Gene description for Ubr4
Gene name ubiquitin protein ligase E3 component n-recognin 4
Gene symbol Ubr4
Other names/aliases 1810009A16Rik
A930005E13Rik
D930005K06Rik
Gm1032
Gm1666
N28143
RBAF600
Zubr1
mKIAA0462
p600
Species Mus musculus
 Database cross references - Ubr4
ExoCarta ExoCarta_69116
Vesiclepedia VP_69116
Entrez Gene 69116
UniProt A2AN08  
 Ubr4 identified in sEVs derived from the following tissue/cell type
Colon cancer cells 37309723    
T-cell lymphoma cells 37309723    
 Gene ontology annotations for Ubr4
Molecular Function
    ubiquitin-protein transferase activity GO:0004842 IBA
    protein binding GO:0005515 IPI
    calmodulin binding GO:0005516 IDA
    zinc ion binding GO:0008270 IEA
    ubiquitin protein ligase activity GO:0061630 IDA
    ubiquitin protein ligase activity GO:0061630 ISO
    ubiquitin protein ligase activity GO:0061630 ISS
Biological Process
    ubiquitin-dependent protein catabolic process GO:0006511 IBA
    ubiquitin-dependent protein catabolic process GO:0006511 ISO
    ubiquitin-dependent protein catabolic process GO:0006511 ISS
    response to oxidative stress GO:0006979 IEA
    endosome organization GO:0007032 IDA
    positive regulation of autophagy GO:0010508 IMP
    protein catabolic process GO:0030163 IMP
    proteasome-mediated ubiquitin-dependent protein catabolic process GO:0043161 ISO
    protein K27-linked ubiquitination GO:0044314 ISO
    protein K27-linked ubiquitination GO:0044314 ISS
    negative regulation of fatty acid biosynthetic process GO:0045717 IEA
    negative regulation of fatty acid biosynthetic process GO:0045717 ISO
    protein stabilization GO:0050821 IMP
    protein K48-linked ubiquitination GO:0070936 ISO
    protein K48-linked ubiquitination GO:0070936 ISS
    protein K11-linked ubiquitination GO:0070979 ISO
    protein K11-linked ubiquitination GO:0070979 ISS
    ubiquitin-dependent protein catabolic process via the N-end rule pathway GO:0071596 IDA
    ubiquitin-dependent protein catabolic process via the N-end rule pathway GO:0071596 IMP
    ubiquitin-dependent protein catabolic process via the N-end rule pathway GO:0071596 ISO
    cytoplasm protein quality control by the ubiquitin-proteasome system GO:0071629 ISO
    cytoplasm protein quality control by the ubiquitin-proteasome system GO:0071629 ISS
    cytoplasm protein quality control GO:0140455 ISO
    cytoplasm protein quality control GO:0140455 ISS
    negative regulation of HRI-mediated signaling GO:0141191 ISS
    protein branched polyubiquitination GO:0141198 ISS
Subcellular Localization
    nucleoplasm GO:0005654 IBA
    nucleoplasm GO:0005654 IEA
    nucleoplasm GO:0005654 ISO
    cytoplasm GO:0005737 ISO
    endosome GO:0005768 IDA
    centrosome GO:0005813 IBA
    centrosome GO:0005813 IEA
    centrosome GO:0005813 ISO
    cytosol GO:0005829 IBA
    cytosol GO:0005829 IEA
    cytosol GO:0005829 ISO
 Experiment description of studies that identified Ubr4 in sEVs
1
Experiment ID 907
MISEV standards
✔
EM
Biophysical techniques
✔
Tsg101|Sdcbp|Cd151|Gapdh|Lamp2|Cd81|Cd82|Cd9|Cd63|Cd80|Flot2|Tfrc|Rab35|Rab5a
Enriched markers
✔
HSPA5
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 37309723    
Organism Mus musculus
Experiment description Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells
Authors "Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S."
Journal name Proteomics
Publication year 2023
Sample Colon cancer cells
Sample name C26
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
2
Experiment ID 908
MISEV standards
✔
EM
Biophysical techniques
✔
Tsg101|Sdcbp|Cd151|Gapdh|Lamp2|Cd81|Cd82|Cd9|Cd63|Cd80|Flot2|Tfrc|Rab35|Rab5a
Enriched markers
✔
HSPA5
Negative markers
✔
NTA
Particle analysis
Identified molecule Protein
Identification method Mass spectrometry
PubMed ID 37309723    
Organism Mus musculus
Experiment description Proteomic analysis of the small extracellular vesicles and soluble secretory proteins from cachexia inducing and non-inducing cancer cells
Authors "Chitti SV, Kang T, Fonseka P, Marzan AL, Stewart S, Shahi S, Bramich K, Ang CS, Pathan M, Gummadi S, Mathivanan S."
Journal name Proteomics
Publication year 2023
Sample T-cell lymphoma cells
Sample name EL4
Isolation/purification methods Differential centrifugation
Ultracentrifugation
Flotation density -
Molecules identified in the study Protein
Methods used in the study Western blotting
Mass spectrometry
 Protein-protein interactions for Ubr4
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 Nphs2  
Affinity Capture-MS Mus musculus
2 Ubc  
Reconstituted Complex Mus musculus
3 Herc4  
Co-fractionation Mus musculus
4 Lars 107045
Co-fractionation Mus musculus
5 Pde4dip  
Affinity Capture-MS Mus musculus
6 Rpl13a 22121
Co-fractionation Mus musculus
7 Dhx29  
Co-fractionation Mus musculus
8 Rps4x 20102
Co-fractionation Mus musculus
9 Rps2 16898
Co-fractionation Mus musculus
10 Fmr1  
Affinity Capture-MS Mus musculus
11 Faf1  
Co-fractionation Mus musculus
12 Psmc6 67089
Co-fractionation Mus musculus
13 Ube2b  
Co-fractionation Mus musculus
14 Chaf1a  
Affinity Capture-MS Mus musculus
15 Herc2  
Affinity Capture-MS Mus musculus
16 Tmem173  
Proximity Label-MS Mus musculus
17 Mycbp2 105689
Affinity Capture-MS Mus musculus
18 Ubxn1  
Co-fractionation Mus musculus
19 Ubxn7  
Co-fractionation Mus musculus
20 AI314180 230249
Co-fractionation Mus musculus
21 Atp9a  
Co-fractionation Mus musculus
22 Eed  
Affinity Capture-MS Mus musculus
23 Rpl15 66480
Co-fractionation Mus musculus
24 Atxn1  
Proximity Label-MS Mus musculus
25 Dock11  
Co-fractionation Mus musculus
26 Ube2a  
Co-fractionation Mus musculus
27 Fancd2  
Affinity Capture-MS Mus musculus
28 Lipt2  
Co-fractionation Mus musculus
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