Gene description for PTCD3
Gene name pentatricopeptide repeat domain 3
Gene symbol PTCD3
Other names/aliases MRP-S39
Species Homo sapiens
 Database cross references - PTCD3
ExoCarta ExoCarta_55037
Vesiclepedia VP_55037
Entrez Gene 55037
HGNC 24717
MIM 614918
UniProt Q96EY7  
 PTCD3 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    
Hepatocellular carcinoma cells 26054723    
Hepatocellular carcinoma cells 26054723    
 Gene ontology annotations for PTCD3
Molecular Function
    RNA binding GO:0003723 HDA
    protein binding GO:0005515 IPI
    rRNA binding GO:0019843 IBA
    rRNA binding GO:0019843 IDA
    ribosomal small subunit binding GO:0043024 IBA
    ribosomal small subunit binding GO:0043024 IDA
Biological Process
    regulation of translation GO:0006417 IEA
    mitochondrial translation GO:0032543 IBA
    mitochondrial translation GO:0032543 IMP
    mitochondrial translation GO:0032543 NAS
Subcellular Localization
    nucleoplasm GO:0005654 IDA
    mitochondrion GO:0005739 HTP
    mitochondrion GO:0005739 IBA
    mitochondrion GO:0005739 IDA
    mitochondrial inner membrane GO:0005743 NAS
    mitochondrial inner membrane GO:0005743 TAS
    mitochondrial matrix GO:0005759 IDA
    mitochondrial small ribosomal subunit GO:0005763 NAS
    cytosol GO:0005829 IDA
    plasma membrane GO:0005886 IDA
 Experiment description of studies that identified PTCD3 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 234
MISEV standards
✔
EM
Biophysical techniques
✔
TSG101|Alix|HSC70|GAPDH
Enriched markers
✔
HSP90B1
Negative markers
✔
qNano
Particle analysis
Identified molecule mRNA
Identification method RNA Sequencing
PubMed ID 26054723    
Organism Homo sapiens
Experiment description Hepatocellular carcinoma-derived exosomes promote motility of immortalized hepatocyte through transfer of oncogenic proteins and RNAs
Authors "He M, Qin H, Poon TC, Sze SC, Ding X, Co NN, Ngai SM, Chan TF, Wong N"
Journal name Carcinogenesis
Publication year 2015
Sample Hepatocellular carcinoma cells
Sample name HKCI-C3
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Sucrose density gradient
Flotation density 1.13-1.19 g/mL
Molecules identified in the study Protein
RNA
Methods used in the study Western blotting
Mass spectrometry
RT-PCR
RNA Sequencing
6
Experiment ID 236
MISEV standards
✔
EM
Biophysical techniques
✔
TSG101|Alix|HSC70|GAPDH
Enriched markers
✔
HSP90B1
Negative markers
✔
qNano
Particle analysis
Identified molecule mRNA
Identification method RNA Sequencing
PubMed ID 26054723    
Organism Homo sapiens
Experiment description Hepatocellular carcinoma-derived exosomes promote motility of immortalized hepatocyte through transfer of oncogenic proteins and RNAs
Authors "He M, Qin H, Poon TC, Sze SC, Ding X, Co NN, Ngai SM, Chan TF, Wong N"
Journal name Carcinogenesis
Publication year 2015
Sample Hepatocellular carcinoma cells
Sample name MHCC97L
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Sucrose density gradient
Flotation density 1.13-1.19 g/mL
Molecules identified in the study Protein
RNA
Methods used in the study Western blotting
Mass spectrometry
RT-PCR
RNA Sequencing
 Protein-protein interactions for PTCD3
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 C9orf78 51759
Affinity Capture-MS Homo sapiens
2 UBE2H 7328
Affinity Capture-MS Homo sapiens
3 ZBTB38 253461
Affinity Capture-MS Homo sapiens
4 SNRPA 6626
Affinity Capture-MS Homo sapiens
5 MRPS27 23107
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
