Gene description for SHMT1
Gene name serine hydroxymethyltransferase 1 (soluble)
Gene symbol SHMT1
Other names/aliases CSHMT
SHMT
Species Homo sapiens
 Database cross references - SHMT1
ExoCarta ExoCarta_6470
Vesiclepedia VP_6470
Entrez Gene 6470
HGNC 10850
MIM 182144
UniProt P34896  
 SHMT1 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    
Chondrocytes 35931686    
Chondrocytes 35931686    
Mesenchymal stem cells 36408942    
Neuroblastoma cells 25944692    
Ovarian cancer cells 23333927    
Ovarian cancer cells 23333927    
Retinal pigment epithelial cells 35333565    
Retinal pigment epithelial cells 35333565    
Thymus 23844026    
Urine 19056867    
 Gene ontology annotations for SHMT1
Molecular Function
    mRNA regulatory element binding translation repressor activity GO:0000900 IDA
    glycine hydroxymethyltransferase activity GO:0004372 IBA
    glycine hydroxymethyltransferase activity GO:0004372 IDA
    protein binding GO:0005515 IPI
    aldehyde-lyase activity GO:0016832 EXP
    pyridoxal phosphate binding GO:0030170 IBA
    pyridoxal phosphate binding GO:0030170 IDA
    small molecule binding GO:0036094 IPI
    identical protein binding GO:0042802 IPI
    protein homodimerization activity GO:0042803 IDA
    mRNA 5'-UTR binding GO:0048027 IDA
    serine binding GO:0070905 IDA
Biological Process
    dTMP biosynthetic process GO:0006231 IEA
    glycine metabolic process GO:0006544 IDA
    L-serine metabolic process GO:0006563 IDA
    L-serine catabolic process GO:0006565 IDA
    purine nucleobase biosynthetic process GO:0009113 IDA
    negative regulation of translation GO:0017148 IDA
    glycine biosynthetic process from serine GO:0019264 IBA
    tetrahydrofolate interconversion GO:0035999 IDA
    tetrahydrofolate interconversion GO:0035999 IEA
    carnitine biosynthetic process GO:0045329 TAS
    tetrahydrofolate metabolic process GO:0046653 IBA
    tetrahydrofolate metabolic process GO:0046653 IDA
    folic acid metabolic process GO:0046655 IDA
    folic acid metabolic process GO:0046655 TAS
    protein homotetramerization GO:0051289 IDA
    cellular response to tetrahydrofolate GO:1904482 IDA
    cellular response to leukemia inhibitory factor GO:1990830 IEA
Subcellular Localization
    nucleus GO:0005634 IBA
    nucleoplasm GO:0005654 IDA
    cytoplasm GO:0005737 IBA
    mitochondrion GO:0005739 IBA
    cytosol GO:0005829 IDA
    cytosol GO:0005829 TAS
    extracellular exosome GO:0070062 HDA
 Experiment description of studies that identified SHMT1 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 497
MISEV standards
✘ Biophysical techniques
✔
CD9|CD151|CD63|CD81|CD82|FLOT1|FLOT2|GAPDH|LAMP1|LAMP2|RAB5A|SDCBP|TFRC|TSG101|UCHL1
Enriched markers
✘ Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 35931686    
Organism Homo sapiens
Experiment description Extracellular vesicles enriched in connexin 43 promote a senescent phenotype in bone and synovial cells contributing to osteoarthritis progression
Authors "Varela-Eirín M, Carpintero-Fernández P, Guitián-Caamaño A, Varela-Vázquez A, García-Yuste A, Sánchez-Temprano A, Bravo-López SB, Yañez-Cabanas J, Fonseca E, Largo R, Mobasheri A, Caeiro JR, Mayán MD."
Journal name Cell Death Dis
Publication year 2022
Sample Chondrocytes
Sample name T/C-28a2
Isolation/purification methods Differential centrifugation
Filtration
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectometry
6
Experiment ID 498
MISEV standards
✔
EM
Biophysical techniques
✔
CD9|CD151|CD63|CD81|CD82|FLOT1|FLOT2|GAPDH|LAMP1|LAMP2|RAB5A|SDCBP|TFRC|TSG101|UCHL1
Enriched markers
✘ Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 35931686    
Organism Homo sapiens
Experiment description Extracellular vesicles enriched in connexin 43 promote a senescent phenotype in bone and synovial cells contributing to osteoarthritis progression
Authors "Varela-Eirín M, Carpintero-Fernández P, Guitián-Caamaño A, Varela-Vázquez A, García-Yuste A, Sánchez-Temprano A, Bravo-López SB, Yañez-Cabanas J, Fonseca E, Largo R, Mobasheri A, Caeiro JR, Mayán MD."
