Gene description for CLN3
Gene name ceroid-lipofuscinosis, neuronal 3
Gene symbol CLN3
Other names/aliases BTS
JNCL
Species Homo sapiens
 Database cross references - CLN3
ExoCarta ExoCarta_1201
Vesiclepedia VP_1201
Entrez Gene 1201
HGNC 2074
MIM 607042
UniProt Q13286  
 CLN3 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    
Colorectal cancer cells 34887515    
Mesenchymal stem cells 36408942    
Ovarian cancer cells 23333927    
Ovarian cancer cells 23333927    
Retinal pigment epithelial cells 35333565    
Retinal pigment epithelial cells 35333565    
 Gene ontology annotations for CLN3
Molecular Function
    protein binding GO:0005515 IPI
    glycolipid transfer activity GO:0017089 TAS
    calcium-dependent protein binding GO:0048306 IEA
    glycolipid binding GO:0051861 IDA
    sulfatide binding GO:0120146 IDA
Biological Process
    action potential GO:0001508 ISS
    receptor-mediated endocytosis GO:0006898 IMP
    lysosome organization GO:0007040 IBA
    lysosome organization GO:0007040 ISS
    lysosomal lumen acidification GO:0007042 IBA
    lysosomal lumen acidification GO:0007042 IMP
    learning or memory GO:0007611 ISS
    associative learning GO:0008306 ISS
    intracellular water homeostasis GO:0009992 ISS
    regulation of fibroblast migration GO:0010762 IMP
    regulation of autophagosome size GO:0016243 IEA
    protein processing GO:0016485 ISS
    actin cytoskeleton organization GO:0030036 IEA
    regulation of synaptic transmission, GABAergic GO:0032228 ISS
    ionotropic glutamate receptor signaling pathway GO:0035235 ISS
    ceramide transport GO:0035627 TAS
    lysosomal lumen pH elevation GO:0035752 IDA
    renal potassium excretion GO:0036359 ISS
    amyloid precursor protein catabolic process GO:0042987 IDA
    positive regulation of Golgi to plasma membrane protein transport GO:0042998 ISS
    negative regulation of apoptotic process GO:0043066 IMP
    negative regulation of apoptotic process GO:0043066 ISS
    negative regulation of neuron apoptotic process GO:0043524 ISS
    blood vessel endothelial cell migration GO:0043534 IEA
    plasma membrane raft organization GO:0044857 ISS
    negative regulation of proteolysis GO:0045861 ISS
    glycerophospholipid biosynthetic process GO:0046474 IMP
    glycolipid transport GO:0046836 IMP
    vesicle transport along microtubule GO:0047496 IMP
    regulation of short-term neuronal synaptic plasticity GO:0048172 ISS
    positive regulation of pinocytosis GO:0048549 ISS
    neuromuscular process controlling balance GO:0050885 ISS
    regulation of cytosolic calcium ion concentration GO:0051480 ISS
    regulation of filopodium assembly GO:0051489 IEA
    regulation of cytoskeleton organization GO:0051493 IMP
    regulation of synaptic transmission, glutamatergic GO:0051966 ISS
    membrane organization GO:0061024 ISS
    autophagosome-lysosome fusion GO:0061909 ISS
    regulation of protein processing GO:0070613 IMP
    protein localization to plasma membrane GO:0072659 IEA
    Golgi to lysosome transport GO:0090160 IMP
    phagosome-lysosome docking GO:0090384 ISS
    phagosome-lysosome fusion GO:0090385 ISS
    autophagosome maturation GO:0097352 ISS
    regulation of cellular response to osmotic stress GO:0106049 IMP
    regulation of arginine biosynthetic process GO:1900079 ISS
    regulation of autophagosome maturation GO:1901096 ISS
    regulation of protein localization to plasma membrane GO:1903076 ISS
    L-arginine transmembrane transport GO:1903826 IDA
    lysosomal protein catabolic process GO:1905146 ISS
    regulation of phagosome maturation GO:1905162 ISS
    regulation of modification of synaptic structure GO:1905244 ISS
    positive regulation of caveolin-mediated endocytosis GO:2001288 ISS
Subcellular Localization
    Golgi membrane GO:0000139 IDA
