Gene description for UBE2D3
Gene name ubiquitin-conjugating enzyme E2D 3
Gene symbol UBE2D3
Other names/aliases E2(17)KB3
UBC4/5
UBCH5C
Species Homo sapiens
 Database cross references - UBE2D3
ExoCarta ExoCarta_7323
Entrez Gene 7323
HGNC 12476
MIM 602963
UniProt P61077  
 UBE2D3 identified in exosomes derived from the following tissue/cell type
Hepatocellular carcinoma cells 26054723    
Hepatocytes 26054723    
Neuroblastoma cells 25944692    
Platelets 25332113    
Platelets 25332113    
Platelets 25332113    
Prostate cancer cells 25844599    
 Gene ontology annotations for UBE2D3
Molecular Function
    ubiquitin conjugating enzyme activity GO:0061631 IDA
    ATP binding GO:0005524 IEA
    ligase activity GO:0016874 IEA
    protein binding GO:0005515 IPI
    ubiquitin-protein transferase activity GO:0004842 IDA
Biological Process
    MyD88-independent toll-like receptor signaling pathway GO:0002756 TAS
    transcription, DNA-templated GO:0006351 TAS
    protein autoubiquitination GO:0051865 IDA
    transcription initiation from RNA polymerase II promoter GO:0006367 TAS
    negative regulation of transcription from RNA polymerase II promoter GO:0000122 TAS
    TRIF-dependent toll-like receptor signaling pathway GO:0035666 TAS
    regulation of transcription from RNA polymerase II promoter in response to hypoxia GO:0061418 TAS
    protein K11-linked ubiquitination GO:0070979 IDA
    positive regulation of protein targeting to mitochondrion GO:1903955 IMP
    DNA repair GO:0006281 IEA
    proteasome-mediated ubiquitin-dependent protein catabolic process GO:0043161 IDA
    toll-like receptor signaling pathway GO:0002224 TAS
    ubiquitin-dependent protein catabolic process GO:0006511 TAS
    innate immune response GO:0045087 TAS
    apoptotic process GO:0006915 IEA
    toll-like receptor 4 signaling pathway GO:0034142 TAS
    cellular protein modification process GO:0006464 TAS
    protein monoubiquitination GO:0006513 IDA
    cellular response to hypoxia GO:0071456 TAS
    gene expression GO:0010467 TAS
    negative regulation of type I interferon production GO:0032480 TAS
    protein K48-linked ubiquitination GO:0070936 IDA
    protein ubiquitination GO:0016567 IDA
    transforming growth factor beta receptor signaling pathway GO:0007179 TAS
    protein polyubiquitination GO:0000209 IDA
    toll-like receptor 3 signaling pathway GO:0034138 TAS
    BMP signaling pathway GO:0030509 TAS
Subcellular Localization
    extracellular exosome GO:0070062 IDA
    plasma membrane GO:0005886 IEA
    nucleoplasm GO:0005654 TAS
    cytosol GO:0005829 TAS
    endosome membrane GO:0010008 IEA
 Experiment description of studies that identified UBE2D3 in exosomes
1
Experiment ID 236
ISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101|Alix|HSC70|GAPDH
EV Cytosolic markers
✘ EV Membrane markers
✔
HSP90B1
EV Negative markers
✔
qNano
EV Particle analysis
Identified molecule mRNA
Identification method RNA Sequencing
PubMed ID 26054723    
Organism Homo sapiens
Experiment description Hepatocellular carcinoma-derived exosomes promote motility of immortalized hepatocyte through transfer of oncogenic proteins and RNAs
Authors He M, Qin H, Poon TC, Sze SC, Ding X, Co NN, Ngai SM, Chan TF, Wong N
Journal name Carcinogenesis
Publication year 2015
Sample Hepatocellular carcinoma cells
Sample name MHCC97L
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Sucrose density gradient
Flotation density 1.13-1.19 g/mL
Molecules identified in the study Protein
RNA
Methods used in the study Western blotting
Mass spectrometry
RT-PCR
RNA Sequencing
2
Experiment ID 237
ISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101|Alix|HSC70|GAPDH
EV Cytosolic markers
✘ EV Membrane markers
✔
HSP90B1
EV Negative markers
✔
qNano
EV Particle analysis
Identified molecule mRNA
Identification method RNA Sequencing
PubMed ID 26054723    
Organism Homo sapiens
Experiment description Hepatocellular carcinoma-derived exosomes promote motility of immortalized hepatocyte through transfer of oncogenic proteins and RNAs
Authors He M, Qin H, Poon TC, Sze SC, Ding X, Co NN, Ngai SM, Chan TF, Wong N
Journal name Carcinogenesis
Publication year 2015
Sample Hepatocytes
Sample name MIHA
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Sucrose density gradient
Flotation density 1.13-1.19 g/mL
Molecules identified in the study Protein
RNA
Methods used in the study Western blotting
Mass spectrometry