Journal name Cell Death Dis
Publication year 2022
Sample Chondrocytes
Sample name T/C-28a2
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 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
8
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
9
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
10
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
11
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
12
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
13
Experiment ID 217
MISEV standards
✔
EM
Biophysical techniques
✔
TSG101|CD81|CD9|CD63
Enriched markers
✘ Negative markers
✔
NTA
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
14
Experiment ID 63
MISEV standards
✘ Biophysical techniques
✔
AQP2
Enriched markers
✘ Negative markers
✘ Particle analysis
Identified molecule protein
Identification method Mass spectrometry
PubMed ID 19056867    
Organism Homo sapiens
Experiment description Large-scale proteomics and phosphoproteomics of urinary exosomes.
Authors "Gonzales PA, Pisitkun T, Hoffert JD, Tchapyjnikov D, Star RA, Kleta R, Wang NS, Knepper MA"
Journal name JASN
Publication year 2009
Sample Urine
Sample name Urine - Normal
Isolation/purification methods Differential centrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Mass spectrometry [LTQ]
Western blotting
 Protein-protein interactions for SHMT1
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 DDX6 1656
Two-hybrid Homo sapiens
2 TRIM21 6737
Affinity Capture-MS Homo sapiens
3 PGK2 5232
Co-fractionation Homo sapiens
4 DLEU1  
Two-hybrid Homo sapiens
5 HSPA1L 3305
Co-fractionation Homo sapiens
6 PLEKHA4 57664
Affinity Capture-MS Homo sapiens
7 IREB2 3658
Co-fractionation Homo sapiens
8 ARFIP1 27236
Co-fractionation Homo sapiens
9 GNPDA2 132789
Co-fractionation Homo sapiens
10 TTC1 7265
Co-fractionation Homo sapiens
11 STK38 11329
Co-fractionation Homo sapiens
12 MCAT 27349
Co-fractionation Homo sapiens
13 FAM129B 64855
Co-fractionation Homo sapiens
14 C18orf25 147339
Co-fractionation Homo sapiens
15 PAWR 5074
Co-fractionation Homo sapiens
16 DPYSL5  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
17 APEH 327
Co-fractionation Homo sapiens
18 HSPE1 3336
Co-fractionation Homo sapiens
19 DNAJA2 10294
Proximity Label-MS Homo sapiens
20 ATP6V1C1 528
Co-fractionation Homo sapiens
21 STXBP1 6812
Co-fractionation Homo sapiens
22 PAICS 10606
Co-fractionation Homo sapiens
23 PBDC1 51260
Co-fractionation Homo sapiens
24 IDE 3416
Co-fractionation Homo sapiens
25 DOCK5 80005
Affinity Capture-MS Homo sapiens
26 MDFI  
Two-hybrid Homo sapiens
27 HIST1H4A 8359
Co-fractionation Homo sapiens
28 EFNB1 1947
Affinity Capture-MS Homo sapiens
29 CTTN 2017
Co-fractionation Homo sapiens
30 SMAD4  
Co-fractionation Homo sapiens
31 ZC3H4 23211
Co-fractionation Homo sapiens
32 HNRNPCL1 343069
Affinity Capture-MS Homo sapiens
33 PARK2  
Affinity Capture-MS Homo sapiens
34 PTK2 5747
Affinity Capture-MS Homo sapiens
35 SHMT2 6472
Co-fractionation Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
36 SHMT1 6470
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
37 PPAT 5471
Co-fractionation Homo sapiens
38 SNX6 58533
Co-fractionation Homo sapiens
39 VPS29 51699
Co-fractionation Homo sapiens
40 PRPS2 5634
Affinity Capture-MS Homo sapiens
41 GARS 2617
Co-fractionation Homo sapiens
42 SULT1A3 6818
Two-hybrid Homo sapiens
43 XPO5 57510
Co-fractionation Homo sapiens
44 CHMP4C 92421
Affinity Capture-MS Homo sapiens
45 GSPT2 23708
Co-fractionation Homo sapiens
46 STAT1 6772
Co-fractionation Homo sapiens
47 AMPD2 271
Affinity Capture-MS Homo sapiens
48 RPA3 6119
Proximity Label-MS Homo sapiens
49 GTF2F2 2963
Co-fractionation Homo sapiens
50 FBXO2 26232
Affinity Capture-MS Homo sapiens
51 MAPK9 5601
Two-hybrid Homo sapiens
52 ITPA 3704
Co-fractionation Homo sapiens
53 DCAF7 10238
Affinity Capture-MS Homo sapiens
54 GORASP2 26003
Two-hybrid Homo sapiens
55 ARNT 405
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
56 TSN 7247
Co-fractionation Homo sapiens
57 PIM1  
Two-hybrid Homo sapiens
58 PRRC1 133619
Co-fractionation Homo sapiens
59 SNX2 6643
Co-fractionation Homo sapiens
60 C9orf72  
Affinity Capture-MS Homo sapiens
61 C7orf60 154743
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
62 HARS 3035
Co-fractionation Homo sapiens
63 PRSS23 11098
Two-hybrid Homo sapiens
64 DEDD  
Two-hybrid Homo sapiens
65 ATIC 471
Co-fractionation Homo sapiens
66 CUL4A 8451
Affinity Capture-MS Homo sapiens
67 CARS 833
Co-fractionation Homo sapiens
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