Standard name
Human Ortholog
Description Component of the nonsense-mediated mRNA decay (NMD) pathway; along with Nam7p and Nmd2p; involved in decay of mRNA containing nonsense codons; involved in telomere maintenance
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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 0.05 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 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 0.05 0 0 0 0.06 0.09 0.06 0 0 0 0 0 0
Cytoplasm 1.0 0.95 0.95 0.9 0.86 0.77 0.66 0.57 0.5 0.57 0.55 0.52 0.98 0.99 0.99 0.92 0.95 0.94 0.95 0.91 0.86 0.88 0.89 0.94
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.05 0 0 0.06 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 0 0 0 0 0 0
Mitochondria 0 0 0.05 0.3 0.28 0.54 0.58 0.62 0.68 0.69 0.68 0.69 0 0 0 0 0 0 0 0 0 0 0 0
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 0 0 0 0 0 0 0.05 0 0 0 0 0 0 0 0 0 0 0.05 0 0.05 0 0
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 1 1 0 1 0 0 1 0 0 1 1 0 0 0 0 1 1 0 2 0 1 0
Bud 1 1 0 0 3 4 14 5 8 24 24 21 0 0 0 0 0 0 0 0 0 0 1 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 1 0
Bud Site 0 0 0 0 0 0 0 0 1 0 1 2 0 0 0 0 0 0 – – – – – –
Cell Periphery 0 3 10 4 7 2 12 6 6 13 13 30 1 14 4 14 25 15 0 0 0 0 0 0
Cytoplasm 262 156 294 214 266 262 297 226 192 346 281 309 279 398 371 216 278 230 253 152 276 111 190 257
Endoplasmic Reticulum 1 4 8 2 3 1 4 3 6 7 2 2 4 2 0 8 10 12 4 1 18 3 2 6
Endosome 0 0 1 0 2 1 1 8 0 1 3 1 0 3 1 0 0 0 1 0 1 0 1 1
Golgi 0 1 0 1 1 0 0 0 0 0 0 0 0 0 0 1 2 0 0 0 2 0 1 0
Mitochondria 5 3 15 72 86 183 263 246 260 414 351 412 1 0 0 5 5 3 0 1 11 1 6 1
Nucleus 0 0 0 2 0 2 1 1 2 1 3 2 0 1 1 3 1 3 0 0 0 0 0 0
Nuclear Periphery 0 0 0 0 0 0 1 1 0 0 2 3 0 0 0 0 0 0 0 0 0 0 0 0
Nucleolus 0 0 0 0 1 0 0 0 0 0 2 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 1 0 1 0 0 0 0 0 0 0 0 0 0
Vac/Vac Membrane 1 1 4 1 2 2 13 9 19 21 18 23 1 1 1 9 7 10 1 7 3 6 3 2
Unique Cell Count 263 164 310 238 311 340 452 397 383 603 514 598 284 403 374 234 293 244 267 168 321 126 215 274
Labelled Cell Count 270 169 333 297 371 458 606 505 495 827 700 807 287 420 378 256 328 274 267 168 321 126 215 274


Cytoplasm

(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) 6.2 8.2 6.5 6.0 5.7 4.9 4.7 4.6 4.3 4.3 4.0 4.0 7.8 7.6 7.5 9.4 9.3 9.4 7.0 8.0 8.8
Std Deviation (1e-4) 0.6 1.0 1.1 1.3 1.4 1.6 1.3 1.1 1.2 1.0 0.9 0.8 1.2 0.9 1.3 1.7 1.3 1.3 1.1 0.9 1.6
Intensity Change (Log2) – – – -0.11 -0.18 -0.39 -0.47 -0.5 -0.58 -0.6 -0.69 -0.7 0.27 0.23 0.21 0.54 0.53 0.54 0.12 0.31 0.44


