Standard name
Human Ortholog
Description Component of the GARP (Golgi-associated retrograde protein) complex; GARP is required for the recycling of proteins from endosomes to the late Golgi, and for mitosis after DNA damage induced checkpoint arrest; required for vacuolar protein sorting; members of the GARP complex are Vps51p-Vps52p-Vps53p-Vps54p; human ortholog is implicated in progressive cerebello-cerebral atrophy type 2 (PCCA2)
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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 0.09 0.05 0 0 0.07 0.09 0 0 0 0 0 0
Bud 0 0 0 0 0 0 0.05 0.06 – 0.06 0.08 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
Bud Site 0 0 0 0 0 0 0 0 – 0 0.05 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
Cytoplasm 0 0 0 0.05 0.05 0 0 0 – 0 0 0 0 0.06 0 0.25 0.17 0.09 0 0 0 0 0 0
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Endosome 0.17 0.05 0.24 0.14 0.26 0.06 0.05 0 – 0 0 0 0.19 0.31 0.29 0.46 0.47 0.43 0.23 0.27 0.23 0.2 0.17 0.16
Golgi 0.11 0.06 0 0 0 0 0 0 – 0 0 0 0.35 0.26 0.4 0 0.14 0.3 0.35 0.4 0.31 0.22 0.29 0.39
Mitochondria 0.74 0.9 0.63 0.72 0.65 0.83 0.83 0.84 – 0.88 0.9 0.87 0.38 0.34 0.17 0.12 0.2 0 0 0 0.05 0.05 0 0
Nucleus 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0.07 0.05 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
Nucleolus 0 0.05 0 0 0 0.06 0.09 0.08 – 0.07 0.05 0.05 0 0 0 0 0 0 0 0 0 0 0 0
Peroxisomes 0.15 0.07 0.4 0.22 0.24 0.12 0.17 0.15 – 0.1 0.1 0.14 0.11 0.25 0 0.12 0.1 0.13 0.31 0.21 0.35 0.46 0.45 0.36
SpindlePole 0.07 0 0.12 0.12 0.12 0.08 0.09 0.1 – 0.08 0.09 0.09 0.15 0.08 0.18 0.32 0.27 0.13 0 0 0 0 0 0
Vac/Vac Membrane 0 0 0 0 0 0 0 0 – 0 0 0 0 0.08 0.07 0 0.05 0.09 0 0 0 0 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 3 14 2 1 0 2 1 5 – 0 1 0 26 8 8 1 4 2 5 10 9 6 18 18
Bud 6 4 13 10 14 17 36 51 – 49 53 56 5 1 4 0 0 0 0 0 0 1 0 0
Bud Neck 0 0 1 0 0 0 0 1 – 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0
Bud Site 2 1 0 1 2 14 21 25 – 26 32 25 0 0 0 0 0 0 – – – – – –
Cell Periphery 1 1 2 0 1 1 1 2 – 7 3 4 1 1 1 2 0 0 0 0 0 0 0 0
Cytoplasm 4 4 20 15 19 15 16 16 – 17 12 2 9 10 9 23 10 2 1 0 0 0 0 1
Endoplasmic Reticulum 1 6 4 0 1 2 0 4 – 0 0 0 10 1 6 3 2 1 1 0 1 2 1 2
Endosome 47 16 113 46 99 33 40 27 – 8 6 17 58 50 59 42 28 10 72 88 113 67 81 92
Golgi 30 20 8 6 9 0 0 0 – 0 0 0 107 42 80 4 8 7 110 130 151 74 140 219
Mitochondria 200 289 301 234 244 453 613 715 – 724 573 629 114 55 34 11 12 1 10 12 25 17 20 17
Nucleus 1 0 3 1 1 1 2 8 – 6 2 2 0 1 1 6 3 0 1 0 0 0 0 0
Nuclear Periphery 0 4 1 1 1 3 4 4 – 6 3 3 4 0 0 0 0 0 0 0 0 0 0 0
Nucleolus 5 16 9 12 6 33 63 72 – 55 35 39 2 3 4 4 1 0 0 1 0 0 1 0
Peroxisomes 41 22 193 71 92 66 126 129 – 79 62 102 33 41 7 11 6 3 97 68 173 154 220 204
SpindlePole 20 11 58 39 47 43 64 82 – 69 56 67 45 13 37 29 16 3 6 8 13 8 3 3
Vac/Vac Membrane 7 4 4 0 8 3 10 8 – 3 4 5 8 13 15 2 3 2 1 1 2 1 1 0
Unique Cell Count 272 321 479 324 378 547 736 850 822 638 723 303 161 201 92 59 23 312 326 497 338 493 565
Labelled Cell Count 368 412 732 437 544 686 997 1149 1050 842 952 422 239 265 138 93 31 312 326 497 338 493 565


