Gene description for Ddb1
Gene name damage specific DNA binding protein 1
Gene symbol Ddb1
Other names/aliases 127kDa
AA408517
p127-Ddb1
Species Mus musculus
 Database cross references - Ddb1
ExoCarta ExoCarta_13194
Vesiclepedia VP_13194
Entrez Gene 13194
UniProt Q3U1J4  
 Ddb1 identified in sEVs derived from the following tissue/cell type
Colon cancer cells 37309723    
T-cell lymphoma cells 37309723    
 Gene ontology annotations for Ddb1
Molecular Function
    damaged DNA binding GO:0003684 IEA
    damaged DNA binding GO:0003684 ISO
    damaged DNA binding GO:0003684 ISO
    protein binding GO:0005515 IPI
    protein-macromolecule adaptor activity GO:0030674 ISO
    protein-containing complex binding GO:0044877 IEA
    protein-containing complex binding GO:0044877 ISO
    WD40-repeat domain binding GO:0071987 IEA
    WD40-repeat domain binding GO:0071987 ISO
    cullin family protein binding GO:0097602 IEA
    cullin family protein binding GO:0097602 ISO
    ubiquitin ligase complex scaffold activity GO:0160072 IEA
    ubiquitin ligase complex scaffold activity GO:0160072 ISO
Biological Process
    DNA repair GO:0006281 IBA
    ubiquitin-dependent protein catabolic process GO:0006511 IMP
    ubiquitin-dependent protein catabolic process GO:0006511 ISO
    apoptotic process GO:0006915 IMP
    DNA damage response GO:0006974 EXP
    DNA damage response GO:0006974 ISO
    DNA damage response GO:0006974 ISS
    spindle assembly involved in female meiosis GO:0007056 IEA
    spindle assembly involved in female meiosis GO:0007056 ISO
    proteasomal protein catabolic process GO:0010498 ISO
    Wnt signaling pathway GO:0016055 IDA
    protein ubiquitination GO:0016567 IEA
    protein ubiquitination GO:0016567 IMP
    protein ubiquitination GO:0016567 ISO
    protein ubiquitination GO:0016567 ISS
    viral release from host cell GO:0019076 IEA
    viral release from host cell GO:0019076 ISO
    cellular response to UV GO:0034644 EXP
    cellular response to UV GO:0034644 ISO
    cellular response to UV GO:0034644 ISS
    ectopic germ cell programmed cell death GO:0035234 IMP
    regulation of circadian rhythm GO:0042752 IMP
    negative regulation of apoptotic process GO:0043066 IMP
    proteasome-mediated ubiquitin-dependent protein catabolic process GO:0043161 IBA
    proteasome-mediated ubiquitin-dependent protein catabolic process GO:0043161 ISO
    proteasome-mediated ubiquitin-dependent protein catabolic process GO:0043161 ISS
    epigenetic programming in the zygotic pronuclei GO:0044725 IEA
    epigenetic programming in the zygotic pronuclei GO:0044725 ISO
    positive regulation of viral genome replication GO:0045070 IEA
    positive regulation of viral genome replication GO:0045070 ISO
    positive regulation of gluconeogenesis GO:0045722 IMP
    positive regulation of protein catabolic process GO:0045732 IEA
    positive regulation of protein catabolic process GO:0045732 ISO
    positive regulation by virus of viral protein levels in host cell GO:0046726 IEA
    positive regulation by virus of viral protein levels in host cell GO:0046726 ISO
    rhythmic process GO:0048511 IEA
    negative regulation of developmental process GO:0051093 IMP
    biological process involved in interaction with symbiont GO:0051702 IEA
    biological process involved in interaction with symbiont GO:0051702 ISO
