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UPF3B (UPF3 regulator of nonsense transcripts homolog B (yeast))

Identity

Alias_namesMRX62
UPF3BP1
UPF3BP2
UPF3BP3
mental retardation, X-linked 62
UPF3B pseudogene 1
UPF3B pseudogene 2
UPF3B pseudogene 3
Alias_symbol (synonym)RENT3B
UPF3X
HUPF3B
Other aliasMRXS14
Upf3p-X
HGNC (Hugo) UPF3B
LocusID (NCBI) 65109
Atlas_Id 75497
Location Xq24  [Link to chromosome band Xq24]
Location_base_pair Starts at 119834026 and ends at 119853028 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)

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)UPF3B   20439
Cards
Entrez_Gene (NCBI)UPF3B  65109  UPF3 regulator of nonsense transcripts homolog B (yeast)
AliasesHUPF3B; MRX62; MRXS14; RENT3B; 
UPF3BP1; UPF3BP2; UPF3BP3; UPF3X; Upf3p-X
GeneCards (Weizmann)UPF3B
Ensembl hg19 (Hinxton)ENSG00000125351 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000125351 [Gene_View]  chrX:119834026-119853028 [Contig_View]  UPF3B [Vega]
ICGC DataPortalENSG00000125351
TCGA cBioPortalUPF3B
AceView (NCBI)UPF3B
Genatlas (Paris)UPF3B
WikiGenes65109
SOURCE (Princeton)UPF3B
Genetics Home Reference (NIH)UPF3B
Genomic and cartography
GoldenPath hg38 (UCSC)UPF3B  -     chrX:119834026-119853028 -  Xq24   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)UPF3B  -     Xq24   [Description]    (hg19-Feb_2009)
EnsemblUPF3B - Xq24 [CytoView hg19]  UPF3B - Xq24 [CytoView hg38]
Mapping of homologs : NCBIUPF3B [Mapview hg19]  UPF3B [Mapview hg38]
OMIM300298   300676   
Gene and transcription
Genbank (Entrez)AF318576 AK093728 AY013251 BC008494 BC121017
RefSeq transcript (Entrez)NM_023010 NM_080632
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)UPF3B
Cluster EST : UnigeneHs.103832 [ NCBI ]
CGAP (NCI)Hs.103832
Alternative Splicing GalleryENSG00000125351
Gene ExpressionUPF3B [ NCBI-GEO ]   UPF3B [ EBI - ARRAY_EXPRESS ]   UPF3B [ SEEK ]   UPF3B [ MEM ]
Gene Expression Viewer (FireBrowse)UPF3B [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)65109
GTEX Portal (Tissue expression)UPF3B
Human Protein AtlasENSG00000125351-UPF3B [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9BZI7   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9BZI7  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9BZI7
Splice isoforms : SwissVarQ9BZI7
PhosPhoSitePlusQ9BZI7
Domains : Interpro (EBI)Nonsense_mediated_decay_UPF3    Nucleotide-bd_a/b_plait    RRM_dom   
Domain families : Pfam (Sanger)Smg4_UPF3 (PF03467)   
Domain families : Pfam (NCBI)pfam03467   
Conserved Domain (NCBI)UPF3B
DMDM Disease mutations65109
Blocks (Seattle)UPF3B
PDB (SRS)1UW4    2XB2   
PDB (PDBSum)1UW4    2XB2   
PDB (IMB)1UW4    2XB2   
PDB (RSDB)1UW4    2XB2   
Structural Biology KnowledgeBase1UW4    2XB2   
SCOP (Structural Classification of Proteins)1UW4    2XB2   
CATH (Classification of proteins structures)1UW4    2XB2   
SuperfamilyQ9BZI7
Human Protein Atlas [tissue]ENSG00000125351-UPF3B [tissue]
Peptide AtlasQ9BZI7
HPRD02247
IPIIPI00023409   IPI00074183   IPI00940805   
Protein Interaction databases
DIP (DOE-UCLA)Q9BZI7
IntAct (EBI)Q9BZI7
FunCoupENSG00000125351
BioGRIDUPF3B
STRING (EMBL)UPF3B
ZODIACUPF3B
Ontologies - Pathways
QuickGOQ9BZI7
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  mRNA splicing, via spliceosome  RNA binding  mRNA binding  nucleocytoplasmic transporter activity  protein binding  nucleus  nucleus  nucleoplasm  nucleolus  cytoplasm  microtubule organizing center  cytosol  cytosol  termination of RNA polymerase II transcription  RNA export from nucleus  mRNA export from nucleus  mRNA 3'-end processing  exon-exon junction complex  exon-exon junction complex  positive regulation of translation  
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  mRNA splicing, via spliceosome  RNA binding  mRNA binding  nucleocytoplasmic transporter activity  protein binding  nucleus  nucleus  nucleoplasm  nucleolus  cytoplasm  microtubule organizing center  cytosol  cytosol  termination of RNA polymerase II transcription  RNA export from nucleus  mRNA export from nucleus  mRNA 3'-end processing  exon-exon junction complex  exon-exon junction complex  positive regulation of translation  
Pathways : KEGGRNA transport    mRNA surveillance pathway   
NDEx NetworkUPF3B
Atlas of Cancer Signalling NetworkUPF3B
Wikipedia pathwaysUPF3B
Orthology - Evolution
OrthoDB65109
GeneTree (enSembl)ENSG00000125351
Phylogenetic Trees/Animal Genes : TreeFamUPF3B
HOVERGENQ9BZI7
HOGENOMQ9BZI7
Homologs : HomoloGeneUPF3B
Homology/Alignments : Family Browser (UCSC)UPF3B
Gene fusions - Rearrangements
Tumor Fusion PortalUPF3B
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerUPF3B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)UPF3B
dbVarUPF3B
ClinVarUPF3B
1000_GenomesUPF3B 
Exome Variant ServerUPF3B
ExAC (Exome Aggregation Consortium)ENSG00000125351
GNOMAD BrowserENSG00000125351
Genetic variants : HAPMAP65109
Genomic Variants (DGV)UPF3B [DGVbeta]
DECIPHERUPF3B [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisUPF3B 
Mutations
ICGC Data PortalUPF3B 
TCGA Data PortalUPF3B 
Broad Tumor PortalUPF3B
OASIS PortalUPF3B [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICUPF3B  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDUPF3B
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 UPF3B
DgiDB (Drug Gene Interaction Database)UPF3B
DoCM (Curated mutations)UPF3B (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)UPF3B (select a term)
intoGenUPF3B
Cancer3DUPF3B(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM300298    300676   
Orphanet972    3256   
DisGeNETUPF3B
MedgenUPF3B
Genetic Testing Registry UPF3B
NextProtQ9BZI7 [Medical]
TSGene65109
GENETestsUPF3B
Target ValidationUPF3B
Huge Navigator UPF3B [HugePedia]
snp3D : Map Gene to Disease65109
BioCentury BCIQUPF3B
ClinGenUPF3B
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD65109
Chemical/Pharm GKB GenePA128394708
Clinical trialUPF3B
Miscellaneous
canSAR (ICR)UPF3B (select the gene name)
Probes
Litterature
PubMed69 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineUPF3B
EVEXUPF3B
GoPubMedUPF3B
iHOPUPF3B
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 20:20:57 CET 2017

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