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RBM39 (RNA binding motif protein 39)

Identity

Alias_namesRNPC2
RNA-binding region (RNP1
Alias_symbol (synonym)CC1.3
HCC1
CAPER
fSAP59
CAPERalpha
Other aliasFSAP59
HGNC (Hugo) RBM39
LocusID (NCBI) 9584
Atlas_Id 50557
Location 20q11.22  [Link to chromosome band 20q11]
Location_base_pair Starts at 35703609 and ends at 35742336 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)
ADCY2 (5p15.31) / RBM39 (20q11.22)ATF6B (6p21.33) / RBM39 (20q11.22)HMG20A (15q24.3) / RBM39 (20q11.22)
PHF20 (20q11.22) / RBM39 (20q11.22)PTPRD (9p24.1) / RBM39 (20q11.22)PXMP4 (20q11.22) / RBM39 (20q11.22)
RBM39 (20q11.22) / DTNB (2p23.3)RBM39 (20q11.22) / GOLGB1 (3q13.33)RBM39 (20q11.22) / PRDM5 (4q27)
RBM39 (20q11.22) / RBM39 (20q11.22)RBM39 (20q11.22) / VMP1 (17q23.1)RBM39 (20q11.22) / WASF2 (1p36.11)
RBM39 20q11.22 / PRDM5 4q27RBM39 20q11.22 / VMP1 17q23.1

