Atlas of Genetics and Cytogenetics in Oncology and Haematology

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RNF38 (ring finger protein 38)

Identity

Other alias-
HGNC (Hugo) RNF38
LocusID (NCBI) 152006
Atlas_Id 47345
Location 9p13.2  [Link to chromosome band 9p13]
Location_base_pair Starts at 36336401 and ends at 36400923 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)
GNE (9p13.3) / RNF38 (9p13.2)RNF38 (9p13.2) / GLIPR2 (9p13.3)RNF38 (9p13.2) / SUPT20H (13q13.3)
SCIN (7p21.3) / RNF38 (9p13.2)WBP5 () / RNF38 (9p13.2)RNF38 9p13.2 / GLIPR2 9p13.3

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 Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(9;9)(p13;p13) PAX5/RNF38

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(9;9)(p13;p13) RNF38/GLIPR2

External links

Nomenclature
HGNC (Hugo)RNF38   18052
Cards
Entrez_Gene (NCBI)RNF38  152006  ring finger protein 38
Aliases
GeneCards (Weizmann)RNF38
Ensembl hg19 (Hinxton)ENSG00000137075 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000137075 [Gene_View]  ENSG00000137075 [Sequence]  chr9:36336401-36400923 [Contig_View]  RNF38 [Vega]
ICGC DataPortalENSG00000137075
TCGA cBioPortalRNF38
AceView (NCBI)RNF38
Genatlas (Paris)RNF38
WikiGenes152006
SOURCE (Princeton)RNF38
Genetics Home Reference (NIH)RNF38
Genomic and cartography
GoldenPath hg38 (UCSC)RNF38  -     chr9:36336401-36400923 -  9p13.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)RNF38  -     9p13.2   [Description]    (hg19-Feb_2009)
EnsemblRNF38 - 9p13.2 [CytoView hg19]  RNF38 - 9p13.2 [CytoView hg38]
Mapping of homologs : NCBIRNF38 [Mapview hg19]  RNF38 [Mapview hg38]
OMIM612488   
Gene and transcription
Genbank (Entrez)AF394047 AK024996 AK025466 AK093480 AK097653
RefSeq transcript (Entrez)NM_022781 NM_194328 NM_194329 NM_194330 NM_194331 NM_194332
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)RNF38
Cluster EST : UnigeneHs.333503 [ NCBI ]
CGAP (NCI)Hs.333503
Alternative Splicing GalleryENSG00000137075
Gene ExpressionRNF38 [ NCBI-GEO ]   RNF38 [ EBI - ARRAY_EXPRESS ]   RNF38 [ SEEK ]   RNF38 [ MEM ]
Gene Expression Viewer (FireBrowse)RNF38 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)152006
GTEX Portal (Tissue expression)RNF38
Human Protein AtlasENSG00000137075-RNF38 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ9H0F5   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ9H0F5  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ9H0F5
Splice isoforms : SwissVarQ9H0F5
Catalytic activity : Enzyme2.3.2.27 [ Enzyme-Expasy ]   2.3.2.272.3.2.27 [ IntEnz-EBI ]   2.3.2.27 [ BRENDA ]   2.3.2.27 [ KEGG ]   
PhosPhoSitePlusQ9H0F5
Domaine pattern : Prosite (Expaxy)ZF_RING_2 (PS50089)   
Domains : Interpro (EBI)Znf_RING    Znf_RING/FYVE/PHD   
Domain families : Pfam (Sanger)zf-RING_2 (PF13639)   
Domain families : Pfam (NCBI)pfam13639   
Domain families : Smart (EMBL)RING (SM00184)  
Conserved Domain (NCBI)RNF38
DMDM Disease mutations152006
Blocks (Seattle)RNF38
PDB (SRS)1X4J    4V3K    4V3L   
PDB (PDBSum)1X4J    4V3K    4V3L   
PDB (IMB)1X4J    4V3K    4V3L   
PDB (RSDB)1X4J    4V3K    4V3L   
Structural Biology KnowledgeBase1X4J    4V3K    4V3L   
SCOP (Structural Classification of Proteins)1X4J    4V3K    4V3L   
CATH (Classification of proteins structures)1X4J    4V3K    4V3L   
SuperfamilyQ9H0F5
Human Protein Atlas [tissue]ENSG00000137075-RNF38 [tissue]
Peptide AtlasQ9H0F5
HPRD11519
IPIIPI00167875   IPI00375419   IPI00478430   IPI00942550   IPI00744793   
Protein Interaction databases
DIP (DOE-UCLA)Q9H0F5
IntAct (EBI)Q9H0F5
FunCoupENSG00000137075
BioGRIDRNF38
STRING (EMBL)RNF38
ZODIACRNF38
Ontologies - Pathways
QuickGOQ9H0F5
Ontology : AmiGOubiquitin-protein transferase activity  nucleus  nucleoplasm  male gonad development  protein ubiquitination  protein ubiquitination  sperm flagellum  proteasome-mediated ubiquitin-dependent protein catabolic process  metal ion binding  ubiquitin protein ligase activity  
Ontology : EGO-EBIubiquitin-protein transferase activity  nucleus  nucleoplasm  male gonad development  protein ubiquitination  protein ubiquitination  sperm flagellum  proteasome-mediated ubiquitin-dependent protein catabolic process  metal ion binding  ubiquitin protein ligase activity  
NDEx NetworkRNF38
Atlas of Cancer Signalling NetworkRNF38
Wikipedia pathwaysRNF38
Orthology - Evolution
OrthoDB152006
GeneTree (enSembl)ENSG00000137075
Phylogenetic Trees/Animal Genes : TreeFamRNF38
HOVERGENQ9H0F5
HOGENOMQ9H0F5
Homologs : HomoloGeneRNF38
Homology/Alignments : Family Browser (UCSC)RNF38
Gene fusions - Rearrangements
Fusion : MitelmanRNF38/GLIPR2 [9p13.2/9p13.3]  
Fusion PortalRNF38 9p13.2 GLIPR2 9p13.3 BRCA
Fusion : QuiverRNF38
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerRNF38 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RNF38
dbVarRNF38
ClinVarRNF38
1000_GenomesRNF38 
Exome Variant ServerRNF38
ExAC (Exome Aggregation Consortium)ENSG00000137075
GNOMAD BrowserENSG00000137075
Genetic variants : HAPMAP152006
Genomic Variants (DGV)RNF38 [DGVbeta]
DECIPHERRNF38 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisRNF38 
Mutations
ICGC Data PortalRNF38 
TCGA Data PortalRNF38 
Broad Tumor PortalRNF38
OASIS PortalRNF38 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICRNF38  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDRNF38
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch RNF38
DgiDB (Drug Gene Interaction Database)RNF38
DoCM (Curated mutations)RNF38 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)RNF38 (select a term)
intoGenRNF38
Cancer3DRNF38(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM612488   
Orphanet
DisGeNETRNF38
MedgenRNF38
Genetic Testing Registry RNF38
NextProtQ9H0F5 [Medical]
TSGene152006
GENETestsRNF38
Target ValidationRNF38
Huge Navigator RNF38 [HugePedia]
snp3D : Map Gene to Disease152006
BioCentury BCIQRNF38
ClinGenRNF38
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD152006
Chemical/Pharm GKB GenePA34438
Clinical trialRNF38
Miscellaneous
canSAR (ICR)RNF38 (select the gene name)
Probes
Litterature
PubMed21 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineRNF38
EVEXRNF38
GoPubMedRNF38
iHOPRNF38
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Jun 22 16:47:31 CEST 2018
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