6 SLIRP 81892
Proximity Label-MS Homo sapiens
7 FOXA1  
Affinity Capture-MS Homo sapiens
8 METTL17  
Proximity Label-MS Homo sapiens
9 APOBEC3D  
Affinity Capture-MS Homo sapiens
10 Ruvbl1 56505
Affinity Capture-MS Mus musculus
11 RIT1 6016
Negative Genetic Homo sapiens
12 BTF3 689
Affinity Capture-MS Homo sapiens
13 Ybx1 22608
Affinity Capture-MS Mus musculus
14 MTG2  
Proximity Label-MS Homo sapiens
15 NGRN  
Proximity Label-MS Homo sapiens
16 RPL10 6134
Affinity Capture-MS Homo sapiens
17 UBE3A 7337
Two-hybrid Homo sapiens
18 CAND1 55832
Affinity Capture-MS Homo sapiens
19 RPUSD4 84881
Proximity Label-MS Homo sapiens
20 DNAJC15  
Proximity Label-MS Homo sapiens
21 MTRF1  
Proximity Label-MS Homo sapiens
22 GFM2 84340
Proximity Label-MS Homo sapiens
23 CCDC90B  
Proximity Label-MS Homo sapiens
24 H1FNT  
Affinity Capture-MS Homo sapiens
25 LRPPRC 10128
Proximity Label-MS Homo sapiens
26 KIAA1429 25962
Affinity Capture-MS Homo sapiens
27 TRUB2  
Proximity Label-MS Homo sapiens
28 RPL4 6124
Affinity Capture-MS Homo sapiens
29 RPS9 6203
Affinity Capture-MS Homo sapiens
30 SNRNP70 6625
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
31 ZBTB2 57621
Affinity Capture-MS Homo sapiens
32 MCU 90550
Proximity Label-MS Homo sapiens
33 CRYZ 1429
Proximity Label-MS Homo sapiens
34 TFAM 7019
Proximity Label-MS Homo sapiens
35 PMPCA 23203
Proximity Label-MS Homo sapiens
36 HINT2 84681
Proximity Label-MS Homo sapiens
37 RFXANK  
Affinity Capture-MS Homo sapiens
38 MRPS23 51649
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
39 MRPS5 64969
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
40 C8orf82  
Proximity Label-MS Homo sapiens
41 HGS 9146
Reconstituted Complex Homo sapiens
42 MRPS24 64951
Affinity Capture-MS Homo sapiens
43 ZNF460  
Affinity Capture-MS Homo sapiens
44 POU5F1  
Affinity Capture-MS Homo sapiens
45 NPM1 4869
Co-fractionation Homo sapiens
46 KLF15  
Affinity Capture-MS Homo sapiens
47 ZNF2  
Affinity Capture-MS Homo sapiens
48 RNF2  
Affinity Capture-MS Homo sapiens
49 MYCN  
Affinity Capture-MS Homo sapiens
50 MRPS26 64949
Proximity Label-MS Homo sapiens
Affinity Capture-MS Homo sapiens
51 SURF1  
Proximity Label-MS Homo sapiens
52 SRSF3 6428
Affinity Capture-MS Homo sapiens
53 CLPB 81570
Proximity Label-MS Homo sapiens
54 EXD2  
Proximity Label-MS Homo sapiens
55 ERAL1  
Affinity Capture-MS Homo sapiens
56 KLF4  
Affinity Capture-MS Homo sapiens
57 E4F1  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
58 ZNF689  
Affinity Capture-MS Homo sapiens
59 ZNF346  
Affinity Capture-MS Homo sapiens
60 SNRPB 6628
Affinity Capture-MS Homo sapiens
61 MECP2 4204
Affinity Capture-MS Homo sapiens
62 PMPCB 9512
Proximity Label-MS Homo sapiens
63 RBM42  
Affinity Capture-MS Homo sapiens
64 FASTKD2  
Proximity Label-MS Homo sapiens
65 RNR1  
Protein-RNA Homo sapiens
66 VWA8 23078
Proximity Label-MS Homo sapiens
67 SRSF6 6431
Affinity Capture-MS Homo sapiens
68 MRPS17 51373
Affinity Capture-MS Homo sapiens
69 MTERF3  
Proximity Label-MS Homo sapiens
70 CTCF  
Affinity Capture-MS Homo sapiens
71 LIN28A  
Affinity Capture-MS Homo sapiens
72 BIRC7  
Two-hybrid Homo sapiens
73 MDH2 4191
Proximity Label-MS Homo sapiens
74 ATF4  
Two-hybrid Homo sapiens
75 KLF16  
Affinity Capture-MS Homo sapiens
76 APOO 79135
Proximity Label-MS Homo sapiens
77 MRPS35 60488
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
78 MRPS25 64432
Affinity Capture-MS Homo sapiens
79 MPV17 4358