    UV-damage excision repair GO:0070914 ISO
    regulation of mitotic cell cycle phase transition GO:1901990 IEA
    regulation of mitotic cell cycle phase transition GO:1901990 ISO
    negative regulation of reproductive process GO:2000242 IMP
Subcellular Localization
    nucleus GO:0005634 IBA
    nucleus GO:0005634 ISO
    nucleus GO:0005634 ISO
    nucleus GO:0005634 ISS
    nucleus GO:0005634 NAS
    nucleoplasm GO:0005654 IEA
    nucleoplasm GO:0005654 ISO
    nucleolus GO:0005730 IEA
    nucleolus GO:0005730 ISO
    cytoplasm GO:0005737 ISO
    cytoplasm GO:0005737 ISS
    Cul4A-RING E3 ubiquitin ligase complex GO:0031464 EXP
    Cul4A-RING E3 ubiquitin ligase complex GO:0031464 ISO
    Cul4A-RING E3 ubiquitin ligase complex GO:0031464 ISS
    Cul4B-RING E3 ubiquitin ligase complex GO:0031465 ISO
    Cul4B-RING E3 ubiquitin ligase complex GO:0031465 ISS
    protein-containing complex GO:0032991 ISO
    site of double-strand break GO:0035861 IBA
    Cul4-RING E3 ubiquitin ligase complex GO:0080008 IDA
    Cul4-RING E3 ubiquitin ligase complex GO:0080008 ISO
    Cul4-RING E3 ubiquitin ligase complex GO:0080008 ISS
 Experiment description of studies that identified Ddb1 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 Ddb1
  Protein Interactor ExoCarta ID Identification method PubMed Species
1 CRBN  
Affinity Capture-MS Homo sapiens
2 Wdr48  
Affinity Capture-MS Mus musculus
3 Dcaf5  
Affinity Capture-MS Mus musculus
4 Smarca2  
Affinity Capture-MS Mus musculus
5 Setd1a  
Affinity Capture-MS Mus musculus
6 Med15  
Affinity Capture-MS Mus musculus
7 Brwd1  
Affinity Capture-MS Mus musculus
8 KRT6A 3853
Affinity Capture-MS Homo sapiens
9 VPRBP 9730
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
10 Wdr46  
Affinity Capture-MS Mus musculus
11 ABL1 25
Two-hybrid Homo sapiens
Reconstituted Complex Homo sapiens
Affinity Capture-Western Homo sapiens
12 Wdr74  
Affinity Capture-MS Mus musculus
13 Cops7b  
Co-fractionation Mus musculus
14 TMEM263 90488
Affinity Capture-MS Homo sapiens
15 Gtf2h2  
Affinity Capture-MS Mus musculus
16 Egln3  
Affinity Capture-MS Mus musculus
17 WDTC1 23038
Affinity Capture-MS Homo sapiens
18 Dcaf17  
Affinity Capture-MS Mus musculus
19 Tmem173  
Proximity Label-MS Mus musculus
20 DDA1  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
21 H2afy 26914
Affinity Capture-MS Mus musculus
22 Ubxn7  
Co-fractionation Mus musculus
23 Wdr91  
Affinity Capture-MS Mus musculus
24 NOLC1 9221
Affinity Capture-MS Homo sapiens
25 DDB1 1642
Affinity Capture-MS Homo sapiens
26 COPS6 10980
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
27 Hist1h1a  
Affinity Capture-MS Mus musculus
28 COPS5 10987
Affinity Capture-MS Homo sapiens
29 Atg16l1  
Affinity Capture-MS Mus musculus
30 Polr2a  
Affinity Capture-Western Mus musculus
Affinity Capture-MS Mus musculus
31 Wdr36 225348
Affinity Capture-MS Mus musculus
32 Elf5  
Affinity Capture-MS Mus musculus
33 Eif3a 13669
Affinity Capture-MS Mus musculus
34 Wdr82  
Affinity Capture-MS Mus musculus
35 Fancd2  
Affinity Capture-Western Mus musculus
Affinity Capture-MS Mus musculus
36 Pde4dip  
Affinity Capture-MS Mus musculus
37 GPS1 2873
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
38 MLXIPL  
Affinity Capture-Western Homo sapiens
39 MRPL47 57129
Affinity Capture-MS Homo sapiens
40 Hdac2  
