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PDE6D (phosphodiesterase 6D)

Identity

Alias_namesphosphodiesterase 6D, cGMP-specific, rod, delta
Alias_symbol (synonym)JBTS22
Other aliasPDED
HGNC (Hugo) PDE6D
LocusID (NCBI) 5147
Atlas_Id 71797
Location 2q37.1  [Link to chromosome band 2q37]
Location_base_pair Starts at 231732425 and ends at 231781327 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
ADAMTS4 (1q23.3) / PDE6D (2q37.1)GNB5 (15q21.2) / PDE6D (2q37.1)NMUR1 (2q37.1) / PDE6D (2q37.1)
PDE6D (2q37.1) / PDE6D (2q37.1)RHBDD2 (7q11.23) / PDE6D (2q37.1)

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)PDE6D   8788
Cards
Entrez_Gene (NCBI)PDE6D  5147  phosphodiesterase 6D
AliasesJBTS22; PDED
GeneCards (Weizmann)PDE6D
Ensembl hg19 (Hinxton)ENSG00000156973 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000156973 [Gene_View]  chr2:231732425-231781327 [Contig_View]  PDE6D [Vega]
ICGC DataPortalENSG00000156973
TCGA cBioPortalPDE6D
AceView (NCBI)PDE6D
Genatlas (Paris)PDE6D
WikiGenes5147
SOURCE (Princeton)PDE6D
Genetics Home Reference (NIH)PDE6D
Genomic and cartography
GoldenPath hg38 (UCSC)PDE6D  -     chr2:231732425-231781327 -  2q37.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PDE6D  -     2q37.1   [Description]    (hg19-Feb_2009)
EnsemblPDE6D - 2q37.1 [CytoView hg19]  PDE6D - 2q37.1 [CytoView hg38]
Mapping of homologs : NCBIPDE6D [Mapview hg19]  PDE6D [Mapview hg38]
OMIM602676   615665   
Gene and transcription
Genbank (Entrez)AF022912 AK311623 BC001054 BC007831 BC017467
RefSeq transcript (Entrez)NM_001291018 NM_002601
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PDE6D
Cluster EST : UnigeneHs.516808 [ NCBI ]
CGAP (NCI)Hs.516808
Alternative Splicing GalleryENSG00000156973
Gene ExpressionPDE6D [ NCBI-GEO ]   PDE6D [ EBI - ARRAY_EXPRESS ]   PDE6D [ SEEK ]   PDE6D [ MEM ]
Gene Expression Viewer (FireBrowse)PDE6D [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5147
GTEX Portal (Tissue expression)PDE6D
Protein : pattern, domain, 3D structure
UniProt/SwissProtO43924   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO43924  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO43924
Splice isoforms : SwissVarO43924
PhosPhoSitePlusO43924
Domains : Interpro (EBI)Ig_E-set    PDED_dom    Rhodop-sen_GMP-Pdiesterase_dsu   
Domain families : Pfam (Sanger)GMP_PDE_delta (PF05351)   
Domain families : Pfam (NCBI)pfam05351   
Conserved Domain (NCBI)PDE6D
DMDM Disease mutations5147
Blocks (Seattle)PDE6D
PDB (SRS)1KSG    1KSH    1KSJ    3T5G    3T5I    4JHP    4JV6    4JV8    4JVB    4JVF    5E80    5E8F    5F2U    5ML2    5ML3    5ML4    5ML6    5ML8    5TAR    5TB5   
PDB (PDBSum)1KSG    1KSH    1KSJ    3T5G    3T5I    4JHP    4JV6    4JV8    4JVB    4JVF    5E80    5E8F    5F2U    5ML2    5ML3    5ML4    5ML6    5ML8    5TAR    5TB5   
PDB (IMB)1KSG    1KSH    1KSJ    3T5G    3T5I    4JHP    4JV6    4JV8    4JVB    4JVF    5E80    5E8F    5F2U    5ML2    5ML3    5ML4    5ML6    5ML8    5TAR    5TB5   
PDB (RSDB)1KSG    1KSH    1KSJ    3T5G    3T5I    4JHP    4JV6    4JV8    4JVB    4JVF    5E80    5E8F    5F2U    5ML2    5ML3    5ML4    5ML6    5ML8    5TAR    5TB5   
Structural Biology KnowledgeBase1KSG    1KSH    1KSJ    3T5G    3T5I    4JHP    4JV6    4JV8    4JVB    4JVF    5E80    5E8F    5F2U    5ML2    5ML3    5ML4    5ML6    5ML8    5TAR    5TB5   