    Golgi membrane GO:0000139 TAS
    nucleus GO:0005634 IDA
    cytoplasm GO:0005737 IDA
    lysosome GO:0005764 IBA
    lysosome GO:0005764 IDA
    lysosome GO:0005764 IMP
    lysosomal membrane GO:0005765 HDA
    lysosomal membrane GO:0005765 IDA
    lysosomal membrane GO:0005765 IMP
    early endosome GO:0005769 IDA
    late endosome GO:0005770 IDA
    late endosome GO:0005770 IMP
    late endosome GO:0005770 ISS
    autophagosome GO:0005776 ISS
    endoplasmic reticulum GO:0005783 IDA
    endoplasmic reticulum membrane GO:0005789 IDA
    Golgi apparatus GO:0005794 IDA
    Golgi apparatus GO:0005794 IMP
    Golgi stack GO:0005795 IDA
    trans-Golgi network GO:0005802 IDA
    cytosol GO:0005829 IEA
    plasma membrane GO:0005886 IDA
    plasma membrane GO:0005886 IMP
    caveola GO:0005901 IDA
    caveola GO:0005901 IMP
    synaptic vesicle GO:0008021 IDA
    membrane GO:0016020 IDA
    early endosome membrane GO:0031901 IMP
    late endosome membrane GO:0031902 IEA
    neuron projection GO:0043005 IDA
    autolysosome GO:0044754 ISS
    membrane raft GO:0045121 IDA
    membrane raft GO:0045121 IMP
    recycling endosome GO:0055037 IDA
 Experiment description of studies that identified CLN3 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 1203
MISEV standards
✔
EM
Biophysical techniques
✔
SDCBP|FLOT1|CD9|CD81|CD63|EPCAM|GAPDH|LAMP1|TFRC|CD151|CD82|LAMP2|RAB35|TSG101|FLOT2|RAB5B|ICAM1|RAB5A
Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 34887515    
Organism Homo sapiens
Experiment description Supermeres are functional extracellular nanoparticles replete with disease biomarkers and therapeutic targets
Authors "Zhang Q, Jeppesen DK, Higginbotham JN, Graves-Deal R, Trinh VQ, Ramirez MA, Sohn Y, Neininger AC, Taneja N, McKinley ET, Niitsu H, Cao Z, Evans R, Glass SE, Ray KC, Fissell WH, Hill S, Rose KL, Huh WJ, Washington MK, Ayers GD, Burnette DT, Sharma S, Rome LH, Franklin JL, Lee YA, Liu Q, Coffey RJ."
Journal name Nat Cell Biol
Publication year 2021
Sample Colorectal cancer cells
Sample name DiFi
Isolation/purification methods Differential centrifugation
Filtration
Centrifugal ultrafiltration
Ultracentrifugation
OptiPrep density gradient centrifugation
Flotation density -
Molecules identified in the study Protein
miRNA
Methods used in the study Western blotting
Mass spectrometry
RNA sequencing
6
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
7
Experiment ID 211
MISEV standards
✔
EM
Biophysical techniques
✔
TSG101|Alix|EpCAM|TFRC
Enriched markers
✔
cytochrome c|GOLGA2
Negative markers
✘ 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
8
Experiment ID 212
MISEV standards
✔
CEM
Biophysical techniques
✔
TSG101|Alix|EpCAM|TFRC
Enriched markers
✔
Cytochrome C|GOLGA2
Negative markers
✘ 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
9
Experiment ID 834
MISEV standards
✔
EM
Biophysical techniques
✔
LAMP2|CD63|FLOT1|ITGA2B|ICAM1|CD9|CD151|TFRC|RAB5A|GAPDH|AQP1|TSG101
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 35333565    
Organism Homo sapiens
Experiment description LAMP2A regulates the loading of proteins into exosomes
Authors "Ferreira JV, da Rosa Soares A, Ramalho J, Máximo Carvalho C, Cardoso MH, Pintado P, Carvalho AS, Beck HC, Matthiesen R, Zuzarte M, Girão H, van Niel G, Pereira P"
Journal name Sci Adv
Publication year 2022
Sample Retinal pigment epithelial cells
Sample name ARPE-19
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
10
Experiment ID 835
MISEV standards
✔
EM
Biophysical techniques
✔
CD63|FLOT1|ITGA2B|ICAM1|CD9|CD151|TFRC|RAB5A|GAPDH|AQP1|TSG101
Enriched markers
✔
CANX
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 35333565    
Organism Homo sapiens
Experiment description LAMP2A regulates the loading of proteins into exosomes