Affinity Capture-MS Mus musculus
41 Phf21a  
Affinity Capture-MS Mus musculus
42 Dcaf11  
Affinity Capture-MS Mus musculus
43 Taf9  
Affinity Capture-MS Mus musculus
44 Dcaf12  
Affinity Capture-MS Mus musculus
45 GMDS 2762
Affinity Capture-MS Homo sapiens
46 RBX1 9978
Affinity Capture-MS Homo sapiens
47 Hdac7  
Affinity Capture-MS Mus musculus
48 CUL4B 8450
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
49 Elk1  
Affinity Capture-Western Mus musculus
Affinity Capture-Western Mus musculus
50 Dnmt1 13433
Affinity Capture-MS Mus musculus
51 Hist1h2bm 319186
Affinity Capture-MS Mus musculus
52 Wdr81  
Affinity Capture-MS Mus musculus
53 Med18  
Affinity Capture-Western Mus musculus
54 Polr2b  
Affinity Capture-Western Mus musculus
Affinity Capture-MS Mus musculus
55 Smarcc1  
Affinity Capture-MS Mus musculus
56 Dcaf4  
Affinity Capture-MS Mus musculus
57 Supt6  
Affinity Capture-MS Mus musculus
58 NUDC 10726
Affinity Capture-MS Homo sapiens
59 H2afy2 404634
Affinity Capture-MS Mus musculus
60 Wdr61  
Co-fractionation Mus musculus
Affinity Capture-MS Mus musculus
61 GTF3C2  
Affinity Capture-MS Homo sapiens
62 Hist1h1b 56702
Affinity Capture-MS Mus musculus
63 DCAF10  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
64 KIAA1522 57648
Affinity Capture-MS Homo sapiens
65 Hdac1 433759
Affinity Capture-MS Mus musculus
66 COPS3 8533
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
67 PRPF18  
Affinity Capture-MS Homo sapiens
68 PNP 4860
Affinity Capture-MS Homo sapiens
69 Med23  
Affinity Capture-MS Mus musculus
70 ZFC3H1 196441
Affinity Capture-MS Homo sapiens
71 Kdm1b  
Affinity Capture-MS Mus musculus
72 COPS7B 64708
Affinity Capture-MS Homo sapiens
73 Dcaf8  
Affinity Capture-MS Mus musculus
74 Eif4a3 192170
Affinity Capture-MS Mus musculus
75 Hist1h1c 50708
Affinity Capture-MS Mus musculus
76 Med1  
Affinity Capture-MS Mus musculus
77 Phf6  
Affinity Capture-MS Mus musculus
78 Brwd3  
Affinity Capture-MS Mus musculus
79 Gtf2i  
Affinity Capture-MS Mus musculus
80 DTL  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
81 Tubgcp2  
Co-fractionation Mus musculus
82 Wdr26 226757
Affinity Capture-MS Mus musculus
83 COPS7A 50813
Affinity Capture-MS Homo sapiens
84 Dcaf7  
Affinity Capture-MS Mus musculus
85 AMBRA1  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
86 Ccnt1  
Affinity Capture-Western Mus musculus
Affinity Capture-MS Mus musculus
87 Wdfy3  
Affinity Capture-MS Mus musculus
88 DCAF12 25853
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
89 UQCRC2 7385
Affinity Capture-MS Homo sapiens
90 Wdtc1  
Affinity Capture-MS Mus musculus
91 Trp53  
Affinity Capture-Western Mus musculus
92 HRNR 388697
Affinity Capture-MS Homo sapiens
93 ERCC8  
Affinity Capture-MS Homo sapiens
94 Wdr59  
Affinity Capture-MS Mus musculus
95 DDB2  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
96 ERCC4  
Affinity Capture-MS Homo sapiens
97 Med9  
Affinity Capture-MS Mus musculus
98 DCAF16 54876
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
99 KPNA2 3838
Affinity Capture-MS Homo sapiens
100 Stat1 20846
Affinity Capture-MS Mus musculus
101 DCAF8 50717
Affinity Capture-MS Homo sapiens
102 Smarcd3  
Affinity Capture-MS Mus musculus
103 DCAF6 55827
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
104 Phf1  
Affinity Capture-MS Mus musculus
105 Ddb2  