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 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 -1.1 -0.7 -2.5 0 0 0 0 0 0 -2.6 0.2 -2.0 1.6 2.8 1.6
Cytoplasm -2.2 -3.9 -6.4 -9.5 -11.3 -12.8 -11.7 -12.2 -13.1 2.2 3.1 3.5 -1.2 0 -0.3
Endoplasmic Reticulum 0 -1.5 0 0 0 0 0 0 0 -1.0 0 0 0.6 0.6 1.5
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 8.1 7.7 13.6 0 0 0 0 0 0 -3.4 -4.5 -4.3 -1.7 -2.1 -2.4
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 0 0 0
SpindlePole 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Vacuole 0 0 0 1.5 1.0 2.7 1.9 1.9 2.1 0 0 0 1.9 1.0 2.1

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 1.7699 2.5818 2.2789 2.1997 2.4704 2.4778 2.0073 2.7967 2.5593 2.2143 2.3919 2.4564 1.9005 2.5526 2.4008 2.3219 1.8981 2.0146
Actin 0.0112 0.0034 0.0065 0.0006 0.0007 0.0075 0.0125 0.0011 0.009 0.0013 0.0273 0.0014 0.0293 0.0004 0.0105 0.0088 0.0423 0.0019
Bud 0.0006 0.0098 0.0058 0.0007 0.0005 0.0016 0.002 0.0019 0.0031 0.0003 0.0027 0.0002 0.001 0.0044 0.0027 0.0029 0.0015 0.0007
Bud Neck 0.0008 0.0007 0.0006 0.0006 0.0007 0.0013 0.0056 0.0005 0.0011 0.0019 0.0015 0.0007 0.0038 0.0002 0.0021 0.0016 0.003 0.0009
Bud Periphery 0.0008 0.0029 0.0032 0.001 0.0005 0.0037 0.003 0.0012 0.0025 0.0001 0.0015 0.0002 0.0011 0.0017 0.0015 0.0042 0.002 0.0005
Bud Site 0.0082 0.0364 0.0046 0.0002 0.0003 0.0007 0.0044 0.0174 0.0079 0.0058 0.0051 0.0002 0.0036 0.0032 0.0069 0.0181 0.015 0.0003
Cell Periphery 0.0007 0.0006 0.0004 0.0004 0.0002 0.0002 0.0004 0.0003 0.0003 0.0001 0.0002 0 0.0005 0.0002 0.0001 0.0008 0.0006 0.0001
Cytoplasm 0.6992 0.7654 0.7675 0.8149 0.702 0.7652 0.6527 0.8896 0.8053 0.873 0.7276 0.8876 0.6935 0.9259 0.8543 0.7655 0.7306 0.8922
Cytoplasmic Foci 0.0446 0.0245 0.032 0.0294 0.0364 0.0352 0.0597 0.0184 0.0373 0.0374 0.036 0.0225 0.0593 0.0155 0.0267 0.0293 0.0487 0.0291
