Standard name
Human Ortholog
Description Clathrin-coated vesicle component, regulator of endocytosis; copurifies with the DSC ubiquitin ligase complex; UBX (ubiquitin regulatory X) domain-containing protein that interacts with Cdc48p; required for efficient clathrin-mediated endocytosis; ortholog of fission yeast Ucp10
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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 0.07 0 0.07 0.07 0.09 0.08 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 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 0.79 0.82 0.8 0.73 0.72 0.66 0.56 0.62 0.57 0.56 0.49 0.55 0.93 0.97 0.96 0.44 0.67 0.52 0.25 0.2 0.12 0.37 0.36 0.27
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.06 0 0 0 0 0 0 0
Endosome 0 0 0.1 0.11 0.11 0 0 0.12 0.07 0 0 0 0 0 0 0.11 0 0.05 0.16 0.16 0.23 0.06 0.06 0.09
Golgi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Mitochondria 0.28 0.07 0.06 0.13 0.16 0.3 0.44 0.28 0.4 0.52 0.58 0.51 0 0 0 0 0 0 0.26 0.16 0.32 0.23 0.19 0.18
Nucleus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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 0.12 0.06 0 0.07 0.13 0.1 0.06 0.08 0.08 0.08 0.1 0 0 0.07 0.62 0.45 0.53 0.23 0.37 0.2 0.26 0.3 0.32
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 1 0 2 2 2 3 4 0 1 0 0 1 4 1 0 0 0 0 4 2 12 5 4 6
Bud 3 3 9 10 18 13 57 32 43 59 60 60 1 0 0 1 0 0 1 6 5 3 6 14
Bud Neck 1 0 0 0 1 0 1 0 0 1 0 1 1 2 1 0 0 0 1 1 1 0 1 3
Bud Site 0 0 0 0 0 0 0 0 1 2 3 1 0 0 0 0 0 0 – – – – – –
Cell Periphery 0 1 0 0 0 4 2 4 3 1 1 3 0 6 1 0 0 0 0 0 0 0 0 0
Cytoplasm 241 338 454 193 322 287 483 513 361 446 312 413 311 493 627 59 110 67 87 97 82 165 208 186
Endoplasmic Reticulum 6 8 5 2 2 4 3 2 0 0 3 8 3 7 2 5 10 4 8 12 17 8 9 21
Endosome 1 15 58 30 50 17 37 99 47 18 19 16 12 4 12 14 7 6 55 76 153 28 37 59
Golgi 0 3 1 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 4 8 24 3 3 7
Mitochondria 87 27 32 34 70 130 381 234 252 418 370 378 1 0 0 4 2 1 93 78 211 103 112 126
Nucleus 0 1 0 1 3 3 4 5 4 4 3 2 0 1 0 1 6 3 0 1 1 4 3 1
Nuclear Periphery 1 0 2 1 1 0 1 2 0 2 1 1 0 0 1 0 0 0 0 3 1 0 1 6
Nucleolus 0 0 1 0 0 0 4 2 2 2 1 1 0 0 0 0 0 0 0 0 0 0 0 1
Peroxisomes 0 0 7 1 2 0 3 8 0 1 1 1 1 0 6 0 0 0 3 0 2 1 0 0
SpindlePole 4 0 14 7 14 14 20 35 15 9 15 19 3 1 2 0 1 0 9 4 7 2 9 15
Vac/Vac Membrane 10 50 36 7 31 56 82 53 50 66 54 75 13 7 46 82 74 69 82 178 130 117 177 221
Unique Cell Count 307 410 571 265 446 433 859 832 633 798 639 748 336 506 656 133 165 129 355 477 663 451 583 686
Labelled Cell Count 355 446 621 288 516 531 1082 989 779 1030 843 980 351 522 698 166 210 150 355 477 663 451 583 686