RNA Sequencing
3
Experiment ID 224
ISEV standards
✔
EM|AFM
EV Biophysical techniques
✔
Alix|TSG101
EV Cytosolic markers
✔
CD63|CD81
EV Membrane markers
✔
GOLGA2
EV Negative markers
✘ EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25944692    
Organism Homo sapiens
Experiment description Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes
Authors Keerthikumar S, Gangoda L, Liem M, Fonseka P, Atukorala I, Ozcitti C, Mechler A, Adda CG, Ang CS, Mathivanan S
Journal name Oncotarget
Publication year 2015
Sample Neuroblastoma cells
Sample name SH-SY5Y
Isolation/purification methods Differential centrifugation
Ultracentrifugation
OptiPrep density gradient
Flotation density 1.10 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
4
Experiment ID 231
ISEV standards
✘ EV Biophysical techniques
✔
Alix
EV Cytosolic markers
✔
CD63|CD9
EV Membrane markers
✘ EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25332113    
Organism Homo sapiens
Experiment description Lipidomic and proteomic characterization of platelet extracellular vesicle subfractions from senescent platelets
Authors Pienimaeki-Roemer A, Kuhlmann K, Bottcher A, Konovalova T, Black A, Orso E, Liebisch G, Ahrens M, Eisenacher M, Meyer HE, Schmitz G.
Journal name Transfusion
Publication year 2015
Sample Platelets
Sample name PL-Exs - Rep 1
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Optiprep density gradient
Flotation density 1.12-1.15 g/mL
Molecules identified in the study Protein
Lipids
Methods used in the study Western blotting
Mass spectrometry
5
Experiment ID 232
ISEV standards
✘ EV Biophysical techniques
✘ EV Cytosolic markers
✘ EV Membrane markers
✘ EV Negative markers
✘ EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25332113    
Organism Homo sapiens
Experiment description Lipidomic and proteomic characterization of platelet extracellular vesicle subfractions from senescent platelets
Authors Pienimaeki-Roemer A, Kuhlmann K, Bottcher A, Konovalova T, Black A, Orso E, Liebisch G, Ahrens M, Eisenacher M, Meyer HE, Schmitz G.
Journal name Transfusion
Publication year 2015
Sample Platelets
Sample name PL-Exs - Rep 2
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Optiprep density gradient
Flotation density 1.12-1.15 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
6
Experiment ID 233
ISEV standards
✘ EV Biophysical techniques
✘ EV Cytosolic markers
✘ EV Membrane markers
✘ EV Negative markers
✘ EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25332113    
Organism Homo sapiens
Experiment description Lipidomic and proteomic characterization of platelet extracellular vesicle subfractions from senescent platelets
Authors Pienimaeki-Roemer A, Kuhlmann K, Bottcher A, Konovalova T, Black A, Orso E, Liebisch G, Ahrens M, Eisenacher M, Meyer HE, Schmitz G.
Journal name Transfusion
Publication year 2015
Sample Platelets
Sample name PL-Exs - Rep 3
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Optiprep density gradient
Flotation density 1.12-1.15 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
7
Experiment ID 274
ISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101|Alix|RAB5A
EV Cytosolic markers
✔
CD9|CD82|CD63|CD81
EV Membrane markers
✔
AIF
EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25844599    
Organism Homo sapiens
Experiment description Molecular profiling of prostate cancer derived exosomes may reveal a predictive signature for response to docetaxel.
Authors Kharaziha P, Chioureas D, Rutishauser D, Baltatzis G, Lennartsson L, Fonseca P, Azimi A, Hultenby K, Zubarev R, Ullen A, Yachnin J, Nilsson S, Panaretakis T.
Journal name Oncotarget
Publication year 2015
Sample Prostate cancer cells
Sample name DU145 - Docetaxel resistant
Isolation/purification methods Filtration
Ultracentrifugation
Sucrose density gradient
Flotation density 1.13-1.18 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Flow cytometry
Western blotting
 Protein-protein interactions for UBE2D3
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 RNF5  
Affinity Capture-MS Homo sapiens
2 RNF126  
Two-hybrid Homo sapiens
3 NEDD4 4734
Biochemical Activity Homo sapiens
4 UBE3A 7337
Affinity Capture-MS Homo sapiens
Biochemical Activity Homo sapiens
5 DTX3L 151636
Affinity Capture-Western Homo sapiens
6 MEX3B 84206
Two-hybrid Homo sapiens
7 TRIM39  
Two-hybrid Homo sapiens
View the network image/svg+xml



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