Gene description for SMPD4
Gene name sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)
Gene symbol SMPD4
Other names/aliases NET13
NSMASE-3
NSMASE3
Species Homo sapiens
 Database cross references - SMPD4
ExoCarta ExoCarta_55627
Vesiclepedia VP_55627
Entrez Gene 55627
HGNC 32949
MIM 610457
UniProt Q9NXE4  
 SMPD4 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 SMPD4
Molecular Function
    sphingomyelin phosphodiesterase activity GO:0004767 IEA
    metal ion binding GO:0046872 IEA
    sphingomyelin phosphodiesterase D activity GO:0050290 IBA
    sphingomyelin phosphodiesterase D activity GO:0050290 IDA
Biological Process
    sphingomyelin catabolic process GO:0006685 IBA
    sphingomyelin catabolic process GO:0006685 IDA
    endoplasmic reticulum organization GO:0007029 IMP
    glycerophospholipid catabolic process GO:0046475 IBA
    glycerophospholipid catabolic process GO:0046475 IDA
    ceramide biosynthetic process GO:0046513 IBA
    ceramide biosynthetic process GO:0046513 IDA
    cellular response to tumor necrosis factor GO:0071356 IDA
Subcellular Localization
    Golgi membrane GO:0000139 IEA
    nuclear envelope GO:0005635 ISS
    nuclear outer membrane GO:0005640 IDA
    endoplasmic reticulum GO:0005783 IDA
    endoplasmic reticulum membrane GO:0005789 TAS
    Golgi apparatus GO:0005794 IDA
    trans-Golgi network GO:0005802 IDA
    sarcolemma GO:0042383 ISS
 Experiment description of studies that identified SMPD4 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 235
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-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
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 SMPD4
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 SGCA  
Affinity Capture-MS Homo sapiens
2 HSD17B11 51170
Proximity Label-MS Homo sapiens
3 FOXA3  
Affinity Capture-MS Homo sapiens
4 METTL7A 25840
Proximity Label-MS Homo sapiens
5 LAMP3  
Proximity Label-MS Homo sapiens
6 ATG9A 79065
Proximity Label-MS Homo sapiens
7 GJA1 2697
Proximity Label-MS Homo sapiens
8 KPNB1 3837
Affinity Capture-MS Homo sapiens
9 CTDNEP1 23399
Proximity Label-MS Homo sapiens
10 GFAP 2670
Proximity Label-MS Homo sapiens
11 GJD3  
Proximity Label-MS Homo sapiens
12 DNAJC25 548645
Proximity Label-MS Homo sapiens
13 PTPN1 5770
Proximity Label-MS Homo sapiens
14 STX4 6810
Proximity Label-MS Homo sapiens
15 B3GAT1  
Proximity Label-MS Homo sapiens
16 HLA-B 3106
Affinity Capture-MS Homo sapiens
17 FAM57A  
Affinity Capture-MS Homo sapiens
18 NUP153 9972
Affinity Capture-MS Homo sapiens
19 RAB3B 5865
Proximity Label-MS Homo sapiens
20 SSR1 6745
Proximity Label-MS Homo sapiens
21 MARCH5  
Proximity Label-MS Homo sapiens
22 PIGH  
Affinity Capture-MS Homo sapiens
23 EXOSC4 54512
Two-hybrid Homo sapiens
24 DNAJC16  
Proximity Label-MS Homo sapiens
25 EED  
Affinity Capture-MS Homo sapiens
26 SLC25A46 91137
Proximity Label-MS Homo sapiens
27 DNAJC7 7266
Proximity Label-MS Homo sapiens
28 BRF2  
Affinity Capture-MS Homo sapiens
29 MECP2 4204
Affinity Capture-MS Homo sapiens
30 RAB35 11021
Proximity Label-MS Homo sapiens
31 EBAG9 9166
Proximity Label-MS Homo sapiens
32 FAM20C 56975
Affinity Capture-MS Homo sapiens
33 MARCKS 4082
Proximity Label-MS Homo sapiens
34 LMAN1 3998
Proximity Label-MS Homo sapiens
35 NUP155 9631
Proximity Label-MS Homo sapiens
36 KIAA1715 80856
Proximity Label-MS Homo sapiens