Early Golgi, 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) 7.2 6.5 6.2 5.7 5.6 4.7 4.6 4.8 – 4.2 4.2 4.4 7.6 7.8 7.9 7.4 8.5 9.9 7.8 8.2 8.2
Std Deviation (1e-4) 0.7 0.9 1.3 1.5 1.2 1.1 1.2 1.0 – 1.1 1.0 1.0 0.9 1.1 0.9 1.7 2.0 1.8 1.4 1.3 1.4
Intensity Change (Log2) – – – -0.12 -0.14 -0.4 -0.42 -0.37 – -0.56 -0.54 -0.48 0.29 0.33 0.35 0.26 0.45 0.68 0.34 0.4 0.41


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 6.0 0 0 0 0 0
Bud 0.3 0.8 0 0 0 – 0 0 0 -1.0 0 -0.6 0 0 0
Bud Neck 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
Cell Periphery 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0
Cytoplasm 0.3 0.6 -1.3 -2.0 -2.5 – -2.2 -2.3 -4.9 -0.9 1.1 0.2 6.9 0 0
Endoplasmic Reticulum 0 0 0 0 0 – 0 0 0 2.5 0 0 0 0 0
Endosome -3.3 0.9 0 0 0 – 0 0 0 -1.5 1.9 1.6 4.4 3.9 2.2
Golgi 0.2 0.7 0 0 0 – 0 0 0 12.9 10.0 13.5 0 0 0
Mitochondria 2.8 0.5 0 0 0 – 0 0 0 -6.9 -6.3 -10.9 -9.0 -6.2 -5.6
Nucleus 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
Nucleolus 1.6 -0.3 0 0 0 – 0 0 0 0 0 0 0 0 0
Peroxisomes -5.4 -4.9 0 0 0 – 0 0 0 -8.8 -3.4 -9.6 -5.2 -4.5 -2.6
SpindlePole 0 0.1 0 0 0 – 0 0 0 1.1 -1.4 2.2 4.7 3.2 0
Vacuole 0 1.6 0 0.8 0 – 0 0 0 0 0 4.8 0 0 0

