Standard name
Human Ortholog
Description Ubiquitin-protein ligase (E3); interacts with Rpt4p and Rpt6p, two subunits of the 19S particle of the 26S proteasome; cytoplasmic E3 involved in the degradation of ubiquitin fusion proteins; relative distribution to the nucleus increases upon DNA replication stress
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Micrographs

ensLOC DeepLoc
Localization WT1 WT2 WT3 RAP60 RAP140 RAP220 RAP300 RAP380 RAP460 RAP540 RAP620 RAP700 HU80 HU120 HU160 rpd3Δ_1 rpd3Δ_2 rpd3Δ_3 WT1 WT2 WT3 AF100 AF140 AF180
Cortical Patches 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Bud 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.05 0.05
Bud Neck 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Bud Site 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 – – – – – –
Cell Periphery 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Cytoplasm 0.77 0.9 0.79 0.31 0.43 0.63 0.47 0.47 0.42 0.4 0.37 0.35 0.35 0.33 0.35 0.65 0.57 0.54 0.77 0.67 0.81 0.6 0.36 0.34
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.05 0.06 0 0 0 0 0 0
Endosome 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Golgi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.05 0 0 0 0 0 0
Mitochondria 0 0 0.08 0.28 0.12 0.25 0.32 0.31 0.51 0.52 0.59 0.61 0 0 0 0 0 0 0 0 0 0 0 0
Nucleus 0.07 0 0 0.11 0.11 0.07 0.08 0.13 0.11 0.11 0.12 0.13 0.17 0.22 0.24 0.1 0.16 0.09 0.19 0.23 0.07 0.28 0.37 0.29
Nuclear Periphery 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Nucleolus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Peroxisomes 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SpindlePole 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Vac/Vac Membrane 0.39 0.18 0.21 0.46 0.51 0.25 0.35 0.32 0.23 0.19 0.17 0.2 0.69 0.56 0.47 0.52 0.47 0.54 0 0.05 0 0.06 0.12 0.17
ensLOC DeepLoc
Localization WT1 WT2 WT3 RAP60 RAP140 RAP220 RAP300 RAP380 RAP460 RAP540 RAP620 RAP700 HU80 HU120 HU160 rpd3Δ_1 rpd3Δ_2 rpd3Δ_3 WT1 WT2 WT3 AF100 AF140 AF180
Cortical Patches 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 1
Bud 0 0 6 6 3 0 3 5 5 9 8 4 0 0 2 1 0 0 0 0 1 3 15 18
Bud Neck 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2
Bud Site 0 0 0 1 0 0 0 2 0 2 0 0 0 0 0 0 0 0 – – – – – –
Cell Periphery 0 0 0 0 0 2 1 1 0 3 3 3 0 0 0 0 1 0 0 0 0 0 0 0
Cytoplasm 68 110 111 54 126 144 208 230 129 156 76 76 47 80 97 82 92 107 93 83 124 80 115 122
Endoplasmic Reticulum 0 0 1 0 0 1 0 1 1 2 1 2 0 1 0 3 8 11 0 0 0 0 2 6
Endosome 0 0 0 6 13 0 9 8 0 1 0 0 2 2 2 3 2 2 0 1 1 2 10 12
Golgi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 5 10 0 0 1 0 0 1
Mitochondria 0 2 11 48 35 57 140 153 156 201 122 135 1 1 5 3 2 5 0 1 0 0 0 2
Nucleus 6 4 2 19 31 15 35 62 35 44 25 28 22 54 67 13 25 18 22 28 11 37 118 103
Nuclear Periphery 0 0 0 0 0 0 1 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 1 3
Nucleolus 0 0 0 0 0 0 1 1 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 2
Peroxisomes 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SpindlePole 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 2 8 11
Vac/Vac Membrane 34 22 29 80 151 57 155 156 70 72 35 45 92 136 128 66 75 106 1 6 5 7 39 59
Unique Cell Count 88 122 141 173 295 229 443 492 305 387 208 220 133 242 275 127 160 197 121 126 155 135 321 354
Labelled Cell Count 108 138 160 214 359 276 553 620 396 490 270 294 164 275 302 173 211 259 121 126 155 135 321 354