SCOP (Structural Classification of Proteins)1KSG    1KSH    1KSJ    3T5G    3T5I    4JHP    4JV6    4JV8    4JVB    4JVF    5E80    5E8F    5F2U    5ML2    5ML3    5ML4    5ML6    5ML8    5TAR    5TB5   
CATH (Classification of proteins structures)1KSG    1KSH    1KSJ    3T5G    3T5I    4JHP    4JV6    4JV8    4JVB    4JVF    5E80    5E8F    5F2U    5ML2    5ML3    5ML4    5ML6    5ML8    5TAR    5TB5   
SuperfamilyO43924
Human Protein AtlasENSG00000156973
Peptide AtlasO43924
HPRD04056
IPIIPI00015161   IPI00916760   IPI00916343   
Protein Interaction databases
DIP (DOE-UCLA)O43924
IntAct (EBI)O43924
FunCoupENSG00000156973
BioGRIDPDE6D
STRING (EMBL)PDE6D
ZODIACPDE6D
Ontologies - Pathways
QuickGOO43924
Ontology : AmiGO3',5'-cyclic-nucleotide phosphodiesterase activity  GTPase inhibitor activity  protein binding  cytosol  cytosol  cytoskeleton  cilium  visual perception  Rab GTPase binding  cytoplasmic vesicle membrane  cytoplasmic vesicle  negative regulation of GTPase activity  response to stimulus  
Ontology : EGO-EBI3',5'-cyclic-nucleotide phosphodiesterase activity  GTPase inhibitor activity  protein binding  cytosol  cytosol  cytoskeleton  cilium  visual perception  Rab GTPase binding  cytoplasmic vesicle membrane  cytoplasmic vesicle  negative regulation of GTPase activity  response to stimulus  
Pathways : KEGGPurine metabolism   
NDEx NetworkPDE6D
Atlas of Cancer Signalling NetworkPDE6D
Wikipedia pathwaysPDE6D
Orthology - Evolution
OrthoDB5147
GeneTree (enSembl)ENSG00000156973
Phylogenetic Trees/Animal Genes : TreeFamPDE6D
HOVERGENO43924
HOGENOMO43924
Homologs : HomoloGenePDE6D
Homology/Alignments : Family Browser (UCSC)PDE6D
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPDE6D [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PDE6D
dbVarPDE6D
ClinVarPDE6D
1000_GenomesPDE6D 
Exome Variant ServerPDE6D
ExAC (Exome Aggregation Consortium)PDE6D (select the gene name)
Genetic variants : HAPMAP5147
Genomic Variants (DGV)PDE6D [DGVbeta]
DECIPHERPDE6D [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPDE6D 
Mutations
ICGC Data PortalPDE6D 
TCGA Data PortalPDE6D 
Broad Tumor PortalPDE6D
OASIS PortalPDE6D [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPDE6D  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPDE6D
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch PDE6D
DgiDB (Drug Gene Interaction Database)PDE6D
DoCM (Curated mutations)PDE6D (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PDE6D (select a term)
intoGenPDE6D
Cancer3DPDE6D(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM602676    615665   
Orphanet2510   
MedgenPDE6D
Genetic Testing Registry PDE6D
NextProtO43924 [Medical]
TSGene5147
GENETestsPDE6D
Target ValidationPDE6D
Huge Navigator PDE6D [HugePedia]
snp3D : Map Gene to Disease5147
BioCentury BCIQPDE6D
ClinGenPDE6D
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5147
Chemical/Pharm GKB GenePA33136
Clinical trialPDE6D
Miscellaneous
canSAR (ICR)PDE6D (select the gene name)
Probes
Litterature
PubMed31 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePDE6D
EVEXPDE6D
GoPubMedPDE6D
iHOPPDE6D
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed May 31 15:35:58 CEST 2017

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