Gene description for EXOSC9
Gene name exosome component 9
Gene symbol EXOSC9
Other names/aliases PM/Scl-75
PMSCL1
RRP45
Rrp45p
p5
p6
Species Homo sapiens
 Database cross references - EXOSC9
ExoCarta ExoCarta_5393
Vesiclepedia VP_5393
Entrez Gene 5393
HGNC 9137
MIM 606180
UniProt Q06265  
 EXOSC9 identified in exosomes derived from the following tissue/cell type
Chondrocytes 35931686    
Chondrocytes 35931686    
Mesenchymal stem cells 36408942    
 Gene ontology annotations for EXOSC9
Molecular Function
    3'-5'-RNA exonuclease activity GO:0000175 NAS
    RNA binding GO:0003723 HDA
    RNA binding GO:0003723 NAS
    RNA exonuclease activity GO:0004532 IDA
    protein binding GO:0005515 IPI
    mRNA 3'-UTR AU-rich region binding GO:0035925 IBA
    mRNA 3'-UTR AU-rich region binding GO:0035925 IDA
    RNA polymerase II-specific DNA-binding transcription factor binding GO:0061629 IEA
Biological Process
    exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) GO:0000467 IBA
    nuclear-transcribed mRNA catabolic process GO:0000956 IMP
    rRNA processing GO:0006364 NAS
    RNA processing GO:0006396 IDA
    RNA catabolic process GO:0006401 IDA
    mRNA catabolic process GO:0006402 IMP
    immune response GO:0006955 NAS
    rRNA catabolic process GO:0016075 IBA
    positive regulation of cell growth GO:0030307 IMP
    U1 snRNA 3'-end processing GO:0034473 IBA
    U4 snRNA 3'-end processing GO:0034475 IBA
    U5 snRNA 3'-end processing GO:0034476 IBA
    positive regulation of transcription by RNA polymerase II GO:0045944 IEA
    nuclear mRNA surveillance GO:0071028 IBA
    nuclear mRNA surveillance GO:0071028 IMP
    nuclear polyadenylation-dependent rRNA catabolic process GO:0071035 IBA
    nuclear polyadenylation-dependent rRNA catabolic process GO:0071035 IMP
    TRAMP-dependent tRNA surveillance pathway GO:0071038 IBA
Subcellular Localization
    nuclear exosome (RNase complex) GO:0000176 IBA
    nuclear exosome (RNase complex) GO:0000176 IDA
    nuclear exosome (RNase complex) GO:0000176 NAS
    cytoplasmic exosome (RNase complex) GO:0000177 IBA
    cytoplasmic exosome (RNase complex) GO:0000177 NAS
    exosome (RNase complex) GO:0000178 IDA
    exosome (RNase complex) GO:0000178 NAS
    nuclear chromosome GO:0000228 IDA
    nucleus GO:0005634 IDA
    nucleoplasm GO:0005654 IDA
    nucleoplasm GO:0005654 TAS
    nucleolus GO:0005730 IDA
    nucleolus GO:0005730 IDA
    cytoplasm GO:0005737 IDA
    cytosol GO:0005829 IDA
    cytosol GO:0005829 TAS
    extracellular exosome GO:0070062 HDA
    nucleolar exosome (RNase complex) GO:0101019 NAS
 Experiment description of studies that identified EXOSC9 in exosomes
1
Experiment ID 497
MISEV standards
Biophysical techniques
CD9|CD151|CD63|CD81|CD82|FLOT1|FLOT2|GAPDH|LAMP1|LAMP2|RAB5A|SDCBP|TFRC|TSG101|UCHL1
Enriched markers
Negative markers
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 35931686    
Organism Homo sapiens
Experiment description Extracellular vesicles enriched in connexin 43 promote a senescent phenotype in bone and synovial cells contributing to osteoarthritis progression
Authors "Varela-Eirín M, Carpintero-Fernández P, Guitián-Caamaño A, Varela-Vázquez A, García-Yuste A, Sánchez-Temprano A, Bravo-López SB, Yañez-Cabanas J, Fonseca E, Largo R, Mobasheri A, Caeiro JR, Mayán MD."
Journal name Cell Death Dis
Publication year 2022
Sample Chondrocytes
Sample name T/C-28a2
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 498
MISEV standards
EM
Biophysical techniques
CD9|CD151|CD63|CD81|CD82|FLOT1|FLOT2|GAPDH|LAMP1|LAMP2|RAB5A|SDCBP|TFRC|TSG101|UCHL1
Enriched markers
Negative markers
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 35931686    
Organism Homo sapiens
Experiment description Extracellular vesicles enriched in connexin 43 promote a senescent phenotype in bone and synovial cells contributing to osteoarthritis progression
Authors "Varela-Eirín M, Carpintero-Fernández P, Guitián-Caamaño A, Varela-Vázquez A, García-Yuste A, Sánchez-Temprano A, Bravo-López SB, Yañez-Cabanas J, Fonseca E, Largo R, Mobasheri A, Caeiro JR, Mayán MD."
