Gene description for TRIM56
Gene name tripartite motif containing 56
Gene symbol TRIM56
Other names/aliases RNF109
Species Homo sapiens
 Database cross references - TRIM56
ExoCarta ExoCarta_81844
Vesiclepedia VP_81844
Entrez Gene 81844
HGNC 19028
UniProt Q9BRZ2  
 TRIM56 identified in sEVs derived from the following tissue/cell type
Mesenchymal stem cells 36408942    
Thymus 23844026    
 Gene ontology annotations for TRIM56
Molecular Function
    RNA binding GO:0003723 HDA
    ubiquitin-protein transferase activity GO:0004842 TAS
    protein binding GO:0005515 IPI
    zinc ion binding GO:0008270 IEA
    ubiquitin protein ligase activity GO:0061630 IBA
    ubiquitin protein ligase activity GO:0061630 IDA
    ubiquitin protein ligase activity GO:0061630 ISS
Biological Process
    protein monoubiquitination GO:0006513 IDA
    regulation of type I interferon production GO:0032479 TAS
    positive regulation of interferon-beta production GO:0032728 ISS
    response to type I interferon GO:0034340 ISS
    innate immune response GO:0045087 IBA
    positive regulation of innate immune response GO:0045089 IDA
    defense response to virus GO:0051607 IDA
    defense response to virus GO:0051607 ISS
    positive regulation of type I interferon-mediated signaling pathway GO:0060340 IBA
    positive regulation of type I interferon-mediated signaling pathway GO:0060340 IDA
    protein K63-linked ubiquitination GO:0070534 ISS
    positive regulation of non-canonical NF-kappaB signal transduction GO:1901224 IDA
Subcellular Localization
    nucleoplasm GO:0005654 IBA
    cytoplasm GO:0005737 ISS
    cytosol GO:0005829 TAS
 Experiment description of studies that identified TRIM56 in sEVs
1
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
2
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
 Protein-protein interactions for TRIM56
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 RPL11 6135
Affinity Capture-MS Homo sapiens
2 UBE2H 7328
Two-hybrid Homo sapiens
3 CNBP 7555
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
4 RPL13 6137
Affinity Capture-MS Homo sapiens
5 FGFBP1 9982
Affinity Capture-MS Homo sapiens
6 ATG16L1 55054
Affinity Capture-MS Homo sapiens
7 ING4  
Affinity Capture-MS Homo sapiens
8 FASN 2194
Negative Genetic Homo sapiens
9 PARP1 142
Proximity Label-MS Homo sapiens
10 USP43  
Affinity Capture-MS Homo sapiens
11 ILF3 3609
Co-fractionation Homo sapiens
12 RPLP0 6175
Affinity Capture-MS Homo sapiens
13 ZNF346  
Affinity Capture-MS Homo sapiens
14 KIF14 9928
Affinity Capture-MS Homo sapiens
15 Espl1  
Affinity Capture-MS Mus musculus
16 LSM2 57819
Co-fractionation Homo sapiens
17 RPL13A 23521
Affinity Capture-MS Homo sapiens
18 DGCR8  
Affinity Capture-MS Homo sapiens
19 SPC24 147841
Affinity Capture-MS Homo sapiens
20 RPL3 6122
Affinity Capture-MS Homo sapiens
21 AGMAT  
Affinity Capture-MS Homo sapiens
22 RPL14 9045
Affinity Capture-MS Homo sapiens
23 CUL3 8452
Affinity Capture-MS Homo sapiens
24 RPL4 6124
Affinity Capture-MS Homo sapiens
25 HSP90AA1 3320
Affinity Capture-Luminescence Homo sapiens
26 SOX2  
Affinity Capture-MS Homo sapiens
27 ILF2 3608
Co-fractionation Homo sapiens
28 SRSF6 6431
Affinity Capture-MS Homo sapiens
29 TMEM173  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
30 PARK2  
Affinity Capture-MS Homo sapiens
31 Cep72  
Affinity Capture-MS Mus musculus
32 FBXW7  
Affinity Capture-MS Homo sapiens
33 PCBP1 5093
Affinity Capture-RNA Homo sapiens
34 MOV10 4343
Affinity Capture-RNA Homo sapiens
35 MYH9 4627
Affinity Capture-MS Homo sapiens
36 DYRK1A 1859
Affinity Capture-MS Homo sapiens
37 TRIM21 6737
Affinity Capture-MS Homo sapiens
38 KIF23 9493
Affinity Capture-MS Homo sapiens
39 RPL7A 6130
Affinity Capture-MS Homo sapiens
40 HIST1H1E 3008
Affinity Capture-MS Homo sapiens
41 NAA10 8260
Co-fractionation Homo sapiens
42 RPL36 25873
Affinity Capture-MS Homo sapiens
43 TICAM1  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
44 SNX2 6643
Co-fractionation Homo sapiens
45 RNF2  
Affinity Capture-MS Homo sapiens
46 Fam60a 56306
Affinity Capture-MS Mus musculus
47 BRPF3  
Affinity Capture-MS Homo sapiens
48 OBSL1 23363
Affinity Capture-MS Homo sapiens
49 MAGEB2 4113
Affinity Capture-MS Homo sapiens
50 FAM188B  
Affinity Capture-MS Homo sapiens
51 HNRNPH1 3187
Affinity Capture-RNA Homo sapiens
52 PPM1G 5496
Affinity Capture-MS Homo sapiens
53 PRKRA 8575
Affinity Capture-MS Homo sapiens
54 C17orf59 54785
Proximity Label-MS Homo sapiens
55 Ccdc9  
Affinity Capture-MS Mus musculus
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