Atlas of Genetics and Cytogenetics in Oncology and Haematology

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RNF40 (ring finger protein 40)

Identity

Alias_namesring finger protein 40
ring finger protein 40, E3 ubiquitin protein ligase
Alias_symbol (synonym)KIAA0661
RBP95
BRE1B
STARING
Other alias
HGNC (Hugo) RNF40
LocusID (NCBI) 9810
Atlas_Id 42138
Location 16p11.2  [Link to chromosome band 16p11]
Location_base_pair Starts at 30761612 and ends at 30776307 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)
GTF3C6 (6q21) / RNF40 (16p11.2)RNF40 (16p11.2) / PLK1 (16p12.2)RNF40 (16p11.2) / RNF40 (16p11.2)
RNF40 16p11.2 / PLK1 16p12.2

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(16;16)(p11;p12) RNF40/PLK1

External links

Nomenclature
HGNC (Hugo)RNF40   16867
Cards
Entrez_Gene (NCBI)RNF40  9810  ring finger protein 40
AliasesBRE1B; RBP95; STARING
GeneCards (Weizmann)RNF40
Ensembl hg19 (Hinxton)ENSG00000103549 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000103549 [Gene_View]  ENSG00000103549 [Sequence]  chr16:30761612-30776307 [Contig_View]  RNF40 [Vega]
ICGC DataPortalENSG00000103549
TCGA cBioPortalRNF40
AceView (NCBI)RNF40
Genatlas (Paris)RNF40
WikiGenes9810
SOURCE (Princeton)RNF40
Genetics Home Reference (NIH)RNF40
Genomic and cartography
GoldenPath hg38 (UCSC)RNF40  -     chr16:30761612-30776307 +  16p11.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)RNF40  -     16p11.2   [Description]    (hg19-Feb_2009)
EnsemblRNF40 - 16p11.2 [CytoView hg19]  RNF40 - 16p11.2 [CytoView hg38]
Mapping of homologs : NCBIRNF40 [Mapview hg19]  RNF40 [Mapview hg38]
OMIM607700   
Gene and transcription
Genbank (Entrez)AB014561 AF122819 AI373490 AK027406 AK054773
RefSeq transcript (Entrez)NM_001207033 NM_001207034 NM_001286572 NM_014771
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)RNF40
Cluster EST : UnigeneHs.65238 [ NCBI ]
CGAP (NCI)Hs.65238
Alternative Splicing GalleryENSG00000103549
Gene ExpressionRNF40 [ NCBI-GEO ]   RNF40 [ EBI - ARRAY_EXPRESS ]   RNF40 [ SEEK ]   RNF40 [ MEM ]
Gene Expression Viewer (FireBrowse)RNF40 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)9810
GTEX Portal (Tissue expression)RNF40
Human Protein AtlasENSG00000103549-RNF40 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO75150   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO75150  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO75150
Splice isoforms : SwissVarO75150
PhosPhoSitePlusO75150
Domaine pattern : Prosite (Expaxy)ZF_RING_1 (PS00518)    ZF_RING_2 (PS50089)   
Domains : Interpro (EBI)E3_ubiquit_lig_Bre1    Znf_RING    Znf_RING/FYVE/PHD    Znf_RING_CS   
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Domain families : Smart (EMBL)RING (SM00184)  
Conserved Domain (NCBI)RNF40
DMDM Disease mutations9810
Blocks (Seattle)RNF40
SuperfamilyO75150
Human Protein Atlas [tissue]ENSG00000103549-RNF40 [tissue]
Peptide AtlasO75150
HPRD07411
IPIIPI00162563   IPI00377273   IPI00290648   IPI01013114   IPI00910246   IPI01012850   IPI00442235   IPI00921437   
Protein Interaction databases
DIP (DOE-UCLA)O75150
IntAct (EBI)O75150
FunCoupENSG00000103549
BioGRIDRNF40
STRING (EMBL)RNF40
ZODIACRNF40
Ontologies - Pathways
QuickGOO75150