Cytoplasm, Nucleus

(Huh et al. Nature 2003 425:686)
Screen WT1 WT2 WT3 RAP60 RAP140 RAP220 RAP300 RAP380 RAP460 RAP540 RAP620 RAP700 HU80 HU120 HU160 rpd3Δ_1 rpd3Δ_2 rpd3Δ_3 AF100 AF140 AF180
Mean Cell GFP Intensity (1e-4) 10.5 6.5 5.9 5.4 5.8 5.4 5.3 5.4 4.8 4.7 4.7 4.4 8.5 8.6 7.6 11.5 12.8 13.1 8.5 8.3 9.2
Std Deviation (1e-4) 1.2 1.2 1.1 0.8 1.3 1.1 1.3 1.4 1.2 1.1 1.2 1.5 1.3 1.5 1.3 2.2 2.8 2.9 1.3 1.5 1.7
Intensity Change (Log2) – – – -0.13 -0.05 -0.13 -0.18 -0.14 -0.32 -0.34 -0.35 -0.43 0.52 0.54 0.35 0.95 1.1 1.14 0.52 0.48 0.63


Localization RAP60 RAP140 RAP220 RAP300 RAP380 RAP460 RAP540 RAP620 RAP700 HU80 HU120 HU160 rpd3Δ_1 rpd3Δ_2 rpd3Δ_3
Cortical Patches 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Bud -0.4 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Bud Neck 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Bud Site 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Cell Periphery 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Cytoplasm -8.4 -7.1 -3.2 -6.6 -6.7 -7.2 -7.8 -7.8 -8.2 -7.3 -8.6 -8.4 -2.6 -3.9 -4.6
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2.4
Endosome 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Golgi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Mitochondria 4.5 1.3 4.1 5.6 5.6 0 0 0 0 -2.8 0 -3.0 -2.0 -2.8 -2.2
Nucleus 3.4 3.4 2.3 2.8 3.9 3.6 3.6 3.6 3.8 4.4 5.6 6.0 3.1 4.3 3.0
Nuclear Periphery 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Nucleolus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Peroxisomes 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SpindlePole 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Vacuole 4.8 6.1 1.0 3.2 2.6 0.6 -0.5 -0.9 0 8.1 6.8 5.2 5.4 4.8 6.2

