Gene description for PRKDC
Gene name protein kinase, DNA-activated, catalytic polypeptide
Gene symbol PRKDC
Other names/aliases DNA-PKcs
DNAPK
DNPK1
HYRC
HYRC1
IMD26
XRCC7
p350
Species Homo sapiens
 Database cross references - PRKDC
ExoCarta ExoCarta_5591
Entrez Gene 5591
HGNC 9413
MIM 600899
UniProt P78527  
 PRKDC identified in exosomes derived from the following tissue/cell type
Colorectal cancer cells 17956143    
Colorectal cancer cells 25890246    
Colorectal cancer cells 25890246    
Colorectal cancer cells 25890246    
Colorectal cancer cells 25890246    
Hepatocellular carcinoma cells 26054723    
Melanoma cells 25950383    
Melanoma cells 25950383    
Melanoma cells 25950383    
Melanoma cells 25950383    
Melanoma cells 25950383    
Nasopharyngeal carcinoma cells 25857718    
Nasopharyngeal carcinoma cells 25857718    
Nasopharyngeal carcinoma cells 25857718    
Neuroblastoma cells 25944692    
Ovarian cancer cells 23333927    
Ovarian cancer cells 23333927    
Thymus 23844026    
 Gene ontology annotations for PRKDC
Molecular Function
    DNA binding GO:0003677 IEA
    protein binding GO:0005515 IPI
    protein serine/threonine kinase activity GO:0004674 IDA
    enzyme binding GO:0019899 IEA
    poly(A) RNA binding GO:0044822 IDA
    DNA-dependent protein kinase activity GO:0004677 IDA
    protein kinase activity GO:0004672 IDA
    transcription factor binding GO:0008134 IPI
    ATP binding GO:0005524 IEA
Biological Process
    somitogenesis GO:0001756 IEA
    T cell differentiation in thymus GO:0033077 IEA
    double-strand break repair via homologous recombination GO:0000724 IBA
    ectopic germ cell programmed cell death GO:0035234 IEA
    double-strand break repair via nonhomologous end joining GO:0006303 TAS
    pro-B cell differentiation GO:0002328 IEA
    cellular protein modification process GO:0006464 TAS
    intrinsic apoptotic signaling pathway in response to DNA damage GO:0008630 IEA
    double-strand break repair GO:0006302 TAS
    positive regulation of apoptotic process GO:0043065 IEA
    positive regulation of transcription from RNA polymerase II promoter GO:0045944 IMP
    response to gamma radiation GO:0010332 IEA
    rhythmic process GO:0048511 IEA
    immunoglobulin V(D)J recombination GO:0033152 IEA
    DNA repair GO:0006281 TAS
    cellular response to insulin stimulus GO:0032869 IMP
    signal transduction involved in mitotic G1 DNA damage checkpoint GO:0072431 IMP
    T cell receptor V(D)J recombination GO:0033153 IEA
    peptidyl-serine phosphorylation GO:0018105 IDA
    T cell lineage commitment GO:0002360 IEA
    innate immune response GO:0045087 TAS
    protein destabilization GO:0031648 IEA
    negative regulation of protein phosphorylation GO:0001933 ISS
    negative regulation of apoptotic process GO:0043066 IMP
    B cell lineage commitment GO:0002326 IEA
    heart development GO:0007507 IEA
    brain development GO:0007420 IEA
    regulation of circadian rhythm GO:0042752 ISS
    positive regulation of type I interferon production GO:0032481 TAS
    telomere maintenance GO:0000723 IEA
Subcellular Localization
    nonhomologous end joining complex GO:0070419 IDA
    nucleolus GO:0005730 IEA
    transcription factor complex GO:0005667 IDA
    DNA-dependent protein kinase-DNA ligase 4 complex GO:0005958 IDA
    membrane GO:0016020 IDA
    nucleoplasm GO:0005654 TAS
    cytosol GO:0005829 TAS
 Experiment description of studies that identified PRKDC in exosomes
1
Experiment ID 20
ISEV standards
✔
EM
EV Biophysical techniques
✔
HSP90
EV Cytosolic markers
✔
CD63|CD81|LAMP1
EV Membrane markers
✔
GOLGA2|cytochrome c
EV Negative markers
✘ EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 17956143    
Organism Homo sapiens
Experiment description Proteomic analysis of microvesicles derived from human colorectal cancer cells.
