Gene description for RNF4
Gene name ring finger protein 4
Gene symbol RNF4
Other names/aliases RES4-26
SLX5
SNURF
Species Homo sapiens
 Database cross references - RNF4
ExoCarta ExoCarta_6047
Vesiclepedia VP_6047
Entrez Gene 6047
HGNC 10067
MIM 602850
UniProt P78317  
 RNF4 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 RNF4
Molecular Function
    DNA binding GO:0003677 ISS
    ubiquitin-protein transferase activity GO:0004842 ISS
    protein binding GO:0005515 IPI
    zinc ion binding GO:0008270 IEA
    nuclear receptor coactivator activity GO:0030374 TAS
    nucleosome binding GO:0031491 ISS
    SUMO polymer binding GO:0032184 IDA
    identical protein binding GO:0042802 IPI
    ubiquitin protein ligase activity GO:0061630 IBA
    ubiquitin protein ligase activity GO:0061630 IDA
Biological Process
    proteasome-mediated ubiquitin-dependent protein catabolic process GO:0043161 IBA
    proteasome-mediated ubiquitin-dependent protein catabolic process GO:0043161 IMP
    positive regulation of DNA-templated transcription GO:0045893 ISS
    positive regulation of transcription by RNA polymerase II GO:0045944 IBA
    positive regulation of transcription by RNA polymerase II GO:0045944 IDA
    response to arsenic-containing substance GO:0046685 IDA
    protein autoubiquitination GO:0051865 ISS
    protein K63-linked ubiquitination GO:0070534 ISS
    protein K48-linked ubiquitination GO:0070936 ISS
    protein K11-linked ubiquitination GO:0070979 ISS
    protein K6-linked ubiquitination GO:0085020 ISS
    regulation of spindle assembly GO:0090169 IMP
    regulation of kinetochore assembly GO:0090234 IMP
    negative regulation of protein localization to chromatin GO:0120186 IDA
Subcellular Localization
    nucleus GO:0005634 IDA
    nucleoplasm GO:0005654 IDA
    nucleoplasm GO:0005654 TAS
    cytoplasm GO:0005737 IDA
    nuclear body GO:0016604 IDA
    PML body GO:0016605 IBA
    PML body GO:0016605 IDA
    microtubule end GO:1990752 IDA
 Experiment description of studies that identified RNF4 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 RNF4
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 TRAIP  
Two-hybrid Homo sapiens
2 UBE2H 7328
Two-hybrid Homo sapiens
3 RALY 22913
Affinity Capture-MS Homo sapiens
4 VPS35 55737
Affinity Capture-MS Homo sapiens
5 HNRNPC 3183
Affinity Capture-MS Homo sapiens
6 KPNA3 3839
Affinity Capture-MS Homo sapiens
7 HIST1H4A 8359
Affinity Capture-MS Homo sapiens
8 SRPK2 6733
Biochemical Activity Homo sapiens
9 TARDBP 23435
Co-localization Homo sapiens
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
10 SP1  
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-Western Homo sapiens
11 ACTC1 70
Affinity Capture-MS Homo sapiens
12 UCHL1 7345
Biochemical Activity Homo sapiens
13 NOP56 10528
Affinity Capture-MS Homo sapiens
14 ARL14EP  
Affinity Capture-MS Homo sapiens
15 UBC 7316
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
16 PGR  
Two-hybrid Homo sapiens
17 HNRNPR 10236
Affinity Capture-MS Homo sapiens
18 ALOX12B  
Affinity Capture-MS Homo sapiens
19 PRKDC 5591
Affinity Capture-MS Homo sapiens
20 ZNF618  
Affinity Capture-MS Homo sapiens
21 APEX1 328
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
22 SAFB 6294
Affinity Capture-MS Homo sapiens
23 TOP2A 7153
Affinity Capture-MS Homo sapiens
24 TRIM28 10155
Affinity Capture-Western Homo sapiens
PCA Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
25 UBE2E2  
Two-hybrid Homo sapiens
Reconstituted Complex Homo sapiens
26 NOLC1 9221
Affinity Capture-MS Homo sapiens
27 UBE2K 3093
Two-hybrid Homo sapiens
28 COPB2 9276
Affinity Capture-MS Homo sapiens
29 RRM2B 50484
Affinity Capture-MS Homo sapiens
30 MDC1  
Affinity Capture-Western Homo sapiens