Authors "Ferreira JV, da Rosa Soares A, Ramalho J, Máximo Carvalho C, Cardoso MH, Pintado P, Carvalho AS, Beck HC, Matthiesen R, Zuzarte M, Girão H, van Niel G, Pereira P"
Journal name Sci Adv
Publication year 2022
Sample Retinal pigment epithelial cells
Sample name ARPE-19
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
 Protein-protein interactions for CLN3
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 IMMT 10989
Affinity Capture-MS Homo sapiens
2 TPRA1  
Affinity Capture-MS Homo sapiens
3 NUP93 9688
Affinity Capture-MS Homo sapiens
4 TRIP13 9319
Affinity Capture-MS Homo sapiens
5 AFG3L2 10939
Affinity Capture-MS Homo sapiens
6 B3GALT2  
Affinity Capture-MS Homo sapiens
7 NPEPPS 9520
Affinity Capture-MS Homo sapiens
8 LGALS9 3965
Affinity Capture-MS Homo sapiens
9 C5AR1  
Affinity Capture-MS Homo sapiens
10 TMPO 7112
Affinity Capture-MS Homo sapiens
11 SLC25A11 8402
Affinity Capture-MS Homo sapiens
12 GRPR  
Affinity Capture-MS Homo sapiens
13 RARS2  
Affinity Capture-MS Homo sapiens
14 PTH1R  
Affinity Capture-MS Homo sapiens
15 RPN2 6185
Affinity Capture-MS Homo sapiens
16 ATG7 10533
Affinity Capture-MS Homo sapiens
17 XPO1 7514
Affinity Capture-MS Homo sapiens
18 OPALIN  
Affinity Capture-MS Homo sapiens
19 TMPRSS11B 132724
Affinity Capture-MS Homo sapiens
20 UNC45A 55898
Affinity Capture-MS Homo sapiens
21 LRRC25  
Affinity Capture-MS Homo sapiens
22 AUP1 550
Affinity Capture-MS Homo sapiens
23 DDOST 1650
Affinity Capture-MS Homo sapiens
24 RIF1  
Affinity Capture-MS Homo sapiens
25 SLC25A10 1468
Affinity Capture-MS Homo sapiens
26 P2RY2 5029
Affinity Capture-MS Homo sapiens
27 SEC61A2 55176
Affinity Capture-MS Homo sapiens
28 COX15 1355
Affinity Capture-MS Homo sapiens
29 GCGR  
Affinity Capture-MS Homo sapiens
30 IRAK1  
Affinity Capture-MS Homo sapiens
31 FANCI 55215
Affinity Capture-MS Homo sapiens
32 ELAVL1 1994
Affinity Capture-RNA Homo sapiens
33 SLC25A22  
Affinity Capture-MS Homo sapiens
34 CAND1 55832
Affinity Capture-MS Homo sapiens
35 B3GALT4  
Affinity Capture-MS Homo sapiens
36 PHB 5245
Affinity Capture-MS Homo sapiens
37 CCDC47 57003
Affinity Capture-MS Homo sapiens
38 OPRL1 4987
Affinity Capture-MS Homo sapiens
39 GEMIN4 50628
Affinity Capture-MS Homo sapiens
40 DNAH17 8632
Affinity Capture-MS Homo sapiens
41 SLC22A9  
Affinity Capture-MS Homo sapiens
42 SBDS 51119
Two-hybrid Homo sapiens
43 ILVBL 10994
Affinity Capture-MS Homo sapiens
44 SYP  
Affinity Capture-MS Homo sapiens
45 ARMC6 93436
Affinity Capture-MS Homo sapiens
46 DDX20 11218
Affinity Capture-MS Homo sapiens
47 GP5 2814
Affinity Capture-MS Homo sapiens
48 VIPR2  
Affinity Capture-MS Homo sapiens
49 HLA-B 3106
Affinity Capture-MS Homo sapiens
50 HSD17B12 51144
Affinity Capture-MS Homo sapiens
51 TELO2 9894
Affinity Capture-MS Homo sapiens
52 XPOT 11260
Affinity Capture-MS Homo sapiens
53 SIGMAR1 10280
Affinity Capture-MS Homo sapiens
54 CYC1 1537
Affinity Capture-MS Homo sapiens
55 GLMP 112770
Affinity Capture-MS Homo sapiens
56 GANAB 23193
Affinity Capture-MS Homo sapiens
57 ABCD3 5825
Affinity Capture-MS Homo sapiens
58 KIAA0368 23392
Affinity Capture-MS Homo sapiens
59 NUP205 23165
Affinity Capture-MS Homo sapiens
60 CKAP4 10970
Affinity Capture-MS Homo sapiens
61 AGPAT2  
Affinity Capture-MS Homo sapiens
62 ESYT2 57488
Affinity Capture-MS Homo sapiens
63 FUCA2 2519
Affinity Capture-MS Homo sapiens
64 SFXN4  
Affinity Capture-MS Homo sapiens
65 GCN1L1 10985
Affinity Capture-MS Homo sapiens
66 VDAC2 7417
Affinity Capture-MS Homo sapiens
67 CPT1A 1374
Affinity Capture-MS Homo sapiens
68 PRKDC 5591
Affinity Capture-MS Homo sapiens
69 MLNR  
Affinity Capture-MS Homo sapiens
View the network image/svg+xml
 Pathways in which CLN3 is involved
PathwayEvidenceSource
Glycosphingolipid transport TAS Reactome
Transport of small molecules TAS Reactome





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