Gene description for USP39
Gene name ubiquitin specific peptidase 39
Gene symbol USP39
Other names/aliases 65K
CGI-21
HSPC332
SAD1
SNRNP65
Species Homo sapiens
 Database cross references - USP39
ExoCarta ExoCarta_10713
Vesiclepedia VP_10713
Entrez Gene 10713
HGNC 20071
MIM 611594
UniProt Q53GS9  
 USP39 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    
Mesenchymal stem cells 36408942    
Thymus 23844026    
Urine 21595033    
Urine 21595033    
Urine 21595033    
 Gene ontology annotations for USP39
Molecular Function
    cysteine-type deubiquitinase activity GO:0004843 IDA
    protein binding GO:0005515 IPI
    zinc ion binding GO:0008270 IEA
Biological Process
    spliceosomal complex assembly GO:0000245 IBA
    spliceosomal complex assembly GO:0000245 IMP
    mRNA splicing, via spliceosome GO:0000398 IDA
    mRNA splicing, via spliceosome GO:0000398 NAS
    mRNA processing GO:0006397 TAS
    RNA splicing GO:0008380 TAS
    protein deubiquitination GO:0016579 IEA
    cell division GO:0051301 IEA
Subcellular Localization
    nucleus GO:0005634 IDA
    nucleus GO:0005634 NAS
    nucleoplasm GO:0005654 IDA
    nucleoplasm GO:0005654 TAS
    spliceosomal complex GO:0005681 IEA
    U4/U6 x U5 tri-snRNP complex GO:0046540 IDA
    U4/U6 x U5 tri-snRNP complex GO:0046540 IPI
 Experiment description of studies that identified USP39 in exosomes
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
7
Experiment ID 193
MISEV standards
✔
EM
Biophysical techniques
✔
CD63|CD9
Enriched markers
✔
PHB
Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 21595033    
Organism Homo sapiens
Experiment description Proteomic analysis of urinary exosomes from patients of early IgA nephropathy and thin basement membrane nephropathy.
Authors "Moon PG, Lee JE, You S, Kim TK, Cho JH, Kim IS, Kwon TH, Kim CD, Park SH, Hwang D, Kim YL, Baek MC."
Journal name Proteomics
Publication year 2011
Sample Urine
Sample name Urine - Normal
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
8
Experiment ID 194
MISEV standards
✘ Biophysical techniques
✘ Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 21595033    
Organism Homo sapiens
Experiment description Proteomic analysis of urinary exosomes from patients of early IgA nephropathy and thin basement membrane nephropathy.
Authors "Moon PG, Lee JE, You S, Kim TK, Cho JH, Kim IS, Kwon TH, Kim CD, Park SH, Hwang D, Kim YL, Baek MC."
Journal name Proteomics
Publication year 2011
Sample Urine
Sample name Urine - Patients of basement membrane nephropathy
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
9
Experiment ID 195
MISEV standards
✘ Biophysical techniques
✘ Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 21595033    
Organism Homo sapiens
Experiment description Proteomic analysis of urinary exosomes from patients of early IgA nephropathy and thin basement membrane nephropathy.
Authors "Moon PG, Lee JE, You S, Kim TK, Cho JH, Kim IS, Kwon TH, Kim CD, Park SH, Hwang D, Kim YL, Baek MC."
