Gene description for EPHB3
Gene name EPH receptor B3
Gene symbol EPHB3
Other names/aliases ETK2
HEK2
TYRO6
Species Homo sapiens
 Database cross references - EPHB3
ExoCarta ExoCarta_2049
Vesiclepedia VP_2049
Entrez Gene 2049
HGNC 3394
MIM 601839
UniProt P54753  
 EPHB3 identified in sEVs 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 19837982    
Colorectal cancer cells 34887515    
Neuroblastoma cells 25944692    
Ovarian cancer cells 23333927    
Ovarian cancer cells 23333927    
 Gene ontology annotations for EPHB3
Molecular Function
    ephrin receptor activity GO:0005003 IDA
    GPI-linked ephrin receptor activity GO:0005004 IEA
    transmembrane-ephrin receptor activity GO:0005005 IBA
    epidermal growth factor receptor activity GO:0005006 IEA
    fibroblast growth factor receptor activity GO:0005007 IEA
    hepatocyte growth factor receptor activity GO:0005008 IEA
    insulin receptor activity GO:0005009 IEA
    insulin-like growth factor receptor activity GO:0005010 IEA
    macrophage colony-stimulating factor receptor activity GO:0005011 IEA
    platelet-derived growth factor alpha-receptor activity GO:0005018 IEA
    platelet-derived growth factor beta-receptor activity GO:0005019 IEA
    stem cell factor receptor activity GO:0005020 IEA
    vascular endothelial growth factor receptor activity GO:0005021 IEA
    protein binding GO:0005515 IPI
    ATP binding GO:0005524 IEA
    axon guidance receptor activity GO:0008046 IEA
    boss receptor activity GO:0008288 IEA
    histone H3Y41 kinase activity GO:0035401 IEA
    placental growth factor receptor activity GO:0036332 IEA
    protein tyrosine kinase collagen receptor activity GO:0038062 IEA
    brain-derived neurotrophic factor receptor activity GO:0060175 IEA
    histone H2AXY142 kinase activity GO:0140801 IEA
Biological Process
    angiogenesis GO:0001525 ISS
    urogenital system development GO:0001655 ISS
    chromatin remodeling GO:0006338 IEA
    epidermal growth factor receptor signaling pathway GO:0007173 IEA
    axon guidance GO:0007411 IBA
    axon guidance GO:0007411 ISS
    axonal fasciculation GO:0007413 ISS
    insulin receptor signaling pathway GO:0008286 IEA
    fibroblast growth factor receptor signaling pathway GO:0008543 IEA
    cell migration GO:0016477 IDA
    central nervous system projection neuron axonogenesis GO:0021952 IEA
    corpus callosum development GO:0022038 ISS
    regulation of cell-cell adhesion GO:0022407 IDA
    retinal ganglion cell axon guidance GO:0031290 IEA
    brain-derived neurotrophic factor receptor signaling pathway GO:0031547 IEA
    substrate adhesion-dependent cell spreading GO:0034446 IDA
    platelet-derived growth factor receptor-alpha signaling pathway GO:0035790 IEA
    platelet-derived growth factor receptor-beta signaling pathway GO:0035791 IEA
    vascular endothelial growth factor receptor-1 signaling pathway GO:0036323 IEA
    collagen-activated tyrosine kinase receptor signaling pathway GO:0038063 IEA
    vascular endothelial growth factor signaling pathway GO:0038084 IEA
    Kit signaling pathway GO:0038109 IEA
    macrophage colony-stimulating factor signaling pathway GO:0038145 IEA
    regulation of GTPase activity GO:0043087 IDA
    protein autophosphorylation GO:0046777 IDA
    insulin-like growth factor receptor signaling pathway GO:0048009 IEA
    hepatocyte growth factor receptor signaling pathway GO:0048012 IEA
    ephrin receptor signaling pathway GO:0048013 IBA
    ephrin receptor signaling pathway GO:0048013 IDA
    thymus development GO:0048538 ISS
    digestive tract morphogenesis GO:0048546 ISS
    regulation of axonogenesis GO:0050770 ISS
    positive regulation of synapse assembly GO:0051965 ISS
    roof of mouth development GO:0060021 ISS
    dendritic spine development GO:0060996 ISS
    dendritic spine morphogenesis GO:0060997 ISS
Subcellular Localization
    extracellular region GO:0005576 TAS
    cytosol GO:0005829 TAS
    plasma membrane GO:0005886 IBA
    plasma membrane GO:0005886 IDA
    plasma membrane GO:0005886 TAS
    dendrite GO:0030425 IBA
 Experiment description of studies that identified EPHB3 in sEVs
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 21
MISEV standards
✔
EM|IEM
Biophysical techniques
✔
Alix|TSG101|HSP70|CD63
Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method
Mass spectrometry   
PubMed ID 19837982    
Organism Homo sapiens
Experiment description Proteomic and bioinformatic analysis of immunoaffinity-purified exosomes derived from the human colon tumor cell line LIM1215.
Authors "Suresh Mathivanan, Justin W.E. Lim, Bow J. Tauro, Hong Ji, Robert L. Moritz and Richard J. Simpson"
Journal name MCP
Publication year 2009
Sample Colorectal cancer cells
Sample name LIM1215
Isolation/purification methods Filtration
Ultracentrifugation
Sucrose density gradient
Flotation density 1.10-1.12 g/mL
Molecules identified in the study Protein
Methods used in the study Mass spectrometry [Orbitrap]
Western blotting
6
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
7
Experiment ID 224
MISEV standards
✔
EM|AFM
Biophysical techniques
✔
Alix|TSG101|CD63|CD81
Enriched markers
✔
GOLGA2
Negative markers
✘ 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
8
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
9
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
 Protein-protein interactions for EPHB3
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 HPCAL1 3241
Two-hybrid Homo sapiens
2 RASA1 5921
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
3 NFRKB  
Two-hybrid Homo sapiens
4 CRK 1398
Reconstituted Complex Homo sapiens
5 LYN 4067
Proximity Label-MS Homo sapiens
6 GJD3  
Proximity Label-MS Homo sapiens
7 EFNB2 1948
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
8 RYK 6259
Affinity Capture-Western Homo sapiens
9 MKRN2 23609
Affinity Capture-RNA Homo sapiens
10 FYN 2534
Reconstituted Complex Homo sapiens
11 GBE1 2632
Two-hybrid Homo sapiens
12 HSF2BP  
Two-hybrid Homo sapiens
13 ERBB2 2064
PCA Homo sapiens
14 GPR114  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
15 MLLT4 4301
Two-hybrid Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
16 EFNB1 1947
Affinity Capture-MS Homo sapiens
17 C16orf58 64755
Affinity Capture-MS Homo sapiens
18 LNX1  
Reconstituted Complex Homo sapiens
19 EFNB3 1949
Reconstituted Complex Homo sapiens
20 GJA1 2697
Proximity Label-MS Homo sapiens
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