Eisosomes 0.0002 0.0001 0.0001 0 0 0.0001 0.0001 0.0001 0 0 0.0001 0 0.0003 0 0.0001 0.0002 0.0006 0
Endoplasmic Reticulum 0.0066 0.0039 0.0044 0.0026 0.0177 0.0031 0.0144 0.0043 0.0057 0.0026 0.0029 0.0039 0.0109 0.0026 0.0029 0.0049 0.0042 0.004
Endosome 0.0437 0.0261 0.0374 0.028 0.0429 0.0456 0.1111 0.015 0.049 0.0507 0.0712 0.0321 0.0738 0.0155 0.0392 0.0542 0.0665 0.0388
Golgi 0.006 0.0033 0.0036 0.0009 0.0017 0.0034 0.0221 0.0016 0.0098 0.003 0.0436 0.0068 0.0152 0.0016 0.0066 0.011 0.0094 0.0033
Lipid Particles 0.0054 0.0005 0.0013 0.0001 0.0003 0.0008 0.0151 0.0004 0.0021 0.0008 0.0292 0.004 0.0137 0.0001 0.0037 0.0069 0.0141 0.0004
Mitochondria 0.0027 0.0014 0.003 0.0007 0.0012 0.0026 0.0137 0.0006 0.0039 0.0007 0.0138 0.0081 0.0105 0.0011 0.0033 0.0381 0.0124 0.0083
None 0.1471 0.109 0.1155 0.111 0.182 0.116 0.0362 0.0388 0.0413 0.0093 0.012 0.0229 0.0443 0.0221 0.0149 0.0118 0.0207 0.0128
Nuclear Periphery 0.0017 0.0008 0.0009 0.0006 0.0012 0.001 0.0085 0.0006 0.0042 0.001 0.0023 0.0009 0.0053 0.0006 0.001 0.0015 0.0014 0.0005
Nucleolus 0.0004 0.0003 0.0003 0.0001 0.0001 0.0001 0.0004 0.0001 0.0003 0.0001 0.0002 0.0001 0.001 0 0.0002 0.0099 0.0003 0
Nucleus 0.0015 0.0015 0.0015 0.0012 0.0013 0.0011 0.0067 0.0012 0.0019 0.0016 0.0014 0.0011 0.0013 0.0009 0.0011 0.0035 0.0013 0.0007
Peroxisomes 0.0087 0.0005 0.0009 0.0002 0.0004 0.004 0.0123 0.0005 0.0042 0.0013 0.0143 0.0033 0.0138 0.0001 0.0141 0.0129 0.0106 0.0018
Punctate Nuclear 0.0019 0.001 0.0014 0.0003 0.0009 0.0008 0.0033 0.0005 0.002 0.0008 0.0028 0.0008 0.0102 0.0001 0.0014 0.0014 0.0033 0.0004
Vacuole 0.0069 0.0069 0.0077 0.0052 0.0074 0.0048 0.0117 0.0055 0.0074 0.0066 0.0027 0.0024 0.0059 0.0033 0.0055 0.01 0.0092 0.0025
Vacuole Periphery 0.001 0.0009 0.0014 0.0011 0.0015 0.0011 0.0043 0.0005 0.0017 0.0014 0.0012 0.0008 0.0019 0.0005 0.0012 0.0024 0.0023 0.0009