Journal name Proteomics
Publication year 2011
Sample Urine
Sample name Urine - Patients of early IgA nephropathy
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
 Protein-protein interactions for USP39
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 UBE2H 7328
Affinity Capture-MS Homo sapiens
2 SLFN11 91607
Affinity Capture-MS Homo sapiens
3 RIT1 6016
Negative Genetic Homo sapiens
4 HNRNPC 3183
Co-fractionation Homo sapiens
5 SNRPE 6635
Affinity Capture-MS Homo sapiens
6 Prpf8 192159
Affinity Capture-MS Mus musculus
7 PRPF8 10594
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
8 GGPS1  
Co-fractionation Homo sapiens
9 KCTD10 83892
Affinity Capture-MS Homo sapiens
10 USP10 9100
Affinity Capture-MS Homo sapiens
11 SP1  
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
12 ZNHIT2 741
Affinity Capture-MS Homo sapiens
13 HIST1H2BG 8339
Proximity Label-MS Homo sapiens
14 C9orf78 51759
Affinity Capture-MS Homo sapiens
15 BRD2  
Affinity Capture-MS Homo sapiens
16 PRPF3  
Affinity Capture-MS Homo sapiens
17 VHL  
Affinity Capture-Western Homo sapiens
18 CAND1 55832
Affinity Capture-MS Homo sapiens
19 SNRPF 6636
Affinity Capture-MS Homo sapiens
20 SNRPD2 6633
Affinity Capture-MS Homo sapiens
21 APP 351
Reconstituted Complex Homo sapiens
22 SAFB 6294
Co-fractionation Homo sapiens
23 DDX23 9416
Proximity Label-MS Homo sapiens
Affinity Capture-MS Homo sapiens
24 PARK2  
Affinity Capture-MS Homo sapiens
25 DDX24 57062
Affinity Capture-MS Homo sapiens
26 SF3B1 23451
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
27 PRC1 9055
Affinity Capture-MS Homo sapiens
28 HSPH1 10808
Co-fractionation Homo sapiens
29 OBSL1 23363
Affinity Capture-MS Homo sapiens
30 SF3A2 8175
Affinity Capture-MS Homo sapiens
31 ADARB1 104
Co-fractionation Homo sapiens
32 SNRPC 6631
Affinity Capture-MS Homo sapiens
33 TRIM26 7726
Two-hybrid Homo sapiens
34 RNU4ATAC 100151683
Affinity Capture-Western Homo sapiens
35 RRP8  
Affinity Capture-MS Homo sapiens
36 MECP2 4204
Affinity Capture-MS Homo sapiens
37 LGALS9 3965
Co-fractionation Homo sapiens
38 MYCN  
Affinity Capture-MS Homo sapiens
39 RBM42  
Affinity Capture-MS Homo sapiens
40 NCSTN 23385
Co-fractionation Homo sapiens
41 GAR1 54433
Affinity Capture-MS Homo sapiens
42 TRIM8  
Two-hybrid Homo sapiens
43 VTN 7448
Co-fractionation Homo sapiens
44 PRPF6 24148
Affinity Capture-MS Homo sapiens
45 NSUN2 54888
Co-fractionation Homo sapiens
46 RPL22L1 200916
Affinity Capture-MS Homo sapiens
47 USP12 219333
Affinity Capture-MS Homo sapiens
48 HIST1H4A 8359
Affinity Capture-MS Homo sapiens
49 DDX21 9188
Affinity Capture-MS Homo sapiens
50 MEPCE 56257
Affinity Capture-MS Homo sapiens
51 SAE1 10055
Biochemical Activity Homo sapiens
52 SRSF3 6428
Co-fractionation Homo sapiens
53 SNRNP200 23020
Affinity Capture-MS Homo sapiens
54 TRIM55  
Co-fractionation Homo sapiens
55 SNRPB 6628
Affinity Capture-MS Homo sapiens
56 NCAPD3 23310
Co-fractionation Homo sapiens
57 NTRK1 4914
Affinity Capture-MS Homo sapiens
58 IFI16 3428
Affinity Capture-MS Homo sapiens
59 RAD18  
Affinity Capture-MS Homo sapiens
60 TPBG 7162
Co-fractionation Homo sapiens
61 GTF3C1  
Co-fractionation Homo sapiens
62 SF3B6 51639
Co-fractionation Homo sapiens
63 COPRS  
Affinity Capture-MS Homo sapiens
64 RNU6ATAC 100151684
Affinity Capture-Western Homo sapiens
65 SNRNP27  
Affinity Capture-MS Homo sapiens
66 DHX9 1660
Co-fractionation Homo sapiens
67 SON 6651
Co-fractionation Homo sapiens
68 DHX38 9785
Affinity Capture-MS Homo sapiens
69 PRPF31 26121
Affinity Capture-MS Homo sapiens
70 CEBPA  
Protein-peptide Homo sapiens
71 SRPK1 6732