Authors Choi DS, Lee JM, Park GW, Lim HW, Bang JY, Kim YK, Kwon KH, Kwon HJ, Kim KP, Gho YS
Journal name JPR
Publication year 2007
Sample Colorectal cancer cells
Sample name HT29
Isolation/purification methods Differential centrifugation
Sucrose density gradient
Diafiltration
Flotation density 1.16 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry [LTQ]
Western blotting
2
Experiment ID 282
ISEV standards
✔
CEM
EV Biophysical techniques
✔
Alix|TSG101
EV Cytosolic markers
✔
CD63|CD81|EpCAM
EV Membrane markers
✘ EV Negative markers
✔
DLS
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors Xu R, Greening DW, Rai A, Ji H, Simpson RJ.
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Ultracentrifugation - Rep 1
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
3
Experiment ID 283
ISEV standards
✔
CEM
EV Biophysical techniques
✔
Alix|TSG101
EV Cytosolic markers
✔
CD63|CD81|EpCAM
EV Membrane markers
✘ EV Negative markers
✔
DLS
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors Xu R, Greening DW, Rai A, Ji H, Simpson RJ.
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Ultracentrifugation - Rep 2
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
4
Experiment ID 285
ISEV standards
✔
CEM
EV Biophysical techniques
✔
Alix|TSG101
EV Cytosolic markers
✔
CD63|CD81|EpCAM
EV Membrane markers
✘ EV Negative markers
✔
DLS
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors Xu R, Greening DW, Rai A, Ji H, Simpson RJ.
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Sequential centrifugal ultrafiltration - Rep 1
Isolation/purification methods Differential centrifugation
Filtration
Sequential centrifugal ultrafiltration
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
5
Experiment ID 286
ISEV standards
✔
CEM
EV Biophysical techniques
✔
Alix|TSG101
EV Cytosolic markers
✔
CD63|CD81|EpCAM
EV Membrane markers
✘ EV Negative markers
✔
DLS
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25890246    
Organism Homo sapiens
Experiment description Highly-purified exosomes and shed microvesicles isolated from the human colon cancer cell line LIM1863 by sequential centrifugal ultrafiltration are biochemically and functionally distinct.
Authors Xu R, Greening DW, Rai A, Ji H, Simpson RJ.
Journal name Methods
Publication year 2015
Sample Colorectal cancer cells
Sample name LIM1863 - Sequential centrifugal ultrafiltration - Rep 2
Isolation/purification methods Differential centrifugation
Filtration
Sequential centrifugal ultrafiltration
Centrifugal concentration
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
6
Experiment ID 235
ISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101|Alix|HSC70|GAPDH
EV Cytosolic markers
✘ EV Membrane markers
✔
HSP90B1
EV Negative markers
✔
qNano
EV 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-8
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
7
Experiment ID 254
ISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101
EV Cytosolic markers
✔
FLOT1|CD81
EV Membrane markers
✘ EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25950383    
Organism Homo sapiens
Experiment description Proteome characterization of melanoma exosomes reveals a specific signature for metastatic cell lines
Authors Lazar I, Clement E, Ducoux-Petit M, Denat L, Soldan V, Dauvillier S, Balor S4, Burlet-Schiltz O1, Larue L, Muller C Nieto L
Journal name Pigment Cell Melanoma Res
Publication year 2015
Sample Melanoma cells
Sample name MNT-1
Isolation/purification methods Differential centrifugation
Unltracentrifugation
Sucrose density gradient
Flotation density 1.13 - 1.19 g/mL
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
8
Experiment ID 255
ISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101
EV Cytosolic markers
✔
FLOT1
EV Membrane markers
✘ EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25950383    
Organism Homo sapiens
Experiment description Proteome characterization of melanoma exosomes reveals a specific signature for metastatic cell lines
Authors Lazar I, Clement E, Ducoux-Petit M, Denat L, Soldan V, Dauvillier S, Balor S4, Burlet-Schiltz O1, Larue L, Muller C Nieto L
Journal name Pigment Cell Melanoma Res
Publication year 2015
Sample Melanoma cells
Sample name G1
Isolation/purification methods Differential centrifugation
Unltracentrifugation
Sucrose density gradient
Flotation density 1.13 - 1.19 g/mL
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
9
Experiment ID 256
ISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101
EV Cytosolic markers
✔
FLOT1
EV Membrane markers
✘ EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25950383    
Organism Homo sapiens
Experiment description Proteome characterization of melanoma exosomes reveals a specific signature for metastatic cell lines
Authors Lazar I, Clement E, Ducoux-Petit M, Denat L, Soldan V, Dauvillier S, Balor S4, Burlet-Schiltz O1, Larue L, Muller C Nieto L
Journal name Pigment Cell Melanoma Res
Publication year 2015
Sample Melanoma cells
Sample name 501mel
Isolation/purification methods Differential centrifugation
Unltracentrifugation
