Gene description for VPS39
Gene name vacuolar protein sorting 39 homolog (S. cerevisiae)
Gene symbol VPS39
Other names/aliases TLP
VAM6
hVam6p
Species Homo sapiens
 Database cross references - VPS39
ExoCarta ExoCarta_23339
Vesiclepedia VP_23339
Entrez Gene 23339
HGNC 20593
MIM 612188
UniProt Q96JC1  
 VPS39 identified in sEVs 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    
Mesenchymal stem cells 36408942    
Thymus 23844026    
 Gene ontology annotations for VPS39
Molecular Function
    protein binding GO:0005515 IPI
Biological Process
    intracellular protein transport GO:0006886 IEA
    autophagy GO:0006914 IBA
    autophagy GO:0006914 IMP
    endosome to lysosome transport GO:0008333 IMP
    endocytic recycling GO:0032456 IMP
    endosomal vesicle fusion GO:0034058 IBA
    endosomal vesicle fusion GO:0034058 IDA
    endosomal vesicle fusion GO:0034058 NAS
    regulation of SNARE complex assembly GO:0035542 NAS
    autophagosome-lysosome fusion GO:0061909 IDA
    late endosome to lysosome transport GO:1902774 IDA
Subcellular Localization
    cytoplasm GO:0005737 IBA
    lysosomal membrane GO:0005765 HDA
    lysosomal membrane GO:0005765 IDA
    late endosome GO:0005770 IDA
    endosome membrane GO:0010008 TAS
    membrane GO:0016020 IBA
    AP-3 adaptor complex GO:0030123 IEA
    HOPS complex GO:0030897 IDA
    HOPS complex GO:0030897 NAS
    late endosome membrane GO:0031902 IDA
    lysosomal HOPS complex GO:1902501 IDA
 Experiment description of studies that identified VPS39 in sEVs
1
Experiment ID 489
MISEV standards
✔
EM
Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
✔
Canx
Negative markers
✔
NTA
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
Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
✔
Canx
Negative markers
✔
NTA
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
Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
✔
Canx
Negative markers
✔
NTA
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
Biophysical techniques
✔
Cd9|Cd81|Cd63|Gapdh|Sdcbp|Lamp1|Aqp1|Rab5a|Icam1|Cd82|Itga2b|Tsg101|Lamp2|Rab35|Flot1|Flot2|Cd151|Rab5b|Tfrc|Uchl1
Enriched markers
✔
Canx
Negative markers
✔
NTA
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
5
Experiment ID 488
MISEV standards
✔
EM
Biophysical techniques
✔
CD9|CD81|CD63|GAPDH|SDCBP|LAMP1|TFRC|UCHL1|FLOT2|LAMP2|FLOT1|ICAM1|RAB5B|CD151|RAB35|TSG101|RAB5A|CD82
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 36408942    
Organism Homo sapiens
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 Mesenchymal stem cells
Sample name UCMSC
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
6
Experiment ID 217
MISEV standards
✔
EM
Biophysical techniques
✔
TSG101|CD81|CD9|CD63
Enriched markers
✘ Negative markers
✔
NTA
Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23844026    
Organism Homo sapiens
Experiment description Characterization of human thymic exosomes.
Authors "Skogberg G, Gudmundsdottir J, van der Post S, Sandstrom K, Bruhn S, Benson M, Mincheva-Nilsson L, Baranov V, Telemo E, Ekwall O."
Journal name PLoS One
Publication year 2013
Sample Thymus
Sample name Normal-Thymus
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
 Protein-protein interactions for VPS39
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 VPS41 27072
Affinity Capture-Western Homo sapiens
2 HOOK1  
Affinity Capture-Western Homo sapiens
3 SIRT6  
Affinity Capture-MS Homo sapiens
4 RILP 83547
Reconstituted Complex Homo sapiens
5 VIPAS39 63894
Co-fractionation Homo sapiens
6 RBM25 58517
Affinity Capture-MS Homo sapiens
7 IL1R1 3554
Affinity Capture-MS Homo sapiens
8 VPS18 57617
Affinity Capture-Western Homo sapiens
9 EDEM1  
Affinity Capture-MS Homo sapiens
10 NPAT  
Affinity Capture-MS Homo sapiens
11 NFRKB  
Affinity Capture-MS Homo sapiens
12 USP54 159195
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
13 CHCHD4  
Affinity Capture-MS Homo sapiens
14 PRPF40A 55660
Affinity Capture-MS Homo sapiens
15 SPATA1  
Affinity Capture-MS Homo sapiens
16 EPN3 55040
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
17 UAP1 6675
Co-fractionation Homo sapiens
18 XPO6 23214
Co-fractionation Homo sapiens
19 UVRAG  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
20 CDK2 1017
Affinity Capture-MS Homo sapiens
21 C12orf49  
Negative Genetic Homo sapiens
22 S100A4 6275
Affinity Capture-MS Homo sapiens
23 RPS6KC1  
Affinity Capture-MS Homo sapiens
24 NTRK1 4914
Affinity Capture-MS Homo sapiens
25 RAB7A 7879
Reconstituted Complex Homo sapiens
26 ZNF655  
Affinity Capture-MS Homo sapiens
27 ZUFSP 221302
Affinity Capture-MS Homo sapiens
28 ARRDC3 57561
Affinity Capture-MS Homo sapiens
29 VPS11 55823
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
30 VPS39 23339
Two-hybrid Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-Western Homo sapiens
Two-hybrid Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-Western Homo sapiens
31 NME8  
Affinity Capture-MS Homo sapiens
32 FAXC  
Affinity Capture-MS Homo sapiens
33 AP3D1 8943
Affinity Capture-Western Homo sapiens
34 GDF3 9573
Affinity Capture-MS Homo sapiens
35 MKI67  
Affinity Capture-MS Homo sapiens
36 STX17 55014
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
37 NOTCH1 4851
Affinity Capture-MS Homo sapiens
38 ZNF263  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
39 UBXN6 80700
Co-fractionation Homo sapiens
40 PTAR1 375743
Synthetic Lethality Homo sapiens
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