Gene description for USP28
Gene name ubiquitin specific peptidase 28
Gene symbol USP28
Other names/aliases -
Species Homo sapiens
 Database cross references - USP28
ExoCarta ExoCarta_57646
Vesiclepedia VP_57646
Entrez Gene 57646
HGNC 12625
MIM 610748
UniProt Q96RU2  
 USP28 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    
 Gene ontology annotations for USP28
Molecular Function
    cysteine-type deubiquitinase activity GO:0004843 IBA
    cysteine-type deubiquitinase activity GO:0004843 IDA
    cysteine-type deubiquitinase activity GO:0004843 IMP
    cysteine-type deubiquitinase activity GO:0004843 TAS
    protein binding GO:0005515 IPI
    deubiquitinase activity GO:0101005 IMP
Biological Process
    DNA damage checkpoint signaling GO:0000077 IBA
    DNA damage checkpoint signaling GO:0000077 IMP
    DNA repair GO:0006281 IEA
    DNA damage response GO:0006974 IDA
    cell population proliferation GO:0008283 IMP
    response to ionizing radiation GO:0010212 IDA
    protein deubiquitination GO:0016579 IDA
    protein deubiquitination GO:0016579 TAS
    regulation of protein stability GO:0031647 IBA
    regulation of protein stability GO:0031647 IMP
    cellular response to UV GO:0034644 IDA
    intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator GO:0042771 IDA
    protein deubiquitination involved in ubiquitin-dependent protein catabolic process GO:0071947 IMP
Subcellular Localization
    nucleus GO:0005634 IBA
    nucleoplasm GO:0005654 IDA
    nucleoplasm GO:0005654 TAS
    cytosol GO:0005829 IBA
    nuclear body GO:0016604 IDA
    protein-containing complex GO:0032991 IDA
 Experiment description of studies that identified USP28 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
 Protein-protein interactions for USP28
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 USP5 8078
Biochemical Activity Homo sapiens
2 UCHL1 7345
Biochemical Activity Homo sapiens
3 UBC 7316
Reconstituted Complex Homo sapiens
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
Co-crystal Structure Homo sapiens
Biochemical Activity Homo sapiens
Reconstituted Complex Homo sapiens
Biochemical Activity Homo sapiens
4 ZC3H4 23211
Co-fractionation Homo sapiens
5 TRIM55  
Biochemical Activity Homo sapiens
6 AQR 9716
Affinity Capture-MS Homo sapiens
7 RFFL 117584
Biochemical Activity Homo sapiens
8 APEX1 328
Affinity Capture-RNA Homo sapiens
9 PJA1  
Biochemical Activity Homo sapiens
10 USO1 8615
Co-fractionation Homo sapiens
11 SENP1  
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
12 Trp53bp1  
Affinity Capture-MS Mus musculus
13 FBXW7  
Affinity Capture-Western Homo sapiens
14 CCDC138  
Affinity Capture-MS Homo sapiens
15 ANOS1 3730
Affinity Capture-MS Homo sapiens
16 OTUB2  
Biochemical Activity Homo sapiens
17 PIK3C3 5289
Affinity Capture-Western Homo sapiens
18 MDC1  
Affinity Capture-Western Homo sapiens
19 DYNLL1 8655
Affinity Capture-MS Homo sapiens
20 USP33  
Biochemical Activity Homo sapiens
21 UCHL5 51377
Biochemical Activity Homo sapiens
22 HYPM  
Affinity Capture-MS Homo sapiens
23 ESPL1  
Biochemical Activity Homo sapiens
24 MRPS7 51081
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
25 MAVS 57506
Affinity Capture-Western Homo sapiens
26 USP7 7874
Biochemical Activity Homo sapiens
27 TWF1 5756
Co-fractionation Homo sapiens
28 GPR17 2840
Affinity Capture-MS Homo sapiens
29 LIN28A  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
30 APPBP2  
Affinity Capture-MS Homo sapiens
31 AURKA 6790
Affinity Capture-Western Homo sapiens
32 ATXN3L  
Biochemical Activity Homo sapiens
