Gene description for USP4
Gene name ubiquitin specific peptidase 4 (proto-oncogene)
Gene symbol USP4
Other names/aliases UNP
Unph
Species Homo sapiens
 Database cross references - USP4
ExoCarta ExoCarta_7375
Vesiclepedia VP_7375
Entrez Gene 7375
HGNC 12627
MIM 603486
UniProt Q13107  
 USP4 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    
 Gene ontology annotations for USP4
Molecular Function
    cysteine-type deubiquitinase activity GO:0004843 IDA
    cysteine-type deubiquitinase activity GO:0004843 TAS
    protein binding GO:0005515 IPI
    adenosine receptor binding GO:0031685 IPI
    identical protein binding GO:0042802 IPI
    metal ion binding GO:0046872 IEA
Biological Process
    spliceosomal tri-snRNP complex assembly GO:0000244 IMP
    proteolysis GO:0006508 IEA
    protein deubiquitination GO:0016579 IDA
    protein deubiquitination GO:0016579 IMP
    protein deubiquitination GO:0016579 TAS
    negative regulation of protein ubiquitination GO:0031397 IMP
    regulation of protein stability GO:0031647 IDA
    protein localization to cell surface GO:0034394 IDA
    positive regulation of TORC1 signaling GO:1904263 IDA
Subcellular Localization
    nucleus GO:0005634 IBA
    nucleus GO:0005634 IDA
    cytoplasm GO:0005737 IDA
    lysosome GO:0005764 TAS
    cytosol GO:0005829 IDA
    cytosol GO:0005829 TAS
    plasma membrane GO:0005886 IDA
 Experiment description of studies that identified USP4 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
 Protein-protein interactions for USP4
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 PSMA6 5687
Two-hybrid Homo sapiens
2 ENSA 2029
Affinity Capture-MS Homo sapiens
3 TCEAL2  
Affinity Capture-MS Homo sapiens
4 TWIST1  
Affinity Capture-Western Homo sapiens
5 HDAC2 3066
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
6 TK1 7083
Two-hybrid Homo sapiens
7 DCP1B  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
8 SART3 9733
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Two-hybrid Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
9 PSMD11 5717
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Two-hybrid Homo sapiens
10 ADSL 158
Affinity Capture-MS Homo sapiens
11 TCF7L2  
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
12 KIF20A 10112
Affinity Capture-MS Homo sapiens
13 LSM4 25804
Affinity Capture-MS Homo sapiens
14 UBC 7316
Affinity Capture-MS Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
Reconstituted Complex Homo sapiens
15 USP11 8237
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
16 PRPF3  
Reconstituted Complex Homo sapiens
Affinity Capture-MS Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-MS Homo sapiens
17 MCCD1  
Affinity Capture-MS Homo sapiens
18 TRIM55  
Biochemical Activity Homo sapiens
19 RIPK1 8737
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
20 NPC2 10577
Two-hybrid Homo sapiens
21 EIF4E2  
Affinity Capture-MS Homo sapiens
22 TRIM54  
Biochemical Activity Homo sapiens
23 WBP5  
Affinity Capture-MS Homo sapiens
24 CUL4B 8450
Affinity Capture-MS Homo sapiens
25 LRRC27  
Affinity Capture-MS Homo sapiens
26 RHEB 6009
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Biochemical Activity Homo sapiens
27 JUNB  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
28 RNPS1 10921
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Two-hybrid Homo sapiens
Affinity Capture-Western Homo sapiens
29 EXOC1 55763
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
30 CT55  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
31 HES6  
Affinity Capture-MS Homo sapiens
32 PGM1 5236
Two-hybrid Homo sapiens
33 ZFYVE1 53349
Affinity Capture-MS Homo sapiens
34 CTC1  
Affinity Capture-MS Homo sapiens
35 RCC1 1104
Two-hybrid Homo sapiens
36 YWHAH 7533
Affinity Capture-Western Homo sapiens
37 TRMT1 55621
Affinity Capture-MS Homo sapiens
38 MAP3K6  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
39 ATP6V0D1 9114
Affinity Capture-MS Homo sapiens
40 FAM196A  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
41 MAVS 57506
Affinity Capture-Western Homo sapiens
42 VDR  
Affinity Capture-MS Homo sapiens
43 PPIA 5478
Two-hybrid Homo sapiens
44 NPAS1  
Affinity Capture-MS Homo sapiens
45 PSAP 5660
Two-hybrid Homo sapiens
46 AKT1 207
Reconstituted Complex Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-Western Homo sapiens
47 LSM2 57819
Affinity Capture-MS Homo sapiens
48 RB1 5925
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Co-fractionation Homo sapiens
49 PDK1 5163
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
50 ANXA7 310
Two-hybrid Homo sapiens
51 TCP10L  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
52 BSPRY 54836
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
53 MRE11A 4361
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
54 USP21  
Biochemical Activity Homo sapiens
55 CDKN1A  
Two-hybrid Homo sapiens
56 MEPCE 56257