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 3.0776 3.6173 3.328 3.0208 2.8036 3.098 5.0385 4.8269 4.4131 3.998 5.2051 4.608 3.8772 5.1581 4.5858 4.9932 4.2495 4.7255
Actin 0.0369 0.0108 0.0164 0.0064 0.0019 0.0163 0.0795 0.0156 0.0399 0.0044 0.0253 0.0184 0.0057 0.0029 0.0085 0.0026 0.0009 0.0086
Bud 0.0005 0.0004 0.0001 0.0001 0.0001 0.0002 0.0008 0.0008 0.0009 0 0.0013 0.0002 0.0001 0.0002 0.0002 0.0001 0 0.0009
Bud Neck 0.0017 0.0008 0.0009 0.0016 0.0005 0.0006 0.0037 0.0008 0.0012 0.0001 0.0006 0.0007 0.0002 0.0003 0.0002 0.0003 0.0002 0.0004
Bud Periphery 0.0005 0.0003 0.0001 0.0002 0.0001 0.0002 0.001 0.0005 0.0008 0 0.0019 0.0003 0.0001 0.0001 0.0001 0.0001 0 0.0003
Bud Site 0.003 0.0055 0.0006 0.0013 0.0022 0.0007 0.016 0.0137 0.0057 0.0001 0.0024 0.0005 0.0004 0.0013 0.0003 0.0004 0.0001 0.0002
Cell Periphery 0.0002 0.0001 0 0.0002 0 0.0001 0.0005 0.0001 0.0001 0 0.0001 0.0001 0 0 0 0 0 0.0001
Cytoplasm 0.0072 0.0034 0.0015 0.0042 0.002 0.0008 0.0064 0.011 0.0023 0.0007 0.0029 0.0021 0.0006 0.0029 0.0014 0.0005 0.0004 0.0042
Cytoplasmic Foci 0.1499 0.2328 0.1981 0.1316 0.2346 0.1355 0.1474 0.2283 0.1806 0.1192 0.113 0.1683 0.1381 0.2275 0.1647 0.16 0.2179 0.1355
Eisosomes 0.0003 0.0001 0.0001 0.0008 0 0 0.0008 0.0002 0.0001 0 0.0001 0.0001 0.0001 0.0001 0 0 0 0
Endoplasmic Reticulum 0.0043 0.0004 0.0009 0.0005 0.0001 0.0003 0.0048 0.0014 0.0009 0.0001 0.001 0.0005 0.0001 0.0004 0.0002 0.0001 0.0001 0.0001
Endosome 0.1652 0.2275 0.1692 0.1828 0.1719 0.1336 0.186 0.1923 0.1596 0.2535 0.1409 0.1219 0.1545 0.1894 0.1633 0.1001 0.1293 0.0977
Golgi 0.1713 0.2591 0.2561 0.317 0.3977 0.3752 0.1026 0.2015 0.2163 0.1387 0.1203 0.2333 0.174 0.274 0.2584 0.1972 0.2707 0.2218
Lipid Particles 0.1311 0.0548 0.0911 0.1392 0.0642 0.1226 0.1203 0.0714 0.1121 0.0386 0.2056 0.0847 0.1371 0.0439 0.0777 0.0834 0.0581 0.0847
Mitochondria 0.013 0.0215 0.0208 0.0076 0.0089 0.0252 0.0192 0.0126 0.0136 0.0043 0.0073 0.0186 0.0134 0.0066 0.0165 0.0301 0.0064 0.0134
None 0.0053 0.0002 0.0009 0.026 0.0002 0.0001 0.0085 0.0029 0.0005 0.0001 0.0022 0.0039 0.0003 0.0085 0.001 0.0001 0.0002 0.0002
Nuclear Periphery 0.0251 0.0002 0.0013 0.0012 0.0001 0.0002 0.0279 0.0006 0.0007 0 0.0248 0.0006 0.0001 0.0002 0.0001 0.0001 0 0.0001
Nucleolus 0.0005 0.0003 0.0002 0.0053 0.0001 0.0014 0.001 0.0003 0.0001 0 0.0023 0.0001 0.0001 0.0001 0 0.0001 0.0001 0.0001
Nucleus 0.0055 0.0002 0.0004 0.0053 0.0001 0.0002 0.0043 0.0003 0.0005 0 0.0576 0.0001 0.0001 0.0001 0 0 0 0.0003
Peroxisomes 0.2685 0.173 0.238 0.1559 0.1132 0.182 0.2501 0.2278 0.2608 0.4376 0.2638 0.3432 0.3647 0.2384 0.3053 0.4227 0.3107 0.4298
Punctate Nuclear 0.0047 0.0023 0.0015 0.0112 0.001 0.0028 0.0147 0.0065 0.0015 0.0003 0.0233 0.0012 0.0088 0.001 0.0004 0.0006 0.003 0.0004
Vacuole 0.0029 0.0049 0.0008 0.0008 0.0006 0.0011 0.0023 0.0099 0.0012 0.0013 0.0018 0.0006 0.0011 0.0015 0.0009 0.0008 0.001 0.0008
Vacuole Periphery 0.0024 0.0014 0.0008 0.0008 0.0006 0.0009 0.0021 0.0014 0.0007 0.0008 0.0014 0.0006 0.0006 0.0007 0.0006 0.0007 0.0007 0.0005

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 25.6969 23.5708 18.6763 21.9823 20.28 24.1194 25.4481 27.2631 22.3429 25.9217
Translational Efficiency 0.4983 0.5709 0.5804 0.4851 0.5298 0.4541 0.4794 0.4577 0.602 0.5423

Hit Data

Dataset Hit
Protein Concentration ✘
Protein Localization ✘
Gene Expression ✔
Translational Efficiency ✔
Standard name
Human Ortholog
Description Component of the GARP (Golgi-associated retrograde protein) complex; GARP is required for the recycling of proteins from endosomes to the late Golgi, and for mitosis after DNA damage induced checkpoint arrest; required for vacuolar protein sorting; members of the GARP complex are Vps51p-Vps52p-Vps53p-Vps54p; human ortholog is implicated in progressive cerebello-cerebral atrophy type 2 (PCCA2)
Localization
Cell Percentages Golgi (5%)
Cell Cycle Regulation No
Subcompartmental Group N/A

Vps53

Vps53


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 (Vps53-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