Journal name Cell Death Dis
Publication year 2022
Sample Chondrocytes
Sample name T/C-28a2
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 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 EXOSC9
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 UBE2H 7328
Affinity Capture-MS Homo sapiens
2 PSMA6 5687
Co-fractionation Homo sapiens
3 SLIT2 9353
Affinity Capture-MS Homo sapiens
4 EXOSC7 23016
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
5 EEF1G 1937
Affinity Capture-MS Homo sapiens
6 DIS3 22894
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
7 ZCCHC8 55596
Affinity Capture-MS Homo sapiens
8 HIST1H2BG 8339
Proximity Label-MS Homo sapiens
9 NOP56 10528
Affinity Capture-MS Homo sapiens
Proximity Label-MS Homo sapiens
10 KIF20A 10112
Affinity Capture-MS Homo sapiens
11 HSP90AB1 3326
Cross-Linking-MS (XL-MS) Homo sapiens
12 CSNK2A1 1457
Biochemical Activity Homo sapiens
13 CAND1 55832
Affinity Capture-MS Homo sapiens
14 EIF4E2  
Affinity Capture-MS Homo sapiens
15 SOX2  
Affinity Capture-MS Homo sapiens
16 PARP8  
Affinity Capture-MS Homo sapiens
17 USP36  
Affinity Capture-MS Homo sapiens
18 CAPZB 832
Affinity Capture-MS Homo sapiens
19 HP 3240
Affinity Capture-MS Homo sapiens
20 EXOSC2 23404
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
21 C1D  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
22 COPS5 10987
Affinity Capture-MS Homo sapiens
23 FBXW8 26259
Affinity Capture-MS Homo sapiens
24 OBSL1 23363
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
25 SRP14 6727
Co-fractionation Homo sapiens
26 RSRC1  
Affinity Capture-MS Homo sapiens
27 EXOSC4 54512
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Two-hybrid Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
28 SRP68 6730
Affinity Capture-MS Homo sapiens
29 EXOSC6 118460
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
30 ARIH2 10425
Affinity Capture-MS Homo sapiens
31 MPHOSPH6 10200
Reconstituted Complex Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
32 KIAA1804  
Affinity Capture-MS Homo sapiens
33 LUM 4060
Affinity Capture-MS Homo sapiens
34 E2F4  
Affinity Capture-MS Homo sapiens
35 ZDHHC17 23390
Two-hybrid Homo sapiens
36 DIS3L  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
37 SRP9 6726
Affinity Capture-MS Homo sapiens
38 CUL3 8452
Affinity Capture-MS Homo sapiens
39 DRG1 4733
Affinity Capture-MS Homo sapiens
40 RBM7  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
41 LYN 4067
Proximity Label-MS Homo sapiens
42 UBE2I 7329
Two-hybrid Homo sapiens
43 RPL5 6125
Affinity Capture-MS Homo sapiens
44 CHMP4B 128866
Two-hybrid Homo sapiens
45 NTRK1 4914
Affinity Capture-MS Homo sapiens
46 RPL31 6160
Proximity Label-MS Homo sapiens
47 EXOSC5 56915
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
48 SUMO2 6613
Reconstituted Complex Homo sapiens
49 HECTD1 25831
Affinity Capture-MS Homo sapiens
50 PSMA5 5686
Co-fractionation Homo sapiens
51 Exosc1  
Affinity Capture-MS Mus musculus
52 ANLN 54443
Affinity Capture-MS Homo sapiens
53 HBS1L 10767
Reconstituted Complex Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
54 C9orf78 51759
Affinity Capture-MS Homo sapiens
55 ECT2 1894
Affinity Capture-MS Homo sapiens
56 EXOSC10 5394
Co-fractionation Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
57 SLC35E1 79939
Affinity Capture-MS Homo sapiens
58 DAB2IP 153090
Affinity Capture-MS Homo sapiens
59 PSMA2 5683
Co-fractionation Homo sapiens
60 EGFR 1956
Negative Genetic Homo sapiens
61 LRRC47 57470
Affinity Capture-MS Homo sapiens
62 PSPC1 55269
Affinity Capture-MS Homo sapiens
63 RPA3 6119
Proximity Label-MS Homo sapiens
64 FAM111B 374393
Affinity Capture-MS Homo sapiens
65 SKIV2L2 23517
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
66 DDRGK1 65992
Affinity Capture-MS Homo sapiens
67 RPS16 6217
Affinity Capture-MS Homo sapiens
68 YBX1 4904
Affinity Capture-MS Homo sapiens
69 USP37  
Proximity Label-MS Homo sapiens
70 GIGYF2 26058
Affinity Capture-MS Homo sapiens
71 SIRT6  
Affinity Capture-MS Homo sapiens
72 TP53 7157
Affinity Capture-MS Homo sapiens
73 EXOSC3 51010
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
74 APEX1 328
Affinity Capture-RNA Homo sapiens
Proximity Label-MS Homo sapiens
75 THOP1 7064
Affinity Capture-MS Homo sapiens
76 SMURF1 57154
Affinity Capture-MS Homo sapiens
77 TKT 7086
Affinity Capture-MS Homo sapiens
78 MKI67  
Affinity Capture-MS Homo sapiens
79 NIFK 84365
Proximity Label-MS Homo sapiens
80 TRIP12 9320
Affinity Capture-MS Homo sapiens
81 STAG1  
Co-fractionation Homo sapiens
82 UFL1 23376
Affinity Capture-MS Homo sapiens
83 NCL 4691
Affinity Capture-MS Homo sapiens
84 ZNF106  
Affinity Capture-MS Homo sapiens
85 PSMA7 5688
Co-fractionation Homo sapiens
86 STAG2 10735
Co-fractionation Homo sapiens
87 CIT 11113
Affinity Capture-MS Homo sapiens
88 KRAS 3845
Negative Genetic Homo sapiens
89 PHF10  
Affinity Capture-MS Homo sapiens
90 PRMT1 3276
Affinity Capture-MS Homo sapiens
91 EXOSC1 51013
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
92 EXOSC8  
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
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