Atlas of Genetics and Cytogenetics in Oncology and Haematology

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PDE6B (phosphodiesterase 6B)

Identity

Alias_namesPDEB
phosphodiesterase 6B, cGMP-specific, rod, beta
Alias_symbol (synonym)CSNB3
rd1
RP40
CSNBAD2
Other aliasGMP-PDEbeta
HGNC (Hugo) PDE6B
LocusID (NCBI) 5158
Atlas_Id 71795
Location 4p16.3  [Link to chromosome band 4p16]
Location_base_pair Starts at 653177 and ends at 670892 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)
INO80 (15q15.1) / PDE6B (4p16.3)PDE6B (4p16.3) / HNRNPA2B1 (7p15.2)PDE6B (4p16.3) / INO80 (15q15.1)

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)PDE6B   8786
Cards
Entrez_Gene (NCBI)PDE6B  5158  phosphodiesterase 6B
AliasesCSNB3; CSNBAD2; GMP-PDEbeta; PDEB; 
RP40; rd1
GeneCards (Weizmann)PDE6B
Ensembl hg19 (Hinxton)ENSG00000133256 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000133256 [Gene_View]  ENSG00000133256 [Sequence]  chr4:653177-670892 [Contig_View]  PDE6B [Vega]
ICGC DataPortalENSG00000133256
TCGA cBioPortalPDE6B
AceView (NCBI)PDE6B
Genatlas (Paris)PDE6B
WikiGenes5158
SOURCE (Princeton)PDE6B
Genetics Home Reference (NIH)PDE6B
Genomic and cartography
GoldenPath hg38 (UCSC)PDE6B  -     chr4:653177-670892 +  4p16.3   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PDE6B  -     4p16.3   [Description]    (hg19-Feb_2009)
GoldenPathPDE6B - 4p16.3 [CytoView hg19]  PDE6B - 4p16.3 [CytoView hg38]
ImmunoBaseENSG00000133256
genome Data Viewer NCBIPDE6B [Mapview hg19]  
OMIM163500   180072   613801   
Gene and transcription
Genbank (Entrez)AI131517 AK295285 AK308789 AK309252 AK316054
RefSeq transcript (Entrez)NM_000283 NM_001145291 NM_001145292 NM_001350154 NM_001350155
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PDE6B
Alternative Splicing GalleryENSG00000133256
Gene ExpressionPDE6B [ NCBI-GEO ]   PDE6B [ EBI - ARRAY_EXPRESS ]   PDE6B [ SEEK ]   PDE6B [ MEM ]
Gene Expression Viewer (FireBrowse)PDE6B [ Firebrowse - Broad ]
GenevisibleExpression of PDE6B in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5158
GTEX Portal (Tissue expression)PDE6B
Human Protein AtlasENSG00000133256-PDE6B [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP35913   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP35913  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP35913
Splice isoforms : SwissVarP35913
Catalytic activity : Enzyme3.1.4.35 [ Enzyme-Expasy ]   3.1.4.353.1.4.35 [ IntEnz-EBI ]   3.1.4.35 [ BRENDA ]   3.1.4.35 [ KEGG ]   [ MEROPS ]
PhosPhoSitePlusP35913
Domaine pattern : Prosite (Expaxy)PDEASE_I_1 (PS00126)    PDEASE_I_2 (PS51845)   
Domains : Interpro (EBI)GAF    GAF-like_dom_sf    HD/PDEase_dom    PDEase    PDEase_catalytic_dom    PDEase_catalytic_dom_sf    PDEase_CS   
Domain families : Pfam (Sanger)GAF (PF01590)    PDEase_I (PF00233)   
Domain families : Pfam (NCBI)pfam01590    pfam00233   
Domain families : Smart (EMBL)GAF (SM00065)  HDc (SM00471)  
Conserved Domain (NCBI)PDE6B
DMDM Disease mutations5158
Blocks (Seattle)PDE6B
SuperfamilyP35913
Human Protein Atlas [tissue]ENSG00000133256-PDE6B [tissue]
Peptide AtlasP35913
HPRD01571
IPIIPI00784027   IPI00922666   IPI00747657   IPI00921912   IPI00946197   IPI00946579   IPI00945707   IPI00945720   IPI00945175   
Protein Interaction databases
DIP (DOE-UCLA)P35913
IntAct (EBI)P35913
FunCoupENSG00000133256
BioGRIDPDE6B
STRING (EMBL)PDE6B
