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Mar 30 15:24:24 CEST 2017

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