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PDE6D (phosphodiesterase 6D)

Identity

Alias (NCBI)JBTS22
PDED
HGNC (Hugo) PDE6D
HGNC Alias symbJBTS22
HGNC Previous namephosphodiesterase 6D, cGMP-specific, rod, delta
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 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
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

 



Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 2 ]
  NMUR1/PDE6D (2q37)
t(2;15)(q37;q21) GNB5/PDE6D


External links

Nomenclature
HGNC (Hugo)PDE6D   8788
Cards
Entrez_Gene (NCBI)PDE6D    phosphodiesterase 6D
AliasesJBTS22; PDED
GeneCards (Weizmann)PDE6D
Ensembl hg19 (Hinxton)ENSG00000156973 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000156973 [Gene_View]  ENSG00000156973 [Sequence]  chr2:231732425-231781327 [Contig_View]  PDE6D [Vega]
ICGC DataPortalENSG00000156973
TCGA cBioPortalPDE6D
AceView (NCBI)PDE6D
Genatlas (Paris)PDE6D
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)
GoldenPathPDE6D - 2q37.1 [CytoView hg19]  PDE6D - 2q37.1 [CytoView hg38]
ImmunoBaseENSG00000156973
genome Data Viewer NCBIPDE6D [Mapview hg19]  
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
Alternative Splicing GalleryENSG00000156973
Gene ExpressionPDE6D [ NCBI-GEO ]   PDE6D [ EBI - ARRAY_EXPRESS ]   PDE6D [ SEEK ]   PDE6D [ MEM ]
Gene Expression Viewer (FireBrowse)PDE6D [ Firebrowse - Broad ]
GenevisibleExpression of PDE6D in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5147
GTEX Portal (Tissue expression)PDE6D
Human Protein AtlasENSG00000156973-PDE6D [pathology]   [cell]   [tissue]
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    PDED_dom_sf    Rhodop-sen_GMP-Pdiesterase_dsu   
Domain families : Pfam (Sanger)GMP_PDE_delta (PF05351)   
Domain families : Pfam (NCBI)pfam05351   
Conserved Domain (NCBI)PDE6D
Blocks (Seattle)PDE6D
PDB (RSDB)1KSG    1KSH    1KSJ    3T5G    3T5I    4JHP    4JV6    4JV8    4JVB    4JVF    5E80    5E8F    5F2U    5ML2    5ML3    5ML4    5ML6    5ML8    5NAL    5TAR    5TB5    5X72    5X73    5X74    5YAV    5YAW   
PDB Europe1KSG    1KSH    1KSJ    3T5G    3T5I    4JHP    4JV6    4JV8    4JVB    4JVF    5E80    5E8F    5F2U    5ML2    5ML3    5ML4    5ML6    5ML8    5NAL    5TAR    5TB5    5X72    5X73    5X74    5YAV    5YAW   
PDB (PDBSum)1KSG    1KSH    1KSJ    3T5G    3T5I    4JHP    4JV6    4JV8    4JVB    4JVF    5E80    5E8F    5F2U    5ML2    5ML3    5ML4    5ML6    5ML8    5NAL    5TAR    5TB5    5X72    5X73    5X74    5YAV    5YAW   
PDB (IMB)1KSG    1KSH    1KSJ    3T5G    3T5I    4JHP    4JV6    4JV8    4JVB    4JVF    5E80    5E8F    5F2U    5ML2    5ML3    5ML4    5ML6    5ML8    5NAL    5TAR    5TB5    5X72    5X73    5X74    5YAV    5YAW   
Structural Biology KnowledgeBase1KSG    1KSH    1KSJ    3T5G    3T5I    4JHP    4JV6    4JV8    4JVB    4JVF    5E80    5E8F    5F2U    5ML2    5ML3    5ML4    5ML6    5ML8    5NAL    5TAR    5TB5    5X72    5X73    5X74    5YAV    5YAW   
SCOP (Structural Classification of Proteins)1KSG    1KSH    1KSJ    3T5G    3T5I    4JHP    4JV6    4JV8    4JVB    4JVF    5E80    5E8F    5F2U    5ML2    5ML3    5ML4    5ML6    5ML8    5NAL    5TAR    5TB5    5X72    5X73    5X74    5YAV    5YAW   
CATH (Classification of proteins structures)1KSG    1KSH    1KSJ    3T5G    3T5I    4JHP    4JV6    4JV8    4JVB    4JVF    5E80    5E8F    5F2U    5ML2    5ML3    5ML4    5ML6    5ML8    5NAL    5TAR    5TB5    5X72    5X73    5X74    5YAV    5YAW   
SuperfamilyO43924
Human Protein Atlas [tissue]ENSG00000156973-PDE6D [tissue]
Peptide AtlasO43924
HPRD04056
IPIIPI00015161   IPI00916760   IPI00916343   
Protein Interaction databases
DIP (DOE-UCLA)O43924
IntAct (EBI)O43924
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
HOGENOMO43924
Homologs : HomoloGenePDE6D
Homology/Alignments : Family Browser (UCSC)PDE6D
Gene fusions - Rearrangements
Fusion : QuiverPDE6D
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPDE6D [hg38]
dbVarPDE6D
ClinVarPDE6D
MonarchPDE6D
1000_GenomesPDE6D 
Exome Variant ServerPDE6D
GNOMAD BrowserENSG00000156973
Varsome BrowserPDE6D
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]  
Somatic Mutations in Cancer : COSMIC3DPDE6D
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] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM602676    615665   
Orphanet2510   
DisGeNETPDE6D
MedgenPDE6D
Genetic Testing Registry PDE6D
NextProtO43924 [Medical]
GENETestsPDE6D
Target ValidationPDE6D
Huge Navigator PDE6D [HugePedia]
ClinGenPDE6D
Clinical trials, drugs, therapy
MyCancerGenomePDE6D
Protein Interactions : CTD
Pharm GKB GenePA33136
Clinical trialPDE6D
Miscellaneous
canSAR (ICR)PDE6D (select the gene name)
HarmonizomePDE6D
DataMed IndexPDE6D
Probes
Litterature
PubMed38 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePDE6D
EVEXPDE6D
GoPubMedPDE6D
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Sat Dec 5 17:22:12 CET 2020

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