Atlas of Genetics and Cytogenetics in Oncology and Haematology

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RNF40 (ring finger protein 40, E3 ubiquitin protein ligase)

Identity

Other namesBRE1B
RBP95
STARING
HGNC (Hugo) RNF40
LocusID (NCBI) 9810
Location 16p11.2
Location_base_pair Starts at 30772933 and ends at 30787628 bp from pter ( according to hg19-Feb_2009)
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, E3 ubiquitin protein ligase
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
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)AC_000148 NC_000016 NC_018927 NT_187260 NW_001838236 NW_004929400
Consensus coding sequences : CCDS (NCBI)RNF40
Cluster EST : UnigeneHs.65238 [ NCBI ]
CGAP (NCI)Hs.65238
Alternative Splicing : Fast-db (Paris)GSHG0011119
Alternative Splicing GalleryENSG00000103549
Gene ExpressionRNF40 [ NCBI-GEO ]     RNF40 [ SEEK ]   RNF40 [ MEM ]
SOURCE (Princeton)Expression in : [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO75150 (Uniprot)
NextProtO75150  [Medical]
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 ]   
Domaine pattern : Prosite (Expaxy)ZF_RING_1 (PS00518)    ZF_RING_2 (PS50089)   
Domains : Interpro (EBI)Znf_C3HC4_RING-type    Znf_RING    Znf_RING/FYVE/PHD    Znf_RING_CS   
Related proteins : CluSTrO75150
Domain families : Pfam (Sanger)zf-C3HC4 (PF00097)   
Domain families : Pfam (NCBI)pfam00097   
Domain families : Smart (EMBL)RING (SM00184)  
DMDM Disease mutations9810
Blocks (Seattle)O75150
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
IntegromeDBRNF40
STRING (EMBL)RNF40
Ontologies - Pathways
QuickGOO75150
Ontology : AmiGOubiquitin ligase complex  ubiquitin-protein transferase activity  protein binding  nucleus  ubiquitin-dependent protein catabolic process  zinc ion binding  histone monoubiquitination  membrane  ligase activity  syntaxin-1 binding  ubiquitin protein ligase binding  protein complex binding  HULC complex  histone H2B ubiquitination  protein homodimerization activity  neuron projection  
Ontology : EGO-EBIubiquitin ligase complex  ubiquitin-protein transferase activity  protein binding  nucleus  ubiquitin-dependent protein catabolic process  zinc ion binding  histone monoubiquitination  membrane  ligase activity  syntaxin-1 binding  ubiquitin protein ligase binding  protein complex binding  HULC complex  histone H2B ubiquitination  protein homodimerization activity  neuron projection  
Protein Interaction DatabaseRNF40
DoCM (Curated mutations)RNF40
Wikipedia pathwaysRNF40
Gene fusion - rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerRNF40 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RNF40
dbVarRNF40
ClinVarRNF40
1000_GenomesRNF40 
Exome Variant ServerRNF40
SNP (GeneSNP Utah)RNF40
SNP : HGBaseRNF40
Genetic variants : HAPMAPRNF40
Genomic VariantsRNF40  RNF40 [DGVbeta]
Mutations
ICGC Data PortalENSG00000103549 
Somatic Mutations in Cancer : COSMICRNF40 
CONAN: Copy Number AnalysisRNF40 
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
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)16:30772933-30787628
Mutations and Diseases : HGMDRNF40
OMIM607700   
MedgenRNF40
NextProtO75150 [Medical]
GENETestsRNF40
Disease Genetic AssociationRNF40
Huge Navigator RNF40 [HugePedia]  RNF40 [HugeCancerGEM]
snp3D : Map Gene to Disease9810
DGIdb (Drug Gene Interaction db)RNF40
General knowledge
Homologs : HomoloGeneRNF40
Homology/Alignments : Family Browser (UCSC)RNF40
Phylogenetic Trees/Animal Genes : TreeFamRNF40
Chemical/Protein Interactions : CTD9810
Chemical/Pharm GKB GenePA34440
Clinical trialRNF40
Cancer Resource (Charite)ENSG00000103549
Other databases
Probes
Litterature
PubMed35 Pubmed reference(s) in Entrez
CoreMineRNF40
GoPubMedRNF40
iHOPRNF40
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

Contributor(s)

Written09-2002Dessen P, Le Minor S
Updated12-2014Dessen P

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Sun Dec 21 01:12:45 CET 2014
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