Affinity Capture-Western Mus musculus
Affinity Capture-MS Mus musculus
106 Nf2  
Co-fractionation Mus musculus
107 Eed  
Affinity Capture-MS Mus musculus
108 DCAF15  
Affinity Capture-MS Homo sapiens
109 Med14  
Affinity Capture-MS Mus musculus
110 Dcaf6  
Affinity Capture-MS Mus musculus
111 Cul4a  
Affinity Capture-Western Mus musculus
Affinity Capture-Western Mus musculus
Affinity Capture-MS Mus musculus
112 ZC3H3  
Affinity Capture-MS Homo sapiens
113 Med24  
Affinity Capture-MS Mus musculus
114 Taf1  
Affinity Capture-MS Mus musculus
115 Vprbp  
Affinity Capture-MS Mus musculus
Affinity Capture-MS Mus musculus
116 RCN1 5954
Affinity Capture-MS Homo sapiens
117 PHGDH 26227
Affinity Capture-MS Homo sapiens
118 Phf8 320595
Affinity Capture-MS Mus musculus
119 Dcaf10  
Affinity Capture-MS Mus musculus
120 Paf1 54624
Affinity Capture-MS Mus musculus
121 Med12  
Affinity Capture-MS Mus musculus
122 SIRT6  
Affinity Capture-MS Homo sapiens
123 Pou5f1  
Affinity Capture-MS Mus musculus
124 Ep300  
Affinity Capture-MS Mus musculus
125 TOR1AIP2 163590
Affinity Capture-MS Homo sapiens
126 Hist1h1e 50709
Affinity Capture-MS Mus musculus
127 Eif4a1 13681
Affinity Capture-MS Mus musculus
128 Wdr3  
Affinity Capture-MS Mus musculus
129 Carm1 59035
Affinity Capture-MS Mus musculus
130 Cdk9  
Affinity Capture-Western Mus musculus
Affinity Capture-MS Mus musculus
131 Med8  
Affinity Capture-Western Mus musculus
132 Wdr1 22388
Affinity Capture-MS Mus musculus
133 Wdr70  
Affinity Capture-MS Mus musculus
134 Kctd13  
Affinity Capture-MS Mus musculus
135 Kdm1a  
Affinity Capture-MS Mus musculus
136 DSC1 1823
Affinity Capture-MS Homo sapiens
137 DCAF11  
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
138 Iqcb1  
Affinity Capture-MS Mus musculus
139 Orai1  
Affinity Capture-Western Mus musculus
140 TRA2B 6434
Affinity Capture-MS Homo sapiens
141 Hdac6  
Affinity Capture-MS Mus musculus
142 Smarcb1  
Affinity Capture-MS Mus musculus
143 Sox2  
Affinity Capture-Western Mus musculus
Affinity Capture-Western Mus musculus
144 Wdfy1  
Affinity Capture-MS Mus musculus
145 Hist2h2ac 319176
Affinity Capture-MS Mus musculus
146 Fzr1  
Affinity Capture-MS Mus musculus
147 Ell  
Affinity Capture-MS Mus musculus
148 Wdr35  
Affinity Capture-MS Mus musculus
149 Crebbp  
Affinity Capture-MS Mus musculus
150 Wdr19  
Affinity Capture-MS Mus musculus
151 Cul4b  
Affinity Capture-Western Mus musculus
Affinity Capture-MS Mus musculus
Affinity Capture-Western Mus musculus
Affinity Capture-Western Mus musculus
Affinity Capture-MS Mus musculus
152 Dcaf15  
Affinity Capture-MS Mus musculus
153 CUL4A 8451
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
154 Sfpq 71514
Co-fractionation Mus musculus
155 Zbtb7b  
Affinity Capture-MS Mus musculus
156 Setd2  
Affinity Capture-MS Mus musculus
157 DCAF4  
Affinity Capture-MS Homo sapiens
158 Gtf2h4  
Affinity Capture-MS Mus musculus
159 COPS4 51138
Affinity Capture-MS Homo sapiens
Affinity Capture-MS Homo sapiens
160 Smarca4  
Affinity Capture-MS Mus musculus
161 Wdr11  
Affinity Capture-MS Mus musculus
162 Med16  
Affinity Capture-MS Mus musculus
163 Smarca1  
Affinity Capture-MS Mus musculus
164 TRPC4AP  
Affinity Capture-MS Homo sapiens
165 PAGE1  
Affinity Capture-MS Homo sapiens
166 FLG2 388698
Affinity Capture-MS Homo sapiens
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