Punctate Nuclear

(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) 3.5 5.1 4.6 4.6 4.8 8.0 4.3 4.3 4.4 4.2 4.0 4.1 6.0 5.7 5.4 6.8 6.7 6.9 5.9 6.2 6.4
Std Deviation (1e-4) 0.5 0.9 0.9 1.4 1.6 9.5 1.1 1.1 1.1 0.9 1.0 0.9 1.0 0.9 0.8 1.3 1.4 1.4 1.3 1.4 1.6
Intensity Change (Log2) – – – 0.0 0.08 0.81 -0.11 -0.08 -0.06 -0.13 -0.19 -0.18 0.38 0.33 0.23 0.58 0.56 0.6 0.35 0.43 0.48


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 0 1.5 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 -2.1 -2.7 -4.7 -9.1 -7.1 -8.3 -9.1 -11.1 -9.2 5.2 9.0 8.7 -8.2 -3.4 -6.5
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 0 0 0.8 0 0 0 0
Endosome 0 0 -3.7 0 0 0 0 0 0 -3.6 -6.6 -6.3 0.1 -2.4 -2.0
Golgi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Mitochondria 0 0 10.4 0 0 0 0 0 0 -4.1 -5.4 -6.1 -1.2 -2.4 -2.3
Nucleus 0 0 0 0 0 0 0 0 0 0 0 0 0 0 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 -0.5 0 0 0
SpindlePole 0 0 0.7 0 0 0 0 0 0 -1.7 -3.2 -3.3 0 0 0
Vacuole -2.2 0.4 3.6 2.2 0 1.1 1.4 1.4 2.4 -1.6 -4.1 0.5 15.4 12.2 13.6