Co-fractionation Homo sapiens
80 C6orf203  
Proximity Label-MS Homo sapiens
81 COX15 1355
Proximity Label-MS Homo sapiens
82 RPA3 6119
Proximity Label-MS Homo sapiens
83 FASTKD5  
Proximity Label-MS Homo sapiens
84 ZNF17  
Affinity Capture-MS Homo sapiens
85 MCAT 27349
Affinity Capture-MS Homo sapiens
86 PARK2  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
87 MRPS34 65993
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
88 ERBB3 2065
Affinity Capture-MS Homo sapiens
89 RBM38  
Affinity Capture-MS Homo sapiens
90 TRA2A 29896
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
91 YBX2 51087
Affinity Capture-MS Homo sapiens
92 MRPS11  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
93 STAU1 6780
Affinity Capture-MS Homo sapiens
94 ACIN1 22985
Co-fractionation Homo sapiens
95 Ar  
Affinity Capture-MS Mus musculus
96 ZBTB48  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
97 DIABLO 56616
Proximity Label-MS Homo sapiens
98 Arhgef17  
Affinity Capture-MS Mus musculus
99 HSCB 150274
Proximity Label-MS Homo sapiens
100 HIST1H2AM 8336
Affinity Capture-MS Homo sapiens
101 RPL35 11224
Affinity Capture-MS Homo sapiens
102 SP110  
Affinity Capture-MS Homo sapiens
103 Klhl21  
Affinity Capture-MS Mus musculus
104 NTRK1 4914
Affinity Capture-MS Homo sapiens
105 FGF8  
Affinity Capture-MS Homo sapiens
106 MRPS6  
Affinity Capture-MS Homo sapiens
107 CCDC109B 55013
Proximity Label-MS Homo sapiens
108 SYNCRIP 10492
Co-fractionation Homo sapiens
109 TBRG4 9238
Proximity Label-MS Homo sapiens
110 LUC7L2 51631
Two-hybrid Homo sapiens
111 FBXL6  
Affinity Capture-MS Homo sapiens
Proximity Label-MS Homo sapiens
112 RPS6 6194
Affinity Capture-MS Homo sapiens
113 MTFMT  
Proximity Label-MS Homo sapiens
114 HNRNPL 3191
Affinity Capture-MS Homo sapiens
115 ZFC3H1 196441
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
116 MTRF1L  
Proximity Label-MS Homo sapiens
117 DNAJC30  
Proximity Label-MS Homo sapiens
118 TMEM70  
Proximity Label-MS Homo sapiens
119 Ksr1  
Affinity Capture-MS Mus musculus
120 GLTSCR2  
Affinity Capture-MS Homo sapiens
121 MRPL2 51069
Affinity Capture-MS Homo sapiens
122 SP100 6672
Affinity Capture-MS Homo sapiens
123 COX4I1 1327
Proximity Label-MS Homo sapiens
124 CCDC59  
Affinity Capture-MS Homo sapiens
125 TLX2  
Proximity Label-MS Homo sapiens
126 Rab5c 19345
Affinity Capture-MS Mus musculus
127 HSPA5 3309
Co-fractionation Homo sapiens
128 OTC 5009
Proximity Label-MS Homo sapiens
129 RBM39 9584
Affinity Capture-MS Homo sapiens
130 HSPA9 3313
Proximity Label-MS Homo sapiens
131 DNAJC21  
Affinity Capture-MS Homo sapiens
132 MRRF  
Proximity Label-MS Homo sapiens
133 ABT1 29777
Affinity Capture-MS Homo sapiens
134 MRPS12  
Proximity Label-MS Homo sapiens
135 AURKAIP1  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
136 MTIF2 4528
Proximity Label-MS Homo sapiens
137 DNAJC4  
Proximity Label-MS Homo sapiens
138 CHCHD1  
Proximity Label-MS Homo sapiens
139 SLC25A51  
Proximity Label-MS Homo sapiens
140 YBX1 4904
Affinity Capture-MS Homo sapiens
141 SIRT7  
Affinity Capture-MS Homo sapiens
142 MTIF3  
Proximity Label-MS Homo sapiens
143 TUFM 7284
Proximity Label-MS Homo sapiens
144 SRSF1 6426
Affinity Capture-MS Homo sapiens
145 SRSF5 6430
Affinity Capture-MS Homo sapiens
146 MRPS14  
Cross-Linking-MS (XL-MS) Homo sapiens
147 CALR 811
Co-fractionation Homo sapiens
148 CUL3 8452
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
149 RPUSD3  
