Atlas of Genetics and Cytogenetics in Oncology and Haematology

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RNF40 (ring finger protein 40)

Identity

Other namesBRE1B
RBP95
STARING
HGNC (Hugo) RNF40
LocusID (NCBI) 9810
Atlas_Id 42138
Location 16p11.2  [Link to chromosome band 16p11]
Location_base_pair Starts at 30772933 and ends at 30787628 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)		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

 

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]  chr16:30772933-30787628 [Contig_View]  RNF40 [Vega]
Ensembl hg38 (Hinxton)ENSG00000103549 [Gene_View]  chr16:30772933-30787628 [Contig_View]  RNF40 [Vega]
ICGC DataPortalENSG00000103549
TCGA cBioPortalRNF40
AceView (NCBI)RNF40
Genatlas (Paris)RNF40
WikiGenes9810
SOURCE (Princeton)RNF40
Genomic and cartography
GoldenPath hg19 (UCSC)RNF40  -     chr16:30772933-30787628 +  16p11.2   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)RNF40  -     16p11.2   [Description]    (hg38-Dec_2013)
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)NC_000016 NC_018927 NT_187260 NW_004929400
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]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)9810
GTEX Portal (Tissue expression)RNF40
Protein : pattern, domain, 3D structure
UniProt/SwissProtO75150 (Uniprot)
NextProtO75150  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO75150
Splice isoforms : SwissVarO75150 (Swissvar)
Catalytic activity : Enzyme6.3.2.- [ Enzyme-Expasy ]   6.3.2.-6.3.2.- [ IntEnz-EBI ]   6.3.2.- [ BRENDA ]   6.3.2.- [ KEGG ]   
PhosPhoSitePlusO75150
Domaine pattern : Prosite (Expaxy)ZF_RING_1 (PS00518)    ZF_RING_2 (PS50089)   
Domains : Interpro (EBI)Znf_RING    Znf_RING/FYVE/PHD    Znf_RING_CS   
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
Domain families : Smart (EMBL)RING (SM00184)  
DMDM Disease mutations9810
Blocks (Seattle)RNF40
SuperfamilyO75150
Human Protein AtlasENSG00000103549
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  cytosol  ubiquitin-dependent protein catabolic process  regulation of mitotic cell cycle  zinc ion binding  histone monoubiquitination  membrane  ligase activity  syntaxin-1 binding  extrinsic component of membrane  ubiquitin conjugating enzyme binding  ubiquitin protein ligase binding  protein complex binding  HULC complex  histone H2B ubiquitination  protein homodimerization activity  neuron projection  response to peptide hormone  axon terminus  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  cytosol  ubiquitin-dependent protein catabolic process  regulation of mitotic cell cycle  zinc ion binding  histone monoubiquitination  membrane  ligase activity  syntaxin-1 binding  extrinsic component of membrane  ubiquitin conjugating enzyme binding  ubiquitin protein ligase binding  protein complex binding  HULC complex  histone H2B ubiquitination  protein homodimerization activity  neuron projection  response to peptide hormone  axon terminus  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
Homologs : HomoloGeneRNF40
Homology/Alignments : Family Browser (UCSC)RNF40
Gene fusions - Rearrangements
Fusion: TCGARNF40 16p11.2 PLK1 16p12.2 BRCA
Polymorphisms : SNP, variants
NCBI Variation ViewerRNF40 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RNF40
dbVarRNF40
ClinVarRNF40
1000_GenomesRNF40 
Exome Variant ServerRNF40
ExAC (Exome Aggregation Consortium)RNF40 (select the gene name)
Genetic variants : HAPMAP9810
Genomic Variants (DGV)RNF40 [DGVbeta]
Mutations
ICGC Data PortalRNF40 
TCGA Data PortalRNF40 
Broad Tumor PortalRNF40
OASIS PortalRNF40 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICRNF40 
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
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)16:30772933-30787628  ENSG00000103549
CONAN: Copy Number AnalysisRNF40 
Mutations and Diseases : HGMDRNF40
OMIM607700   
MedgenRNF40
Genetic Testing Registry RNF40
NextProtO75150 [Medical]
TSGene9810
GENETestsRNF40
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)
Probes
Litterature
PubMed44 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 : Mon Sep 19 19:11:17 CEST 2016
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