Gene description for PDE6D
Gene name phosphodiesterase 6D, cGMP-specific, rod, delta
Gene symbol PDE6D
Other names/aliases JBTS22
PDED
Species Homo sapiens
 Database cross references - PDE6D
ExoCarta ExoCarta_5147
Vesiclepedia VP_5147
Entrez Gene 5147
HGNC 8788
MIM 602676
UniProt O43924  
 PDE6D identified in exosomes derived from the following tissue/cell type
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
Bone marrow mesenchymal stem cells 36408942    
 Gene ontology annotations for PDE6D
Molecular Function
    Rab GTPase binding GO:0017137 IPI
    GTPase inhibitor activity GO:0005095 ISS
    3',5'-cyclic-nucleotide phosphodiesterase activity GO:0004114 IEA
    protein binding GO:0005515 IPI
Biological Process
    negative regulation of GTPase activity GO:0034260 ISS
    metabolic process GO:0008152 IEA
    visual perception GO:0007601 IEA
    response to stimulus GO:0050896 IEA
    organelle organization GO:0006996 TAS
Subcellular Localization
    primary cilium GO:0072372 TAS
    cytoplasmic vesicle membrane GO:0030659 IEA
    cytoplasmic vesicle GO:0031410 IDA
    cytoskeleton GO:0005856 IEA
    cytosol GO:0005829 TAS
 Experiment description of studies that identified PDE6D in exosomes
1
Experiment ID 489
MISEV standards
✔
EM
EV Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
EV Enriched markers
✔
Canx
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ.
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 6
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
2
Experiment ID 490
MISEV standards
✔
EM
EV Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
EV Enriched markers
✔
Canx
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ.
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 7
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
3
Experiment ID 491
MISEV standards
✔
EM
EV Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
EV Enriched markers
✔
Canx
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ.
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 8
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
4
Experiment ID 492
MISEV standards
✔
EM
EV Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
EV Enriched markers
✔
Canx
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Rattus norvegicus
Experiment description Quantitative proteomic analysis of exosomes from umbilical cord mesenchymal stem cells and rat bone marrow stem cells
Authors Xu X, Yin F, Guo M, Gan G, Lin G, Wen C, Wang J, Song P, Wang J, Qi ZQ, Zhong CQ.
Journal name Proteomics
Publication year 2023
Sample Bone marrow mesenchymal stem cells
Sample name BMSC - Passage 9
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
 Protein-protein interactions for PDE6D
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 RAB18 22931
Two-hybrid Homo sapiens
2 RASA1 5921
Affinity Capture-MS Homo sapiens
3 Arl3 56350
Two-hybrid Mus musculus
4 CDC42 998
Two-hybrid Homo sapiens
5 RAP2B 5912
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
6 ARL15 54622
Two-hybrid Homo sapiens
7 FAM219A 203259
Two-hybrid Homo sapiens
8 RPGR  
Invitro Homo sapiens
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
9 Arl2 56327
Two-hybrid Mus musculus
10 RHEB 6009
Affinity Capture-MS Homo sapiens
Two-hybrid Homo sapiens
11 ARL3 403
Two-hybrid Homo sapiens
Invitro Homo sapiens
Invivo Homo sapiens
Two-hybrid Homo sapiens
12 CETN3  
Two-hybrid Homo sapiens
13 RHOA 387
Affinity Capture-MS Homo sapiens
Two-hybrid Homo sapiens
14 HRAS 3265
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
15 RAD23A 5886
Two-hybrid Homo sapiens
16 RHOB 388
Two-hybrid Homo sapiens
17 RND1  
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
18 RAB13 5872
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
19 ARL2 402
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
Co-crystal Structure Homo sapiens
20 RAP1A 5906
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
Two-hybrid Homo sapiens
21 GNAI1 2770
Affinity Capture-MS Homo sapiens
View the network image/svg+xml
 Pathways in which PDE6D is involved
PathwayEvidenceSource
ARL13B-mediated ciliary trafficking of INPP5E TAS Reactome





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