37 DNAJC14  
Proximity Label-MS Homo sapiens
38 RAB5A 5868
Proximity Label-MS Homo sapiens
39 LMNB1 4001
Proximity Label-MS Homo sapiens
40 EMD 2010
Proximity Label-MS Homo sapiens
41 FOXI2  
Affinity Capture-MS Homo sapiens
42 PARK2  
Affinity Capture-MS Homo sapiens
43 CXADR 1525
Proximity Label-MS Homo sapiens
44 MAPRE1 22919
Affinity Capture-MS Homo sapiens
45 RAB4A 5867
Proximity Label-MS Homo sapiens
46 FOXL2  
Affinity Capture-MS Homo sapiens
47 NTRK1 4914
Affinity Capture-MS Homo sapiens
48 GPR182  
Affinity Capture-MS Homo sapiens
49 TEAD2  
Affinity Capture-MS Homo sapiens
50 STX6 10228
Proximity Label-MS Homo sapiens
51 RPN1 6184
Proximity Label-MS Homo sapiens
52 CUL2 8453
Affinity Capture-MS Homo sapiens
53 Ube2i  
Affinity Capture-MS Mus musculus
54 RHOT2 89941
Proximity Label-MS Homo sapiens
55 ELOVL5 60481
Proximity Label-MS Homo sapiens
56 SEC61B 10952
Proximity Label-MS Homo sapiens
57 RMDN3 55177
Proximity Label-MS Homo sapiens
58 REEP5 7905
Proximity Label-MS Homo sapiens
59 FOXH1  
Affinity Capture-MS Homo sapiens
60 SEC63 11231
Proximity Label-MS Homo sapiens
61 RPN2 6185
Proximity Label-MS Homo sapiens
62 Nup98  
Affinity Capture-MS Mus musculus
63 LRRC59 55379
Proximity Label-MS Homo sapiens
64 PANX1 24145
Proximity Label-MS Homo sapiens
65 LAMP1 3916
Proximity Label-MS Homo sapiens
66 FOXI1  
Affinity Capture-MS Homo sapiens
67 BCAP31 10134
Proximity Label-MS Homo sapiens
68 HSD3B7 80270
Proximity Label-MS Homo sapiens
69 FOXG1  
Affinity Capture-MS Homo sapiens
70 STIM1 6786
Proximity Label-MS Homo sapiens
71 FKBP8 23770
Proximity Label-MS Homo sapiens
72 ARF6 382
Proximity Label-MS Homo sapiens
73 FOXL1  
Affinity Capture-MS Homo sapiens
74 AQP3  
Affinity Capture-MS Homo sapiens
75 OCIAD1 54940
Proximity Label-MS Homo sapiens
76 Nup107  
Affinity Capture-MS Mus musculus
77 RPA3 6119
Proximity Label-MS Homo sapiens
78 ATP2A1 487
Proximity Label-MS Homo sapiens
79 GPR45  
Affinity Capture-MS Homo sapiens
80 RAB9A 9367
Proximity Label-MS Homo sapiens
81 DHFRL1  
Proximity Label-MS Homo sapiens
82 CYP2C9  
Proximity Label-MS Homo sapiens
83 HAX1  
Proximity Label-MS Homo sapiens
84 LMNA 4000
Proximity Label-MS Homo sapiens
Proximity Label-MS Homo sapiens
85 PEX3 8504
Proximity Label-MS Homo sapiens
86 ACBD5 91452
Proximity Label-MS Homo sapiens
87 MAGEA8  
Affinity Capture-MS Homo sapiens
88 RNF43  
Proximity Label-MS Homo sapiens
89 PLEKHA4 57664
Affinity Capture-MS Homo sapiens
90 OPALIN  
Affinity Capture-MS Homo sapiens
91 MFSD4  
Affinity Capture-MS Homo sapiens
92 FOXB1  
Affinity Capture-MS Homo sapiens
93 NUP35 129401
Proximity Label-MS Homo sapiens
94 ERGIC1 57222
Proximity Label-MS Homo sapiens
95 ANAPC2 29882
Proximity Label-MS Homo sapiens
96 PXMP2  
Proximity Label-MS Homo sapiens
97 ERGIC2 51290
Proximity Label-MS Homo sapiens
98 NUP107 57122
Affinity Capture-MS Homo sapiens
99 SEC62 7095
Proximity Label-MS Homo sapiens
100 CEP135  
Proximity Label-MS Homo sapiens
101 RAB11A 8766
Proximity Label-MS Homo sapiens
102 DNAJC1 64215
Proximity Label-MS Homo sapiens
103 RAB5C 5878
Proximity Label-MS Homo sapiens
104 C9orf72  
Affinity Capture-MS Homo sapiens
105 CCDC47 57003
Affinity Capture-MS Homo sapiens
106 CKAP4 10970
Proximity Label-MS Homo sapiens
107 FOXE1  
Affinity Capture-MS Homo sapiens
108 DERL1 79139
Proximity Label-MS Homo sapiens
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