Sucrose density gradient
Flotation density 1.13 - 1.19 g/mL
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
10
Experiment ID 257
ISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101
EV Cytosolic markers
✔
FLOT1
EV Membrane markers
✘ EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25950383    
Organism Homo sapiens
Experiment description Proteome characterization of melanoma exosomes reveals a specific signature for metastatic cell lines
Authors Lazar I, Clement E, Ducoux-Petit M, Denat L, Soldan V, Dauvillier S, Balor S4, Burlet-Schiltz O1, Larue L, Muller C Nieto L
Journal name Pigment Cell Melanoma Res
Publication year 2015
Sample Melanoma cells
Sample name Daju
Isolation/purification methods Differential centrifugation
Unltracentrifugation
Sucrose density gradient
Flotation density 1.13 - 1.19 g/mL
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
11
Experiment ID 259
ISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101
EV Cytosolic markers
✔
FLOT1
EV Membrane markers
✘ EV Negative markers
✔
NTA
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25950383    
Organism Homo sapiens
Experiment description Proteome characterization of melanoma exosomes reveals a specific signature for metastatic cell lines
Authors Lazar I, Clement E, Ducoux-Petit M, Denat L, Soldan V, Dauvillier S, Balor S4, Burlet-Schiltz O1, Larue L, Muller C Nieto L
Journal name Pigment Cell Melanoma Res
Publication year 2015
Sample Melanoma cells
Sample name A375M
Isolation/purification methods Differential centrifugation
Unltracentrifugation
Sucrose density gradient
Flotation density 1.13 - 1.19 g/mL
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
12
Experiment ID 219
ISEV standards
✔
EM
EV Biophysical techniques
✘ EV Cytosolic markers
✔
CD63|CD9
EV Membrane markers
✔
HSP90B1
EV Negative markers
✔
qNano
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25857718    
Organism Homo sapiens
Experiment description Proteomic analysis of exosomes from nasopharyngeal carcinoma cell identifies intercellular transfer of angiogenic proteins
Authors Chan YK, Zhang H, Liu P, Tsao GS, Li Lung M, Mak NK, Ngok-Shun Wong R, Ying-Kit Yue P
Journal name Int J Cancer
Publication year 2015
Sample Nasopharyngeal carcinoma cells
Sample name C666-1
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Sucrose density gradient
Flotation density 1.17-1.19 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
13
Experiment ID 220
ISEV standards
✔
EM
EV Biophysical techniques
✘ EV Cytosolic markers
✔
CD63|CD9
EV Membrane markers
✔
HSP90B1
EV Negative markers
✔
qNano
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25857718    
Organism Homo sapiens
Experiment description Proteomic analysis of exosomes from nasopharyngeal carcinoma cell identifies intercellular transfer of angiogenic proteins
Authors Chan YK, Zhang H, Liu P, Tsao GS, Li Lung M, Mak NK, Ngok-Shun Wong R, Ying-Kit Yue P
Journal name Int J Cancer
Publication year 2015
Sample Nasopharyngeal carcinoma cells
Sample name NP69
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Sucrose density gradient
Flotation density 1.17-1.19 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
14
Experiment ID 221
ISEV standards
✔
EM
EV Biophysical techniques
✘ EV Cytosolic markers
✔
CD63|CD9
EV Membrane markers
✔
HSP90B1
EV Negative markers
✔
qNano
EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25857718    
Organism Homo sapiens
Experiment description Proteomic analysis of exosomes from nasopharyngeal carcinoma cell identifies intercellular transfer of angiogenic proteins
Authors Chan YK, Zhang H, Liu P, Tsao GS, Li Lung M, Mak NK, Ngok-Shun Wong R, Ying-Kit Yue P
Journal name Int J Cancer
Publication year 2015
Sample Nasopharyngeal carcinoma cells
Sample name NP460
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Sucrose density gradient
Flotation density 1.17-1.19 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
15
Experiment ID 224
ISEV standards
✔
EM|AFM
EV Biophysical techniques
✔
Alix|TSG101
EV Cytosolic markers
✔
CD63|CD81
EV Membrane markers
✔
GOLGA2
EV Negative markers
✘ EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 25944692    
Organism Homo sapiens
Experiment description Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes
Authors Keerthikumar S, Gangoda L, Liem M, Fonseka P, Atukorala I, Ozcitti C, Mechler A, Adda CG, Ang CS, Mathivanan S
Journal name Oncotarget
Publication year 2015
Sample Neuroblastoma cells
Sample name SH-SY5Y
Isolation/purification methods Differential centrifugation
Ultracentrifugation
OptiPrep density gradient
Flotation density 1.10 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
Western blotting
16
Experiment ID 211
ISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101|Alix
EV Cytosolic markers
✔
EpCAM|TFRC
EV Membrane markers
✔
cytochrome c|GOLGA2
EV Negative markers
✘ EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23333927    
Organism Homo sapiens
Experiment description Characterization and proteomic analysis of ovarian cancer-derived exosomes.