Biochemical Activity Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
72 TSR2  
Affinity Capture-MS Homo sapiens
73 SNRPB2 6629
Affinity Capture-MS Homo sapiens
74 SCARNA22  
Affinity Capture-RNA Homo sapiens
75 SRSF11 9295
Co-fractionation Homo sapiens
76 RBM39 9584
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
77 LSM8 51691
Affinity Capture-MS Homo sapiens
78 PRPF4B 8899
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
79 FANCD2  
Affinity Capture-MS Homo sapiens
80 NOC3L 64318
Affinity Capture-MS Homo sapiens
81 WWTR1 25937
Affinity Capture-RNA Homo sapiens
82 TRMT10C 54931
Affinity Capture-MS Homo sapiens
83 PTEN 5728
Affinity Capture-MS Homo sapiens
84 SIRT7  
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
85 EPAS1  
Affinity Capture-Western Homo sapiens
86 CD2BP2 10421
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
87 SRSF1 6426
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
88 TRAF6 7189
Two-hybrid Homo sapiens
89 NR3C1 2908
Proximity Label-MS Homo sapiens
90 SRSF5 6430
Co-fractionation Homo sapiens
91 EGFR 1956
Negative Genetic Homo sapiens
92 FUS 2521
Affinity Capture-MS Homo sapiens
93 SART1 9092
Affinity Capture-MS Homo sapiens
94 FN1 2335
Affinity Capture-MS Homo sapiens
95 SF3A1 10291
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
96 AURKB 9212
Affinity Capture-MS Homo sapiens
97 EFTUD2 9343
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
98 PRPF19 27339
Co-fractionation Homo sapiens
99 RPA3 6119
Proximity Label-MS Homo sapiens
100 FXR2 9513
Two-hybrid Homo sapiens
101 Chmp3  
Affinity Capture-MS Mus musculus
102 ZC3H18  
Co-fractionation Homo sapiens
103 APEH 327
Co-fractionation Homo sapiens
104 TOP1 7150
Affinity Capture-MS Homo sapiens
105 HSPA4 3308
Co-fractionation Homo sapiens
106 SART3 9733
Affinity Capture-MS Homo sapiens
107 SRSF10 10772
Co-fractionation Homo sapiens
108 DDRGK1 65992
Affinity Capture-MS Homo sapiens
109 CSNK1E 1454
Co-fractionation Homo sapiens
110 TRIM39  
Two-hybrid Homo sapiens
111 CETN2 1069
Co-fractionation Homo sapiens
112 BRD3 8019
Affinity Capture-MS Homo sapiens
113 SUPT16H 11198
Co-fractionation Homo sapiens
114 CCDC8  
Affinity Capture-MS Homo sapiens
115 Sart1  
Affinity Capture-MS Mus musculus
116 PA2G4 5036
Affinity Capture-MS Homo sapiens
117 TRIM5 85363
Two-hybrid Homo sapiens
118 EAPP  
Affinity Capture-MS Homo sapiens
119 KAT8  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
120 ZRANB2 9406
Affinity Capture-MS Homo sapiens
121 CPSF6 11052
Affinity Capture-MS Homo sapiens
122 TP53 7157
Affinity Capture-MS Homo sapiens
123 WWOX 51741
Affinity Capture-MS Homo sapiens
124 SNRPA 6626
Affinity Capture-MS Homo sapiens
125 TXNL4A 10907
Affinity Capture-MS Homo sapiens
126 RUVBL2 10856
Co-fractionation Homo sapiens
127 MKI67  
Affinity Capture-MS Homo sapiens
128 TRIM25 7706
Two-hybrid Homo sapiens
129 PCNA 5111
Co-fractionation Homo sapiens
130 SNRNP40 9410
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
131 LSM7  
Affinity Capture-MS Homo sapiens
132 NCL 4691
Affinity Capture-MS Homo sapiens
133 EZH2  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
134 RNMTL1  
Affinity Capture-MS Homo sapiens
135 ARHGAP36  
Affinity Capture-MS Homo sapiens
136 SRSF7 6432
Co-fractionation Homo sapiens
137 ARF1 375
Co-fractionation Homo sapiens
138 PRPF4 9128
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
139 CUL7 9820
Affinity Capture-MS Homo sapiens
140 KRAS 3845
Negative Genetic Homo sapiens
141 HNRNPU 3192
Co-fractionation Homo sapiens
142 SSRP1 6749
Affinity Capture-MS Homo sapiens
143 CDC5L 988
Affinity Capture-MS Homo sapiens
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