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
57 TCEAL1  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
58 FAM96B 51647
Two-hybrid Homo sapiens
59 PRPS2 5634
Affinity Capture-MS Homo sapiens
60 PPIH 10465
Affinity Capture-MS Homo sapiens
61 PTP4A3  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
62 RAB30 27314
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
63 RIPPLY2  
Affinity Capture-MS Homo sapiens
64 TRIM21 6737
Two-hybrid Homo sapiens
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
Two-hybrid Homo sapiens
65 NTRK1 4914
Affinity Capture-MS Homo sapiens
66 SLX1A  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
67 CABP1 9478
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
68 DCP1A 55802
Affinity Capture-MS Homo sapiens
69 AKAP7 9465
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
70 BRAP  
Two-hybrid Homo sapiens
Affinity Capture-Western Homo sapiens
Two-hybrid Homo sapiens
71 PRPF31 26121
Affinity Capture-MS Homo sapiens
72 USP28 57646
Biochemical Activity Homo sapiens
73 TRIM63  
Biochemical Activity Homo sapiens
74 UBXN6 80700
Affinity Capture-MS Homo sapiens
75 USP32 84669
Affinity Capture-MS Homo sapiens
76 SNAP29 9342
Affinity Capture-MS Homo sapiens
77 RBL1  
Reconstituted Complex Homo sapiens
78 PICK1  
Affinity Capture-MS Homo sapiens
79 DDX6 1656
Affinity Capture-MS Homo sapiens
80 LSM8 51691
Affinity Capture-MS Homo sapiens
81 USP4 7375
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
82 SFN 2810
Affinity Capture-Western Homo sapiens
83 ELMO1 9844
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
84 LGALS1 3956
Two-hybrid Homo sapiens
85 USP15 9958
Biochemical Activity Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
86 CDPF1  
Affinity Capture-MS Homo sapiens
87 CTNNB1 1499
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
88 MIS18A  
Affinity Capture-MS Homo sapiens
89 TNFRSF1A 7132
Affinity Capture-Western Homo sapiens
90 TRAF6 7189
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-Western Homo sapiens
91 ASS1 445
Two-hybrid Homo sapiens
92 PTEN 5728
Affinity Capture-MS Homo sapiens
93 OBFC1 79991
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
94 ATP1B3 483
Two-hybrid Homo sapiens
95 METTL21B  
Affinity Capture-MS Homo sapiens
96 LGALS7 3963
Affinity Capture-MS Homo sapiens
97 PRPF19 27339
Affinity Capture-Western Homo sapiens
98 RBL2 5934
Reconstituted Complex Homo sapiens
99 LGALS7B 653499
Affinity Capture-MS Homo sapiens
100 FAM46A  
Affinity Capture-MS Homo sapiens
101 ATP1B1 481
Two-hybrid Homo sapiens
102 PSMC5 5705
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
103 PLA2G2A 5320
Biochemical Activity Homo sapiens
104 PRKY  
Affinity Capture-MS Homo sapiens
105 MAP3K7  
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
106 BDKRB2  
Two-hybrid Homo sapiens
107 IGKV2D-29  
Two-hybrid Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
108 TRPS1  
Affinity Capture-Western Homo sapiens
109 HUWE1 10075
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
110 RBBP8  
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
111 USP19 10869
Affinity Capture-Western Homo sapiens
112 PADI6  
Affinity Capture-MS Homo sapiens
113 PLEKHA4 57664
Affinity Capture-MS Homo sapiens
114 TP53BP2  
Two-hybrid Homo sapiens
115 TRAF2 7186
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
116 SMN1 6606
Two-hybrid Homo sapiens
117 SUPT20H 55578
Affinity Capture-Western Homo sapiens
118 TP53 7157
Negative Genetic Homo sapiens
119 USP1 7398
Affinity Capture-MS Homo sapiens
120 TGFBR1 7046
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
121 BFSP1  
Affinity Capture-MS Homo sapiens
122 RNF19B  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
123 INSR 3643
Affinity Capture-Western Homo sapiens
124 PLOD1 5351
Two-hybrid Homo sapiens
125 EDC3 80153
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
126 DDX58 23586
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
127 TUT1  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
128 RAD50 10111
Affinity Capture-Western Homo sapiens
129 PCNA 5111
Biochemical Activity Homo sapiens
130 C6orf141  
Affinity Capture-MS Homo sapiens
131 LSM7  
Affinity Capture-MS Homo sapiens
132 FAM110D  
Affinity Capture-MS Homo sapiens
133 AURKA 6790
Affinity Capture-Western Homo sapiens
134 C16orf72 29035
Affinity Capture-MS Homo sapiens
135 NLK  
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
136 LAMA5 3911
Two-hybrid Homo sapiens
137 LSM6 11157
Affinity Capture-MS Homo sapiens
138 PRPF4 9128
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
139 KRAS 3845
Synthetic Lethality Homo sapiens
140 CYCS 54205
Affinity Capture-MS Homo sapiens
141 SRP9 6726
Affinity Capture-MS Homo sapiens
142 IKBKB 3551
Affinity Capture-Western Homo sapiens
143 CUL4A 8451
Affinity Capture-MS Homo sapiens
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