33 SENP2 59343
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
34 USP14 9097
Biochemical Activity Homo sapiens
35 USP21  
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
36 RB1CC1 9821
Affinity Capture-MS Homo sapiens
37 PARK2  
Affinity Capture-MS Homo sapiens
38 C14orf80  
Affinity Capture-MS Homo sapiens
39 Ppp6c 67857
Affinity Capture-MS Mus musculus
40 COMTD1 118881
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
41 OFD1 8481
Affinity Capture-MS Homo sapiens
42 USP8 9101
Biochemical Activity Homo sapiens
43 SENP8  
Biochemical Activity Homo sapiens
44 ST6GAL1 6480
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
45 SUMO2 6613
Affinity Capture-MS Homo sapiens
Co-crystal Structure Homo sapiens
Reconstituted Complex Homo sapiens
46 BRAF  
Affinity Capture-MS Homo sapiens
47 DYNLL2 140735
Affinity Capture-MS Homo sapiens
48 STAMBP 10617
Biochemical Activity Homo sapiens
49 USP28 57646
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
50 TRIM63  
Biochemical Activity Homo sapiens
51 PFAS 5198
Co-fractionation Homo sapiens
52 STAM 8027
Biochemical Activity Homo sapiens
53 ZCCHC8 55596
Co-fractionation Homo sapiens
54 NUMA1 4926
Affinity Capture-Western Homo sapiens
55 BRF1  
Affinity Capture-MS Homo sapiens
56 USP4 7375
Biochemical Activity Homo sapiens
57 TP53BP1 7158
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
58 USP15 9958
Biochemical Activity Homo sapiens
59 NSMCE2  
Biochemical Activity Homo sapiens
60 PRKD1 5587
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-Western Homo sapiens
61 MTNR1A  
Two-hybrid Homo sapiens
62 ATM 472
Affinity Capture-Western Homo sapiens
63 MAP3K1 4214
Biochemical Activity Homo sapiens
64 BAP1 8314
Biochemical Activity Homo sapiens
65 Paxip1  
Affinity Capture-MS Mus musculus
66 GUCY1B3  
Affinity Capture-MS Homo sapiens
67 HAUS5 23354
Affinity Capture-MS Homo sapiens
68 PIM2  
Affinity Capture-Western Homo sapiens
69 MYC  
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
70 MSGN1  
Affinity Capture-MS Homo sapiens
71 TP63  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
72 RPL35A 6165
Affinity Capture-MS Homo sapiens
73 PLA2G2A 5320
Biochemical Activity Homo sapiens
74 PCM1 5108
Affinity Capture-MS Homo sapiens
75 FOXK1 221937
Affinity Capture-MS Homo sapiens
76 KLHL2 11275
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
77 USP51  
Biochemical Activity Homo sapiens
78 HIF1A 3091
Biochemical Activity Homo sapiens
79 CLSPN  
Affinity Capture-Western Homo sapiens
80 USP25  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
81 PIM1  
Affinity Capture-Western Homo sapiens
82 ELAVL1 1994
Affinity Capture-RNA Homo sapiens
83 RCHY1  
Affinity Capture-Western Homo sapiens
84 OTUB1 55611
Biochemical Activity Homo sapiens
85 PAFAH2 5051
Affinity Capture-MS Homo sapiens
86 UCHL3 7347
Biochemical Activity Homo sapiens
87 CEP44  
Affinity Capture-MS Homo sapiens
88 NUP50 10762
Proximity Label-MS Homo sapiens
89 KDM1A 23028
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
90 TRIM23 373
Affinity Capture-MS Homo sapiens
91 SPPL2B 56928
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
92 JOSD1  
Biochemical Activity Homo sapiens
93 ZNF304  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
94 CIT 11113
Co-fractionation Homo sapiens
95 SERBP1 26135
Affinity Capture-MS Homo sapiens
96 AR 367
Proximity Label-MS Homo sapiens
97 UCK1  
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-Western Homo sapiens
98 USP20  
Biochemical Activity Homo sapiens
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