Ontology : AmiGOubiquitin ligase complex  mRNA 3'-UTR binding  ubiquitin-protein transferase activity  protein binding  nucleus  nucleoplasm  nucleoplasm  cytosol  ubiquitin-dependent protein catabolic process  regulation of mitotic cell cycle  histone monoubiquitination  membrane  protein ubiquitination  syntaxin-1 binding  extrinsic component of membrane  ubiquitin conjugating enzyme binding  ubiquitin protein ligase binding  HULC complex  histone H2B ubiquitination  protein homodimerization activity  neuron projection  response to peptide hormone  axon terminus  protein-containing complex binding  metal ion binding  negative regulation of mRNA polyadenylation  positive regulation of proteasomal protein catabolic process  positive regulation of protein polyubiquitination  positive regulation of histone H2B ubiquitination  
Ontology : EGO-EBIubiquitin ligase complex  mRNA 3'-UTR binding  ubiquitin-protein transferase activity  protein binding  nucleus  nucleoplasm  nucleoplasm  cytosol  ubiquitin-dependent protein catabolic process  regulation of mitotic cell cycle  histone monoubiquitination  membrane  protein ubiquitination  syntaxin-1 binding  extrinsic component of membrane  ubiquitin conjugating enzyme binding  ubiquitin protein ligase binding  HULC complex  histone H2B ubiquitination  protein homodimerization activity  neuron projection  response to peptide hormone  axon terminus  protein-containing complex binding  metal ion binding  negative regulation of mRNA polyadenylation  positive regulation of proteasomal protein catabolic process  positive regulation of protein polyubiquitination  positive regulation of histone H2B ubiquitination  
NDEx NetworkRNF40
Atlas of Cancer Signalling NetworkRNF40
Wikipedia pathwaysRNF40
Orthology - Evolution
OrthoDB9810
GeneTree (enSembl)ENSG00000103549
Phylogenetic Trees/Animal Genes : TreeFamRNF40
HOGENOMO75150
Homologs : HomoloGeneRNF40
Homology/Alignments : Family Browser (UCSC)RNF40
Gene fusions - Rearrangements
Fusion : MitelmanRNF40/PLK1 [16p11.2/16p12.2]  
Fusion PortalRNF40 16p11.2 PLK1 16p12.2 BRCA
Fusion : QuiverRNF40
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerRNF40 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RNF40
dbVarRNF40
ClinVarRNF40
1000_GenomesRNF40 
Exome Variant ServerRNF40
ExAC (Exome Aggregation Consortium)ENSG00000103549
GNOMAD BrowserENSG00000103549
Varsome BrowserRNF40
Genetic variants : HAPMAP9810
Genomic Variants (DGV)RNF40 [DGVbeta]
DECIPHERRNF40 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisRNF40 
Mutations
ICGC Data PortalRNF40 
TCGA Data PortalRNF40 
Broad Tumor PortalRNF40
OASIS PortalRNF40 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICRNF40  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDRNF40
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 RNF40
DgiDB (Drug Gene Interaction Database)RNF40
DoCM (Curated mutations)RNF40 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)RNF40 (select a term)
intoGenRNF40
Cancer3DRNF40(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM607700   
Orphanet
DisGeNETRNF40
MedgenRNF40
Genetic Testing Registry RNF40
NextProtO75150 [Medical]
TSGene9810
GENETestsRNF40
Target ValidationRNF40
Huge Navigator RNF40 [HugePedia]
snp3D : Map Gene to Disease9810
BioCentury BCIQRNF40
ClinGenRNF40
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD9810
Chemical/Pharm GKB GenePA34440
Clinical trialRNF40
Miscellaneous
canSAR (ICR)RNF40 (select the gene name)
DataMed IndexRNF40
Probes
Litterature
PubMed60 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineRNF40
EVEXRNF40
GoPubMedRNF40
iHOPRNF40
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Feb 14 16:54:42 CET 2019
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