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 14.6931 14.4058 10.6898 12.2211 9.2179 14.2113 12.8521 13.5898 11.0179 13.2041
Translational Efficiency 1.4159 1.2338 1.4361 1.1407 1.6285 1.2198 1.3198 1.0264 1.3422 1.1833

Hit Data

Dataset Hit
Protein Concentration ✔
Protein Localization ✘
Gene Expression ✔
Translational Efficiency ✘

Micrographs

Cell Count

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
1668 1489 191 1342 1304 940 1153 97 2972 2429 1344 1439

Protein Abundance

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Mean 859.32 908.38 1102.71 931.10 851.05 905.26 1007.34 1153.00 855.69 907.17 1020.89 946.06
Standard Deviation 106.62 229.97 119.99 134.73 105.50 118.25 124.65 151.16 106.21 194.51 128.39 146.85
Intensity Change Log 2 — 0.080100 0.359786 0.115741 — 0.089088 0.243235 0.438077 — 0.084580 0.302969 0.285116

Localization Score (DeepLoc)

R1 R2 R1 & R2
WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14 WT UBP2 UBP14 UBP2UBP14
Actin 0.000237 0.000186 0.000705 0.000381 0.000192 0.000240 0.000166 0.002615 0.000217 0.000207 0.000242 0.000532
Bud Neck 0.004001 0.003308 0.002130 0.002095 0.003371 0.006224 0.000931 0.002675 0.003725 0.004437 0.001102 0.002134
Bud Site 0.015136 0.024643 0.018374 0.027394 0.015605 0.022370 0.007354 0.027958 0.015342 0.023763 0.008920 0.027432
Cell Periphery 0.000192 0.000186 0.000235 0.000111 0.000204 0.000160 0.000062 0.000108 0.000197 0.000176 0.000086 0.000111
Cytoplasm 0.520446* 0.649806* 0.572803* 0.704499* 0.598250* 0.554172* 0.747874* 0.444774* 0.554583* 0.612797* 0.722994* 0.686992*
Cytoplasmic Foci 0.307876* 0.196920* 0.106070 0.088253 0.267461* 0.216988* 0.070821 0.167514 0.290143* 0.204686* 0.075830 0.093595
Eisosomes 0.000092 0.000022 0.000058 0.000016 0.000068 0.000059 0.000017 0.000045 0.000082 0.000036 0.000023 0.000018
Endoplasmic Reticulum 0.005875 0.001316 0.002396 0.000479 0.007359 0.002784 0.000869 0.000336 0.006526 0.001884 0.001086 0.000469
Endosome 0.026752 0.019507 0.017308 0.007795 0.016666 0.028016 0.006509 0.020675 0.022327 0.022800 0.008043 0.008663
Golgi 0.022358 0.010229 0.000592 0.001508 0.019720 0.009323 0.000544 0.001247 0.021201 0.009878 0.000551 0.001491
Lipid Particles 0.004103 0.001459 0.002935 0.000871 0.003338 0.002757 0.000983 0.001601 0.003768 0.001961 0.001260 0.000920
Mitochondria 0.004249 0.002092 0.000055 0.000267 0.003671 0.001862 0.000398 0.008394 0.003996 0.002003 0.000349 0.000815
Mitotic Spindle 0.000944 0.002777 0.003085 0.003184 0.000197 0.002937 0.001996 0.006482 0.000616 0.002839 0.002151 0.003406
None 0.000532 0.002665 0.000394 0.001328 0.000779 0.001796 0.001281 0.000277 0.000640 0.002329 0.001155 0.001258
Nuclear Periphery 0.000065 0.000077 0.000401 0.000067 0.000067 0.000137 0.000266 0.000122 0.000066 0.000100 0.000285 0.000070
Nuclear Periphery Foci 0.000318 0.000440 0.012084 0.001153 0.000385 0.000362 0.003566 0.002658 0.000347 0.000410 0.004776 0.001254
Nucleolus 0.000308 0.000366 0.000116 0.000142 0.000134 0.000268 0.000147 0.000059 0.000231 0.000328 0.000143 0.000136
Nucleus 0.008109 0.019004 0.030744 0.010731 0.008092 0.011344 0.031209 0.006258 0.008101 0.016039 0.031143 0.010430
Peroxisomes 0.001517 0.001451 0.000789 0.001406 0.001014 0.001372 0.000359 0.011027 0.001297 0.001420 0.000420 0.002054
Vacuole 0.066891 0.057250 0.228186* 0.147246 0.043050 0.130085 0.124318 0.294475* 0.056430 0.085436 0.139079 0.157170
Vacuole Periphery 0.010000 0.006296 0.000542 0.001076 0.010376 0.006746 0.000331 0.000699 0.010165 0.006470 0.000361 0.001050

Localization Changes (T-score)

