Gene description for NPHP4
Gene name nephronophthisis 4
Gene symbol NPHP4
Other names/aliases POC10
SLSN4
Species Homo sapiens
 Database cross references - NPHP4
ExoCarta ExoCarta_261734
Vesiclepedia VP_261734
Entrez Gene 261734
HGNC 19104
MIM 607215
UniProt O75161  
 NPHP4 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    
 Gene ontology annotations for NPHP4
Molecular Function
    structural molecule activity GO:0005198 NAS
    protein binding GO:0005515 IPI
Biological Process
    signal transduction GO:0007165 NAS
    visual behavior GO:0007632 NAS
    actin cytoskeleton organization GO:0030036 NAS
    flagellated sperm motility GO:0030317 IEA
    photoreceptor cell outer segment organization GO:0035845 IEA
    photoreceptor cell maintenance GO:0045494 IEA
    retina development in camera-type eye GO:0060041 IEA
    negative regulation of canonical Wnt signaling pathway GO:0090090 IBA
    negative regulation of canonical Wnt signaling pathway GO:0090090 IDA
    cell-cell adhesion GO:0098609 NAS
    positive regulation of bicellular tight junction assembly GO:1903348 IMP
    protein localization to ciliary transition zone GO:1904491 IBA
Subcellular Localization
    nucleoplasm GO:0005654 IDA
    centrosome GO:0005813 IDA
    centriole GO:0005814 IEA
    cytosol GO:0005829 IDA
    cytosol GO:0005829 TAS
    cell-cell junction GO:0005911 IDA
    bicellular tight junction GO:0005923 IEA
    nuclear body GO:0016604 IDA
    ciliary transition zone GO:0035869 IBA
    ciliary basal body GO:0036064 IBA
    intracellular membrane-bounded organelle GO:0043231 IDA
    ribbon synapse GO:0097470 IEA
    ciliary base GO:0097546 IBA
    non-motile cilium GO:0097730 IBA
    photoreceptor distal connecting cilium GO:0120206 IEA
 Experiment description of studies that identified NPHP4 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
 Protein-protein interactions for NPHP4
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 DNAJC7 7266
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
2 FTL 2512
Affinity Capture-MS Homo sapiens
3 PPP4R2  
Affinity Capture-MS Homo sapiens
4 IGHA1 3493
Affinity Capture-MS Homo sapiens
5 BAG2 9532
Affinity Capture-MS Homo sapiens
6 RPP25L  
Affinity Capture-MS Homo sapiens
7 Iqgap3 404710
Affinity Capture-MS Mus musculus
8 JADE1  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
9 SULT1C4  
Affinity Capture-MS Homo sapiens
10 RPGRIP1  
Affinity Capture-Western Homo sapiens
11 EGFR 1956
Affinity Capture-MS Homo sapiens
12 NPHP1  
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
13 ECT2 1894
Affinity Capture-MS Homo sapiens
14 RPGRIP1L 23322
Affinity Capture-MS Homo sapiens
15 CLUH 23277
Affinity Capture-MS Homo sapiens
16 TUBB1 81027
Affinity Capture-MS Homo sapiens
17 LATS1  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
18 PRPS2 5634
Affinity Capture-MS Homo sapiens
19 TRIM52  
Affinity Capture-MS Homo sapiens
20 SKAP1 8631
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
21 RPGR  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
22 TRIM37  
Proximity Label-MS Homo sapiens
23 TEFM  
Affinity Capture-MS Homo sapiens
24 DDB1 1642
Affinity Capture-Western Homo sapiens
25 Vcpip1  
Affinity Capture-MS Mus musculus
26 NEK4  
Affinity Capture-MS Homo sapiens
27 SSSCA1 10534
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
28 PNMA2  
Affinity Capture-MS Homo sapiens
29 CEP164  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
30 GKAP1  
Affinity Capture-MS Homo sapiens
31 Setd2  
Affinity Capture-MS Mus musculus
32 PTGES3 10728
Affinity Capture-MS Homo sapiens
33 LCN1 3933
Affinity Capture-MS Homo sapiens
34 RAF1 5894
Affinity Capture-MS Homo sapiens
35 CCDC140  
Affinity Capture-MS Homo sapiens
36 Eea1  
Affinity Capture-MS Mus musculus
37 PIPSL 266971
Affinity Capture-MS Homo sapiens
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