ZODIACPDE6B
Ontologies - Pathways
QuickGOP35913
Ontology : AmiGOcell  plasma membrane  G protein-coupled receptor signaling pathway  G protein-coupled receptor signaling pathway  Wnt signaling pathway, calcium modulating pathway  visual perception  phototransduction, visible light  rhodopsin mediated signaling pathway  regulation of rhodopsin mediated signaling pathway  metal ion binding  3',5'-cyclic-GMP phosphodiesterase activity  3',5'-cyclic-GMP phosphodiesterase activity  regulation of cytosolic calcium ion concentration  regulation of cytosolic calcium ion concentration  retina development in camera-type eye  photoreceptor disc membrane  
Ontology : EGO-EBIcell  plasma membrane  G protein-coupled receptor signaling pathway  G protein-coupled receptor signaling pathway  Wnt signaling pathway, calcium modulating pathway  visual perception  phototransduction, visible light  rhodopsin mediated signaling pathway  regulation of rhodopsin mediated signaling pathway  metal ion binding  3',5'-cyclic-GMP phosphodiesterase activity  3',5'-cyclic-GMP phosphodiesterase activity  regulation of cytosolic calcium ion concentration  regulation of cytosolic calcium ion concentration  retina development in camera-type eye  photoreceptor disc membrane  
Pathways : BIOCARTAVisual Signal Transduction [Genes]   
NDEx NetworkPDE6B
Atlas of Cancer Signalling NetworkPDE6B
Wikipedia pathwaysPDE6B
Orthology - Evolution
OrthoDB5158
GeneTree (enSembl)ENSG00000133256
Phylogenetic Trees/Animal Genes : TreeFamPDE6B
HOGENOMP35913
Homologs : HomoloGenePDE6B
Homology/Alignments : Family Browser (UCSC)PDE6B
Gene fusions - Rearrangements
Fusion : QuiverPDE6B
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPDE6B [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PDE6B
dbVarPDE6B
ClinVarPDE6B
1000_GenomesPDE6B 
Exome Variant ServerPDE6B
GNOMAD BrowserENSG00000133256
Varsome BrowserPDE6B
Genetic variants : HAPMAP5158
Genomic Variants (DGV)PDE6B [DGVbeta]
DECIPHERPDE6B [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPDE6B 
Mutations
ICGC Data PortalPDE6B 
TCGA Data PortalPDE6B 
Broad Tumor PortalPDE6B
OASIS PortalPDE6B [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPDE6B  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DPDE6B
Mutations and Diseases : HGMDPDE6B
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
LOVD (Leiden Open Variation Database)Eye diseases - LOVD
BioMutasearch PDE6B
DgiDB (Drug Gene Interaction Database)PDE6B
DoCM (Curated mutations)PDE6B (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PDE6B (select a term)
intoGenPDE6B
Cancer3DPDE6B(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM163500    180072    613801   
Orphanet659    923   
DisGeNETPDE6B
MedgenPDE6B
Genetic Testing Registry PDE6B
NextProtP35913 [Medical]
TSGene5158
GENETestsPDE6B
Target ValidationPDE6B
Huge Navigator PDE6B [HugePedia]
snp3D : Map Gene to Disease5158
BioCentury BCIQPDE6B
ClinGenPDE6B
Clinical trials, drugs, therapy
Protein Interactions : CTD5158
Pharm GKB GenePA33134
Clinical trialPDE6B
Miscellaneous
canSAR (ICR)PDE6B (select the gene name)
HarmonizomePDE6B
DataMed IndexPDE6B
Probes
Litterature
PubMed47 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePDE6B
EVEXPDE6B
GoPubMedPDE6B
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Jul 10 20:30:59 CEST 2020
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