Proximity Label-MS Homo sapiens
150 RMND1 55005
Proximity Label-MS Homo sapiens
151 ZEB1  
Affinity Capture-MS Homo sapiens
152 EGFR 1956
Negative Genetic Homo sapiens
153 HNRNPA1 3178
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
154 DHX30 22907
Proximity Label-MS Homo sapiens
155 SUZ12  
Affinity Capture-MS Homo sapiens
156 C17orf80 55028
Proximity Label-MS Homo sapiens
157 MRPS28  
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
158 C12orf65  
Proximity Label-MS Homo sapiens
159 FBXW11  
Affinity Capture-MS Homo sapiens
160 CEP250 11190
Affinity Capture-MS Homo sapiens
161 TACO1  
Proximity Label-MS Homo sapiens
162 MTG1  
Proximity Label-MS Homo sapiens
163 MYC  
Affinity Capture-MS Homo sapiens
164 Mta2 23942
Affinity Capture-MS Mus musculus
165 YBX3 8531
Co-fractionation Homo sapiens
166 DNAJC9 23234
Proximity Label-MS Homo sapiens
167 NOL12 79159
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
168 TSFM 10102
Proximity Label-MS Homo sapiens
169 DAP3 7818
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
170 ACAD9 28976
Proximity Label-MS Homo sapiens
171 AMOTL1 154810
Affinity Capture-MS Homo sapiens
172 DDRGK1 65992
Affinity Capture-MS Homo sapiens
173 PLP2 5355
Co-fractionation Homo sapiens
174 BMI1  
Affinity Capture-MS Homo sapiens
175 CD55 1604
Co-fractionation Homo sapiens
176 NANOG  
Affinity Capture-MS Homo sapiens
177 METTL15  
Proximity Label-MS Homo sapiens
178 ZC3H3  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
179 MCUR1 63933
Proximity Label-MS Homo sapiens
180 RBMS2 5939
Affinity Capture-MS Homo sapiens
181 SOX2  
Proximity Label-MS Homo sapiens
182 EIF3H 8667
Co-fractionation Homo sapiens
183 H2AFX 3014
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
184 RPL19 6143
Affinity Capture-MS Homo sapiens
185 ZNF574  
Affinity Capture-MS Homo sapiens
186 RPL13 6137
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
187 CLPP 8192
Proximity Label-MS Homo sapiens
188 DNAJC28  
Proximity Label-MS Homo sapiens
189 CS 1431
Proximity Label-MS Homo sapiens
Proximity Label-MS Homo sapiens
190 ZNF707  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
191 PLEKHA4 57664
Affinity Capture-MS Homo sapiens
192 ESR2  
Affinity Capture-MS Homo sapiens
193 RC3H1 149041
Affinity Capture-MS Homo sapiens
194 AUH 549
Proximity Label-MS Homo sapiens
195 TP53 7157
Affinity Capture-MS Homo sapiens
196 PDGFB  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
197 MRPL11 65003
Proximity Label-MS Homo sapiens
198 DNAJC19 131118
Proximity Label-MS Homo sapiens
199 LNX2  
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
200 MRPS2 51116
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
201 RRS1 23212
Affinity Capture-MS Homo sapiens
202 PRR3  
Affinity Capture-MS Homo sapiens
203 Pcgf1  
Affinity Capture-MS Mus musculus
204 ICT1 3396
Affinity Capture-MS Homo sapiens
Proximity Label-MS Homo sapiens
205 SOX15  
Proximity Label-MS Homo sapiens
Affinity Capture-MS Homo sapiens
206 RPL6 6128
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
207 ZNF746  
Affinity Capture-MS Homo sapiens
208 SRP14 6727
Affinity Capture-MS Homo sapiens
209 MRPS18C  
Affinity Capture-MS Homo sapiens
210 MRPS31  
Affinity Capture-MS Homo sapiens
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
211 FAM3C 10447
Co-fractionation Homo sapiens
212 PDHA1 5160
Proximity Label-MS Homo sapiens
213 DNAJA3 9093
Proximity Label-MS Homo sapiens
214 SMURF1 57154
Affinity Capture-MS Homo sapiens