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)RBM39   15923
Cards
Entrez_Gene (NCBI)RBM39  9584  RNA binding motif protein 39
AliasesCAPER; CAPERalpha; FSAP59; HCC1; 
RNPC2
GeneCards (Weizmann)RBM39
Ensembl hg19 (Hinxton)ENSG00000131051 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000131051 [Gene_View]  chr20:35703609-35742336 [Contig_View]  RBM39 [Vega]
ICGC DataPortalENSG00000131051
TCGA cBioPortalRBM39
AceView (NCBI)RBM39
Genatlas (Paris)RBM39
WikiGenes9584
SOURCE (Princeton)RBM39
Genetics Home Reference (NIH)RBM39
Genomic and cartography
GoldenPath hg38 (UCSC)RBM39  -     chr20:35703609-35742336 -  20q11.22   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)RBM39  -     20q11.22   [Description]    (hg19-Feb_2009)
EnsemblRBM39 - 20q11.22 [CytoView hg19]  RBM39 - 20q11.22 [CytoView hg38]
Mapping of homologs : NCBIRBM39 [Mapview hg19]  RBM39 [Mapview hg38]
OMIM604739   
Gene and transcription
Genbank (Entrez)AK126158 AK130283 AK297520 AK299165 AK299678
RefSeq transcript (Entrez)NM_001242599 NM_001242600 NM_001323422 NM_001323423 NM_001323424 NM_004902 NM_184234 NM_184237 NM_184241 NM_184244
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)RBM39
Cluster EST : UnigeneHs.731837 [ NCBI ]
CGAP (NCI)Hs.731837
Alternative Splicing GalleryENSG00000131051
Gene ExpressionRBM39 [ NCBI-GEO ]   RBM39 [ EBI - ARRAY_EXPRESS ]   RBM39 [ SEEK ]   RBM39 [ MEM ]
Gene Expression Viewer (FireBrowse)RBM39 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)9584
GTEX Portal (Tissue expression)RBM39
Human Protein AtlasENSG00000131051-RBM39 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ14498   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ14498  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ14498
Splice isoforms : SwissVarQ14498
PhosPhoSitePlusQ14498
Domaine pattern : Prosite (Expaxy)RRM (PS50102)   
Domains : Interpro (EBI)Nucleotide-bd_a/b_plait    RBM39_linker    RBM39_SF    RRM_dom    RRM_dom_euk   
Domain families : Pfam (Sanger)RBM39linker (PF15519)    RRM_1 (PF00076)   
Domain families : Pfam (NCBI)pfam15519    pfam00076   
Domain families : Smart (EMBL)RRM (SM00360)  RRM_1 (SM00361)  
Conserved Domain (NCBI)RBM39
DMDM Disease mutations9584
Blocks (Seattle)RBM39
PDB (SRS)2JRS    2MHN    4OO6    4OZ0    4OZ1    4YUD   
PDB (PDBSum)2JRS    2MHN    4OO6    4OZ0    4OZ1    4YUD   
PDB (IMB)2JRS    2MHN    4OO6    4OZ0    4OZ1    4YUD   
PDB (RSDB)2JRS    2MHN    4OO6    4OZ0    4OZ1    4YUD   
Structural Biology KnowledgeBase2JRS    2MHN    4OO6    4OZ0    4OZ1    4YUD   
SCOP (Structural Classification of Proteins)2JRS    2MHN    4OO6    4OZ0    4OZ1    4YUD   
CATH (Classification of proteins structures)2JRS    2MHN    4OO6    4OZ0    4OZ1    4YUD   
SuperfamilyQ14498
Human Protein Atlas [tissue]ENSG00000131051-RBM39 [tissue]
Peptide AtlasQ14498
HPRD09201
IPIIPI00163505   IPI00215801   IPI00514831   IPI01015916   IPI00644764   IPI00647282   IPI00942853   IPI00513959   IPI00853448   IPI00852586   IPI00915257   IPI00746554   IPI00878725   IPI00879910   IPI00893285   
Protein Interaction databases
DIP (DOE-UCLA)Q14498
IntAct (EBI)Q14498
FunCoupENSG00000131051
BioGRIDRBM39
STRING (EMBL)RBM39
ZODIACRBM39
Ontologies - Pathways
QuickGOQ14498
Ontology : AmiGORNA binding  protein binding  nucleoplasm  microtubule organizing center  transcription, DNA-templated  regulation of transcription, DNA-templated  RNA processing  mRNA processing  RNA splicing  microtubule cytoskeleton  nuclear speck  
Ontology : EGO-EBIRNA binding  protein binding  nucleoplasm  microtubule organizing center  transcription, DNA-templated  regulation of transcription, DNA-templated  RNA processing  mRNA processing  RNA splicing  microtubule cytoskeleton  nuclear speck  
NDEx NetworkRBM39
Atlas of Cancer Signalling NetworkRBM39
Wikipedia pathwaysRBM39
Orthology - Evolution
OrthoDB9584
GeneTree (enSembl)ENSG00000131051
Phylogenetic Trees/Animal Genes : TreeFamRBM39
HOVERGENQ14498
HOGENOMQ14498
Homologs : HomoloGeneRBM39
Homology/Alignments : Family Browser (UCSC)RBM39
Gene fusions - Rearrangements
Fusion : MitelmanRBM39/PRDM5 [20q11.22/4q27]  
Fusion : MitelmanRBM39/VMP1 [20q11.22/17q23.1]  [t(17;20)(q23;q11)]  
Fusion: TCGA_MDACCRBM39 20q11.22 PRDM5 4q27 BLCA
Fusion: TCGA_MDACCRBM39 20q11.22 VMP1 17q23.1 BRCA
Tumor Fusion PortalRBM39
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerRBM39 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)RBM39
dbVarRBM39
ClinVarRBM39
1000_GenomesRBM39 
Exome Variant ServerRBM39
ExAC (Exome Aggregation Consortium)ENSG00000131051
GNOMAD BrowserENSG00000131051
Genetic variants : HAPMAP9584
Genomic Variants (DGV)RBM39 [DGVbeta]
DECIPHERRBM39 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisRBM39 
Mutations
ICGC Data PortalRBM39 
TCGA Data PortalRBM39 
Broad Tumor PortalRBM39
OASIS PortalRBM39 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICRBM39  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDRBM39
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 RBM39
DgiDB (Drug Gene Interaction Database)RBM39
DoCM (Curated mutations)RBM39 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)RBM39 (select a term)
intoGenRBM39
Cancer3DRBM39(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604739   
Orphanet
DisGeNETRBM39
MedgenRBM39
Genetic Testing Registry RBM39
NextProtQ14498 [Medical]
TSGene9584
GENETestsRBM39
Target ValidationRBM39
Huge Navigator RBM39 [HugePedia]
snp3D : Map Gene to Disease9584
BioCentury BCIQRBM39
ClinGenRBM39
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD9584
Chemical/Pharm GKB GenePA34450
Clinical trialRBM39
Miscellaneous
canSAR (ICR)RBM39 (select the gene name)
Probes
Litterature
PubMed83 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineRBM39
EVEXRBM39
GoPubMedRBM39
iHOPRBM39
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 14:31:56 CET 2017

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