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 2.0585 1.9796 1.7831 1.4214 1.7918 1.8847 0.8385 1.1162 0.9983 0.8511 0.686 1.1715 -0.1206 0.6182 0.1066 0.431 0.1971 0.342
Actin 0.024 0.0002 0.0053 0.0005 0.015 0.008 0.0194 0.0028 0.0035 0.0018 0.0033 0.0053 0.0051 0.0009 0.0012 0 0.0121 0.002
Bud 0.0006 0.0002 0.0006 0.0005 0.0008 0.0031 0.0003 0.0028 0.001 0.0051 0.0005 0.0017 0.0007 0.0019 0.0033 0.0005 0.0007 0.003
Bud Neck 0.0056 0.0001 0.0009 0.0003 0.0005 0.0013 0.0015 0.001 0.0045 0.0004 0.0007 0.001 0.0022 0.0004 0.0005 0.0003 0.0019 0.0016
Bud Periphery 0.0009 0.0002 0.0007 0.0006 0.0019 0.0035 0.0003 0.0033 0.001 0.0107 0.0004 0.004 0.0008 0.0014 0.0023 0.0003 0.0005 0.0043
Bud Site 0.0042 0.0007 0.0015 0.0004 0.001 0.0003 0.0015 0.0154 0.0101 0.0022 0.0004 0.001 0.0048 0.0069 0.008 0.0002 0.0008 0.0008
Cell Periphery 0.0007 0.0002 0.0004 0.0002 0.0003 0.0002 0.0003 0.0017 0.0002 0.0001 0.0001 0.0001 0.0003 0.0004 0.0002 0 0.0002 0.0001
Cytoplasm 0.1675 0.2957 0.2377 0.2875 0.2713 0.3137 0.2457 0.3359 0.3453 0.2669 0.3246 0.4367 0.3191 0.4005 0.3553 0.3774 0.2929 0.4181
Cytoplasmic Foci 0.0993 0.0556 0.0737 0.077 0.0809 0.0842 0.0937 0.0868 0.0711 0.0593 0.0749 0.0844 0.0941 0.0904 0.0935 0.1162 0.0763 0.1063
Eisosomes 0.0005 0.0001 0.0009 0.0001 0.0014 0.0001 0.0005 0.0001 0 0 0 0.0001 0.0002 0.0001 0.0001 0 0.0013 0
Endoplasmic Reticulum 0.0066 0.0029 0.0124 0.0035 0.0061 0.0094 0.0072 0.0055 0.0063 0.0045 0.0032 0.0051 0.0084 0.0038 0.0043 0.002 0.0048 0.0039
Endosome 0.1704 0.1036 0.1572 0.1902 0.3135 0.1444 0.1674 0.1702 0.1421 0.2956 0.3455 0.1788 0.2177 0.1732 0.2239 0.3329 0.2333 0.2106
Golgi 0.0157 0.0022 0.0057 0.0054 0.0137 0.0046 0.0078 0.0054 0.0064 0.0047 0.0107 0.0038 0.0057 0.006 0.0104 0.0086 0.0087 0.0048
Lipid Particles 0.0189 0.0024 0.0097 0.0033 0.0202 0.0036 0.0072 0.0023 0.0026 0.0014 0.011 0.0026 0.0056 0.002 0.0024 0.0017 0.0053 0.002
Mitochondria 0.0164 0.0011 0.0081 0.0064 0.0327 0.0028 0.0028 0.0036 0.0037 0.0061 0.003 0.0038 0.0045 0.0049 0.0031 0.0029 0.0037 0.004
None 0.3738 0.4997 0.4347 0.3714 0.1649 0.3738 0.3882 0.3197 0.359 0.1989 0.13 0.2309 0.2833 0.2715 0.2553 0.0947 0.2142 0.2086
Nuclear Periphery 0.0039 0.0014 0.0037 0.0024 0.0111 0.0058 0.0089 0.0037 0.004 0.0307 0.0065 0.006 0.0057 0.0013 0.0016 0.0009 0.0098 0.0016
Nucleolus 0.0033 0.0003 0.0009 0.0005 0.0016 0.0003 0.0007 0.0005 0.0005 0.0009 0.0005 0.0003 0.0005 0.0005 0.0004 0.0002 0.0046 0.0002
Nucleus 0.004 0.0012 0.0021 0.002 0.0036 0.0031 0.0056 0.003 0.0023 0.009 0.0031 0.0032 0.0026 0.0021 0.0019 0.0021 0.0736 0.0015
Peroxisomes 0.0096 0.0005 0.0046 0.0012 0.0026 0.0042 0.0074 0.0019 0.0015 0.0016 0.0032 0.0009 0.0023 0.0009 0.0013 0.0007 0.0021 0.0019
Punctate Nuclear 0.0242 0.0008 0.0023 0.0009 0.0047 0.0051 0.0066 0.0021 0.0018 0.0052 0.0117 0.0017 0.0018 0.0013 0.0015 0.0004 0.0158 0.0012
Vacuole 0.0447 0.0271 0.0291 0.0359 0.0376 0.023 0.0231 0.0274 0.0266 0.0692 0.0508 0.0228 0.028 0.0247 0.0245 0.0486 0.0297 0.0175
Vacuole Periphery 0.0055 0.0038 0.0077 0.0098 0.0146 0.0054 0.0038 0.0048 0.0064 0.0255 0.016 0.0058 0.0065 0.0049 0.0053 0.0092 0.0078 0.0058

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 6.4527 4.3262 6.4205 6.9928 6.2746 2.4184 6.9259 8.3649 9.3749 8.362
Translational Efficiency 0.5075 0.8929 0.5129 0.5587 0.5105 1.9765 0.6487 0.5225 0.6148 0.7096

Hit Data

Dataset Hit
Protein Concentration ✔
Protein Localization ✘
Gene Expression ✘
Translational Efficiency ✘
Standard name
Human Ortholog
Description Clathrin-coated vesicle component, regulator of endocytosis; copurifies with the DSC ubiquitin ligase complex; UBX (ubiquitin regulatory X) domain-containing protein that interacts with Cdc48p; required for efficient clathrin-mediated endocytosis; ortholog of fission yeast Ucp10
Localization
Cell Percentages —
Cell Cycle Regulation No
Subcompartmental Group N/A

Ubx3

Ubx3


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 (Ubx3-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