31 FBL 2091
Affinity Capture-MS Homo sapiens
32 TDG 6996
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
33 GPX1 2876
Affinity Capture-MS Homo sapiens
34 HIST2H2AC 8338
Affinity Capture-MS Homo sapiens
35 SNRPD3 6634
Affinity Capture-MS Homo sapiens
36 UCHL5 51377
Biochemical Activity Homo sapiens
37 DDX18 8886
Affinity Capture-MS Homo sapiens
38 YEATS2  
Affinity Capture-MS Homo sapiens
39 UBE2W  
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
Reconstituted Complex Homo sapiens
40 MECP2 4204
Biochemical Activity Homo sapiens
41 NCOA1  
Phenotypic Enhancement Homo sapiens
42 UBE2E3 10477
Two-hybrid Homo sapiens
Reconstituted Complex Homo sapiens
43 NSUN2 54888
Affinity Capture-MS Homo sapiens
44 POF1B 79983
Affinity Capture-MS Homo sapiens
45 ATF7IP 55729
Affinity Capture-MS Homo sapiens
46 HNRNPA0 10949
Affinity Capture-MS Homo sapiens
47 RNF4 6047
Co-crystal Structure Homo sapiens
FRET Homo sapiens
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-Western Homo sapiens
FRET Homo sapiens
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
Co-crystal Structure Homo sapiens
FRET Homo sapiens
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-Western Homo sapiens
FRET Homo sapiens
Biochemical Activity Homo sapiens
Biochemical Activity Homo sapiens
48 UBE2T  
Two-hybrid Homo sapiens
49 USP11 8237
Affinity Capture-MS Homo sapiens
50 UBE2D4  
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
51 TAB3 257397
Affinity Capture-Western Homo sapiens
52 COPG1 22820
Affinity Capture-MS Homo sapiens
53 MGME1  
Affinity Capture-MS Homo sapiens
54 NOP2 4839
Affinity Capture-MS Homo sapiens
55 KPNA4 3840
Affinity Capture-MS Homo sapiens
56 UBE2I 7329
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
57 TSR3  
Affinity Capture-MS Homo sapiens
58 RAN 5901
Affinity Capture-MS Homo sapiens
59 ACTN4 81
Affinity Capture-MS Homo sapiens
60 NKRF 55922
Affinity Capture-MS Homo sapiens
61 GYS1 2997
Affinity Capture-MS Homo sapiens
62 TAB2  
Affinity Capture-Western Homo sapiens
63 REXO4  
Affinity Capture-MS Homo sapiens
64 SUMO2 6613
Affinity Capture-Western Homo sapiens
FRET Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Biochemical Activity Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Co-crystal Structure Homo sapiens
Reconstituted Complex Homo sapiens
Biochemical Activity Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Biochemical Activity Homo sapiens
Protein-peptide Homo sapiens
Affinity Capture-MS Homo sapiens
Reconstituted Complex Homo sapiens
65 GAMT  
Affinity Capture-MS Homo sapiens
66 ACTB 60
Affinity Capture-MS Homo sapiens
67 PML 5371
FRET Homo sapiens
FRET Homo sapiens
PCA Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
Biochemical Activity Homo sapiens
68 UBE2D3 7323
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
Reconstituted Complex Homo sapiens
69 L3MBTL2  
Affinity Capture-MS Homo sapiens
70 HNRNPA3 220988
Affinity Capture-MS Homo sapiens
71 ACSL4 2182
Affinity Capture-MS Homo sapiens
72 DDX27 55661
Affinity Capture-MS Homo sapiens
73 GTPBP4 23560
Affinity Capture-MS Homo sapiens
74 DAXX  
Affinity Capture-Western Homo sapiens
75 ZNF326 284695
Affinity Capture-MS Homo sapiens
76 ATXN1 6310
Co-localization Homo sapiens
Biochemical Activity Homo sapiens
77 LIMA1 51474
Affinity Capture-MS Homo sapiens
78 UBE2N 7334
Co-crystal Structure Homo sapiens
Reconstituted Complex Homo sapiens
79 SF3B2 10992
Affinity Capture-MS Homo sapiens
80 SERPINB3 6317
Affinity Capture-MS Homo sapiens
81 UEVLD 55293
Two-hybrid Homo sapiens
82 HIST2H3C 126961
Biochemical Activity Homo sapiens
83 EIF4G1 1981
Affinity Capture-MS Homo sapiens
84 SMARCA5 8467
Affinity Capture-MS Homo sapiens
85 MGA  
Affinity Capture-MS Homo sapiens