Images

Circle plot not available

Protein Concentration and Protein Localization Data

R1 R2 R3
G1 Pre-START G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Pre-START G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Pre-START G1 Post-START S/G2 Metaphase Anaphase Telophase
Concentration 3.5926 5.1785 4.43 3.8715 3.5201 4.7463 4.7454 7.1734 6.4647 6.6788 5.8377 6.6439 4.2122 5.9172 4.9296 4.8582 4.9453 4.9224
Actin 0.0256 0.0004 0.0112 0.045 0.0014 0.0003 0.0515 0.0003 0.0187 0.0243 0.0297 0.0021 0.0047 0.0005 0.0035 0.0005 0.0181 0.0021
Bud 0.0013 0.0004 0.0004 0.0008 0.0004 0.0002 0.0007 0.0005 0.0015 0.0033 0.0004 0.0003 0.001 0.0002 0.0047 0.0002 0.0002 0.0003
Bud Neck 0.0034 0.0013 0.0046 0.0251 0.0472 0.0023 0.0034 0.0004 0.002 0.0035 0.0064 0.0021 0.0134 0.0007 0.001 0.0013 0.001 0.0034
Bud Periphery 0.0017 0.0003 0.0004 0.0009 0.0003 0.0001 0.0007 0.0001 0.0005 0.0046 0.0006 0.0002 0.0005 0 0.0015 0.0001 0.0001 0.0001
Bud Site 0.0029 0.0146 0.0059 0.0038 0.0009 0.0002 0.0044 0.0014 0.002 0.0063 0.0009 0.0003 0.0051 0.0009 0.0019 0.0003 0.0005 0.0002
Cell Periphery 0.0003 0.0003 0.0003 0.0005 0.0002 0.0001 0.0002 0 0.0001 0.0003 0.0001 0 0.0001 0.0001 0.0001 0 0 0
Cytoplasm 0.2578 0.3779 0.465 0.3793 0.6019 0.2734 0.2449 0.4221 0.3391 0.534 0.5016 0.2073 0.3124 0.4029 0.4563 0.5566 0.6133 0.2215
Cytoplasmic Foci 0.0105 0.0009 0.013 0.0106 0.0031 0.0009 0.0238 0.0041 0.0101 0.0043 0.02 0.001 0.0237 0.0015 0.0047 0.0017 0.0037 0.0021
Eisosomes 0.0002 0 0.0001 0.0005 0 0 0.0009 0 0.0001 0.0004 0.0001 0 0.0001 0 0 0 0.0001 0
Endoplasmic Reticulum 0.0108 0.003 0.0042 0.0017 0.0071 0.0028 0.0083 0.0022 0.0021 0.002 0.0036 0.0017 0.0048 0.0052 0.0033 0.0059 0.0034 0.0025
Endosome 0.0209 0.001 0.0049 0.0078 0.0204 0.003 0.0389 0.0008 0.0127 0.0105 0.0215 0.0013 0.0078 0.0025 0.0034 0.0018 0.0038 0.0032
Golgi 0.0061 0.0001 0.0034 0.0109 0.0185 0.0006 0.0159 0 0.0068 0.0023 0.0074 0.0003 0.0016 0.0001 0.0019 0.0001 0.0028 0.0002
Lipid Particles 0.0053 0.0001 0.0095 0.0209 0.0012 0.0018 0.0175 0.0001 0.0026 0.0003 0.0228 0 0.0108 0.0002 0.0011 0.0001 0.0025 0.0001
Mitochondria 0.0151 0.0004 0.0023 0.0288 0.0098 0.0157 0.0111 0.0006 0.0038 0.0037 0.022 0.0054 0.0009 0.0004 0.0038 0.0004 0.0009 0.0089
None 0.0049 0.0096 0.0035 0.002 0.0014 0.0026 0.01 0.0027 0.0016 0.0031 0.0096 0.0006 0.0353 0.0213 0.0135 0.0154 0.0564 0.0021
Nuclear Periphery 0.0382 0.0147 0.0169 0.0117 0.0127 0.0144 0.0305 0.0116 0.0102 0.0088 0.0149 0.0135 0.0126 0.0166 0.0142 0.01 0.0104 0.0131
Nucleolus 0.0019 0.0011 0.0011 0.0024 0.0007 0.0006 0.0012 0.0013 0.0004 0.0003 0.0007 0.0005 0.0019 0.0005 0.0009 0.0004 0.0002 0.0008
Nucleus 0.5711 0.5671 0.4292 0.4173 0.2659 0.6742 0.5082 0.5465 0.5766 0.3755 0.306 0.7547 0.5336 0.5391 0.4639 0.3992 0.2751 0.7294
Peroxisomes 0.0052 0 0.0097 0.0183 0.0004 0.0004 0.0072 0.0001 0.0009 0.001 0.0149 0.0004 0.008 0.0001 0.0012 0.0001 0.0019 0.0007
Punctate Nuclear 0.0048 0.004 0.0112 0.0073 0.0025 0.0016 0.0163 0.0041 0.0065 0.006 0.0134 0.0068 0.0188 0.0056 0.0176 0.0048 0.0042 0.0075
Vacuole 0.0092 0.0029 0.0027 0.0034 0.0031 0.004 0.0026 0.0007 0.0012 0.0041 0.002 0.0011 0.0024 0.0017 0.0011 0.001 0.0011 0.0015
Vacuole Periphery 0.0029 0.0003 0.0004 0.0011 0.001 0.0008 0.0017 0.0002 0.0005 0.0013 0.0013 0.0002 0.0003 0.0002 0.0003 0.0002 0.0002 0.0003

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 26.3955 24.1498 27.6201 34.5912 26.0287 28.2387 27.8901 32.0536 34.2922 30.5171
Translational Efficiency 0.8325 0.7485 0.7298 0.7001 0.6091 0.7886 0.753 0.5383 0.6236 0.5712

Hit Data

Dataset Hit
Protein Concentration ✘
Protein Localization ✘
Gene Expression ✘
Translational Efficiency ✘
Standard name
Human Ortholog
Description Ubiquitin-protein ligase (E3); interacts with Rpt4p and Rpt6p, two subunits of the 19S particle of the 26S proteasome; cytoplasmic E3 involved in the degradation of ubiquitin fusion proteins; relative distribution to the nucleus increases upon DNA replication stress
Localization
Cell Percentages cytoplasm (76%)
Cell Cycle Regulation No
Subcompartmental Group cytoplasm-9

Ufd4

Ufd4


Nearest neighbours ( genes)

correlation threshold

0.6

1.0

0.80


Biological Process (Gene Ontology)
Molecular Function (Gene Ontology)
Cellular Component (Gene Ontology)

Endocytosis
Temp Actin Patch (Sac6-tdTomato) Cortical Patch (Sla1-GFP) Late Endosome (Snf7-GFP) Vacuole (Vph1-GFP)
37℃
RT
Cell Cycle Omics

CYCLoPs (Ufd4-GFP)
Gene / Allele Actin Patch (Sac6-tdTomato) Cortical Patch (Sla1-GFP) Late Endosome (Snf7-GFP) Vacuole (Sac6-tdTomato)
Gene Images
Gene Images
Images are not yet available
Images are not yet available