R1 R2 R1 & R2
UBP2_WT UBP14_WT UBP2UBP14_WT UBP2UBP14_UBP2 UBP2UBP14_UBP14 UBP2_WT UBP14_WT UBP2UBP14_WT UBP2UBP14_UBP2 UBP2UBP14_UBP14 UBP2_WT UBP14_WT UBP2UBP14_WT UBP2UBP14_UBP2 UBP2UBP14_UBP14
Actin 2.46 -4.30 -4.30 -6.24 3.17 -0.72 0.83 -1.28 -1.21 -1.30 0.34 -1.41 -3.55 -3.46 -2.72
Bud Neck 1.71 5.32 6.85 4.58 1.27 -2.83 7.28 3.30 4.24 -4.00 -1.63 11.85 7.27 5.84 -5.51
Bud Site -6.56 -1.53 -4.33 0.35 -1.79 -2.98 7.41 -1.89 0.04 -4.35 -6.74 7.02 -4.52 0.02 -7.72
Cell Periphery -0.23 -1.53 4.23 3.16 6.79 1.38 8.12 6.07 3.08 -1.44 0.49 8.14 6.14 3.81 -1.66
Cytoplasm -13.75 -0.82 -17.25 -3.26 -7.00 3.94 -11.83 6.26 4.67 10.15 -7.96 -16.09 -12.95 -5.66 2.62
Cytoplasmic Foci 16.14 25.99 39.89 19.85 1.65 6.36 34.82 11.69 7.57 -3.96 16.42 51.14 45.22 25.04 -4.06
Eisosomes 11.42 4.26 12.45 3.70 10.12 0.93 11.33 6.38 2.44 -4.50 8.32 14.36 16.07 4.71 4.59
Endoplasmic Reticulum 7.53 5.26 9.38 4.84 7.04 4.43 7.09 7.72 5.45 4.78 8.28 10.42 11.72 6.79 5.38
Endosome 4.42 6.12 16.36 9.55 5.69 -6.87 11.94 1.95 5.21 -1.62 -0.35 18.19 17.18 14.73 0.04
Golgi 11.39 25.88 22.96 11.76 -1.76 8.98 23.41 22.38 9.82 -0.41 14.47 34.06 29.20 13.81 -1.85
Lipid Particles 11.36 4.02 16.60 3.72 7.04 1.59 10.38 4.61 3.00 -0.88 8.92 15.74 18.60 6.64 2.50
Mitochondria 2.48 5.75 5.47 3.78 -1.37 2.73 5.68 0.17 -0.41 -0.91 3.46 7.24 6.78 3.92 -0.48
Mitotic Spindle -1.80 -1.58 -2.52 -0.23 -0.23 -2.81 -2.08 -1.19 0.01 -0.30 -3.05 -1.95 -3.16 -0.23 -0.73
None -4.22 1.19 -1.24 2.47 -1.52 -1.26 -1.55 3.45 1.85 3.45 -3.88 -2.01 -0.94 2.25 0.09
Nuclear Periphery -1.13 -10.87 -2.25 -0.66 10.44 -1.79 -6.19 -2.84 -0.59 4.12 -2.02 -9.76 -1.95 0.72 9.60
Nuclear Periphery Foci -1.91 -10.67 -9.63 -7.11 9.81 0.10 -9.91 -5.04 -5.59 2.08 -0.65 -15.17 -7.69 -8.84 11.87
Nucleolus -0.43 1.43 1.24 3.11 -1.24 -2.45 -0.61 6.58 3.85 6.19 -1.09 1.23 1.26 3.78 0.21
Nucleus -5.01 -9.40 -6.08 3.09 7.85 -3.49 -16.65 1.56 4.02 16.22 -5.72 -18.69 -6.61 2.87 15.25
Peroxisomes 0.44 3.80 1.84 1.45 -2.32 -3.18 9.78 -1.27 -1.15 -1.50 -1.05 10.31 -0.68 -0.19 -4.61
Vacuole 2.82 -12.33 -18.23 -19.52 5.33 -14.38 -18.81 -12.65 -9.49 -8.52 -9.19 -20.23 -22.76 -16.73 -2.40
Vacuole Periphery 4.50 14.50 13.66 10.16 -2.49 3.18 14.55 14.06 6.85 -0.25 5.54 20.65 18.87 11.40 -3.85
Standard name
Human Ortholog
Description Component of the nonsense-mediated mRNA decay (NMD) pathway; along with Nam7p and Nmd2p; involved in decay of mRNA containing nonsense codons; involved in telomere maintenance
Localization
Cell Percentages cytoplasm (97%)
Cell Cycle Regulation No
Subcompartmental Group cytoplasm-4

Upf3

Upf3


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 (Upf3-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