86 ZZZ3  
Affinity Capture-MS Homo sapiens
87 LMO7 4008
Affinity Capture-MS Homo sapiens
88 CTNNB1 1499
Reconstituted Complex Homo sapiens
89 UBE2L6 9246
Two-hybrid Homo sapiens
90 BLM 641
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
91 CUL3 8452
Affinity Capture-MS Homo sapiens
92 CSRP2BP  
Affinity Capture-MS Homo sapiens
93 CTTN 2017
Affinity Capture-MS Homo sapiens
94 UBE2E1  
Two-hybrid Homo sapiens
Reconstituted Complex Homo sapiens
95 HNRNPA1 3178
Affinity Capture-MS Homo sapiens
96 FUS 2521
Affinity Capture-MS Homo sapiens
Affinity Capture-Western Homo sapiens
97 MAP3K7  
Affinity Capture-Western Homo sapiens
Affinity Capture-MS Homo sapiens
98 KPNA2 3838
Affinity Capture-MS Homo sapiens
99 SART1 9092
Affinity Capture-Western Homo sapiens
100 MYO1C 4641
Affinity Capture-MS Homo sapiens
101 TBP  
Reconstituted Complex Homo sapiens
Phenotypic Enhancement Homo sapiens
102 HNF4A  
Biochemical Activity Homo sapiens
103 BIRC6 57448
Biochemical Activity Homo sapiens
104 MYC  
Reconstituted Complex Homo sapiens
105 HNRNPAB 3182
Affinity Capture-MS Homo sapiens
106 PATZ1  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Two-hybrid Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
107 UBE2D2 7322
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
Biochemical Activity Homo sapiens
Reconstituted Complex Homo sapiens
108 DDX1 1653
Affinity Capture-MS Homo sapiens
109 SETDB1  
Affinity Capture-MS Homo sapiens
110 HIST1H2BI 8346
Affinity Capture-MS Homo sapiens
111 LARP4 113251
Affinity Capture-MS Homo sapiens
112 ILF3 3609
Affinity Capture-MS Homo sapiens
113 SUMO1 7341
Reconstituted Complex Homo sapiens
PCA Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Co-crystal Structure Homo sapiens
114 UBE2D1 7321
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
Affinity Capture-MS Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
Reconstituted Complex Homo sapiens
115 KRT18 3875
Affinity Capture-MS Homo sapiens
116 TRAF7  
Affinity Capture-MS Homo sapiens
117 TRIP6 7205
Affinity Capture-MS Homo sapiens
118 SPTBN1 6711
Affinity Capture-MS Homo sapiens
119 TERF2  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
120 PARP1 142
Affinity Capture-Western Homo sapiens
Biochemical Activity Homo sapiens
121 SKIL  
Two-hybrid Homo sapiens
122 TRPS1  
Affinity Capture-Western Homo sapiens
123 H3F3A 3020
Affinity Capture-MS Homo sapiens
124 RBM25 58517
Affinity Capture-MS Homo sapiens
125 BLK 640
Affinity Capture-MS Homo sapiens
126 MISP 126353
Affinity Capture-MS Homo sapiens
127 RPA1 6117
Affinity Capture-Western Homo sapiens
128 IKBKG 8517
Two-hybrid Homo sapiens
129 HNRNPM 4670
Affinity Capture-MS Homo sapiens
130 SQSTM1 8878
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
131 ELAVL1 1994
Affinity Capture-MS Homo sapiens
132 S100A9 6280
Affinity Capture-MS Homo sapiens
133 DDX58 23586
Affinity Capture-RNA Homo sapiens
134 H2AFY 9555
Affinity Capture-MS Homo sapiens
135 ESR1  
Two-hybrid Homo sapiens
136 EIF3J 8669
Affinity Capture-MS Homo sapiens
137 TCF20  
Two-hybrid Homo sapiens
Reconstituted Complex Homo sapiens
138 GSX2  
Affinity Capture-MS Homo sapiens
139 UHRF1 29128
Affinity Capture-Western Homo sapiens
140 SUMO3 6612
Affinity Capture-MS Homo sapiens
141 AR 367
Two-hybrid Homo sapiens
Two-hybrid Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
Reconstituted Complex Homo sapiens
142 LGALS3 3958
Affinity Capture-MS Homo sapiens
143 VIM 7431
Affinity Capture-MS Homo sapiens
144 DNMT1 1786
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
145 FANCA  
Affinity Capture-Western Homo sapiens
Affinity Capture-Western Homo sapiens
146 HNRNPA2B1 3181
Affinity Capture-MS Homo sapiens
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