Authors Liang B, Peng P, Chen S, Li L, Zhang M, Cao D, Yang J, Li H, Gui T, Li X, Shen K.
Journal name J Proteomics
Publication year 2013
Sample Ovarian cancer cells
Sample name IGROV1
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density 1.09-1.15 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
17
Experiment ID 212
ISEV standards
✔
CEM
EV Biophysical techniques
✔
TSG101|Alix
EV Cytosolic markers
✔
EpCAM|TFRC
EV Membrane markers
✔
Cytochrome C|GOLGA2
EV Negative markers
✘ EV Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 23333927    
Organism Homo sapiens
Experiment description Characterization and proteomic analysis of ovarian cancer-derived exosomes.
Authors Liang B, Peng P, Chen S, Li L, Zhang M, Cao D, Yang J, Li H, Gui T, Li X, Shen K.
Journal name J Proteomics
Publication year 2013
Sample Ovarian cancer cells
Sample name OVCAR-3
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Sucrose density gradient
Flotation density 1.09-1.15 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry
18
Experiment ID 217
ISEV standards
✔
EM
EV Biophysical techniques
✔
TSG101
EV Cytosolic markers
✔
CD81|CD9|CD63
EV Membrane markers
✘ EV Negative markers
✔
NTA
EV 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 PRKDC
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 E4F1  
Protein-peptide Homo sapiens
2 NCOA6  
Affinity Capture-MS Homo sapiens
Invitro Homo sapiens
Biochemical Activity Homo sapiens
3 NCF4  
Biochemical Activity Homo sapiens
4 RAD17  
Protein-peptide Homo sapiens
5 ILF3 3609
Affinity Capture-Western Homo sapiens
Co-purification Homo sapiens
6 HMGB1 3146
Invitro Homo sapiens
7 PCNA 5111
Invitro Homo sapiens
8 LIG4  
Protein-peptide Homo sapiens
9 RPA2 6118
Affinity Capture-Western Homo sapiens
Invitro Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
10 GCN5L2  
Biochemical Activity Homo sapiens
11 RPA1 6117
Reconstituted Complex Homo sapiens
12 BRCA1 672
Protein-peptide Homo sapiens
13 IKBKB 3551
Biochemical Activity Homo sapiens
14 ABL1 25
Reconstituted Complex Homo sapiens
15 MRE11A 4361
Protein-peptide Homo sapiens
16 DCLRE1C  
Invitro Homo sapiens
17 WRN  
Affinity Capture-Western Homo sapiens
Protein-peptide Homo sapiens
Biochemical Activity Homo sapiens
18 NCF1  
Biochemical Activity Homo sapiens
19 NCF2 4688
Biochemical Activity Homo sapiens
20 LYN 4067
Reconstituted Complex Homo sapiens
21 ILF2 3608
Affinity Capture-Western Homo sapiens
Co-purification Homo sapiens
22 XRCC6 2547
Invivo Homo sapiens
Invitro Homo sapiens
Affinity Capture-Western Homo sapiens
23 ATM  
Invitro Homo sapiens
Protein-peptide Homo sapiens
24 HSF1  
Invitro Homo sapiens
25 TP53  
Invitro Homo sapiens
Protein-peptide Homo sapiens
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
26 CHEK1  
Reconstituted Complex Homo sapiens
Protein-peptide Homo sapiens
27 AKT2 208
Biochemical Activity Homo sapiens
28 AP1B1 162
Protein-peptide Homo sapiens
29 C1D  
Reconstituted Complex Homo sapiens
Two-hybrid Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-Western Homo sapiens
30 CIB1 10519
Invitro Homo sapiens
Two-hybrid Homo sapiens
31 EIF2S2 8894
Co-purification Homo sapiens
32 AR 367
Affinity Capture-MS Homo sapiens
33 PTS  
Protein-peptide Homo sapiens
34 RBBP8  
Protein-peptide Homo sapiens
35 MAPK8 5599
Invivo Homo sapiens
Invitro Homo sapiens
36 CHUK 1147
Reconstituted Complex Homo sapiens
Biochemical Activity Homo sapiens
37 XRCC5 7520
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Invivo Homo sapiens
Invitro Homo sapiens
38 HMGB2 3148
Invitro Homo sapiens
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