Standard name
Human Ortholog
Description Vacuolar protein component of the retromer; forms part of the multimeric membrane-associated retromer complex involved in vacuolar protein sorting along with Vps35p, Vps29p, Vps17p, and Vps5p; essential for endosome-to-Golgi retrograde protein transport; interacts with Ypt7p; protein abundance increases in response to 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 0.05 0 0 0 0 0 0 0 0
Bud 0 0 0.06 0 0.09 0.07 0.06 0.07 – 0.09 0.09 0.09 0.05 0.05 0 0.06 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 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 0.18 0.09 0.13 0.15 0.25 0.19 0.17 – 0.17 0.16 0.15 0.05 0.12 0.16 0.06 0.11 0.09 0 0 0 0 0 0
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 – 0 0 0 0.07 0 0 0.06 0 0 0 0 0 0 0 0
Endosome 0.47 0.24 0.31 0.23 0.24 0.08 0.08 0.11 – 0.12 0.12 0.12 0.56 0.54 0.57 0.58 0.55 0.59 0.67 0.45 0.58 0.69 0.67 0.75
Golgi 0 0.15 0 0 0 0 0 0 – 0 0 0 0.13 0.1 0.1 0.16 0.13 0.16 0.05 0 0 0 0 0
Mitochondria 0.27 0.23 0.57 0.68 0.66 0.64 0.75 0.69 – 0.64 0.68 0.67 0.18 0.05 0.09 0.16 0.13 0.15 0 0.05 0.08 0.05 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
Nuclear Periphery 0 0.1 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0.08 0.1 0 0 0
Nucleolus 0.19 0.05 0.05 0 0 0 0 0 – 0 0 0 0.05 0.05 0 0.11 0.08 0.1 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
SpindlePole 0.05 0 0.11 0 0.08 0.09 0.09 0.06 – 0.11 0.09 0.1 0.05 0.09 0.13 0.12 0.13 0.17 0 0 0 0 0 0
Vac/Vac Membrane 0.27 0.29 0.11 0.07 0.07 0 0.08 0.06 – 0.08 0.09 0.05 0.11 0.16 0.23 0.2 0.27 0.18 0.15 0.31 0.17 0.13 0.1 0.1
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 2 0 1 1 3 6 0 0 – 1 4 2 1 3 2 5 1 1 1 2 2 1 7 1
Bud 2 1 11 11 29 16 22 29 – 36 29 38 3 6 3 6 6 2 0 1 0 0 1 0
Bud Neck 0 0 0 0 0 1 0 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Bud Site 0 0 0 0 1 2 0 0 – 1 1 2 0 0 0 0 0 0 – – – – – –
Cell Periphery 0 0 0 1 0 0 2 2 – 5 3 3 0 0 0 1 0 0 0 0 0 0 0 0
Cytoplasm 4 27 17 33 47 56 72 75 – 72 53 60 3 16 18 6 17 16 1 1 0 3 3 2
Endoplasmic Reticulum 0 6 3 5 2 10 6 10 – 3 2 8 4 1 1 6 4 4 0 3 0 3 2 5
Endosome 53 36 62 58 76 18 32 46 – 48 39 47 31 70 65 59 85 103 87 81 122 123 144 174
Golgi 4 22 3 6 2 1 0 2 – 1 0 0 7 13 12 16 20 28 5 6 5 5 7 2
Mitochondria 31 34 113 171 206 147 292 297 – 263 227 269 10 7 10 16 20 26 3 9 15 9 7 9
Nucleus 2 3 0 1 1 1 1 5 – 3 0 3 0 0 0 0 0 0 0 0 0 0 0 1
Nuclear Periphery 3 15 5 0 1 1 0 2 – 1 0 0 0 2 0 2 2 1 3 13 20 2 5 3
Nucleolus 21 7 10 3 9 4 7 17 – 11 11 17 3 6 1 11 13 17 0 0 0 0 1 1
Peroxisomes 1 0 1 1 4 1 3 3 – 10 4 5 0 4 3 3 2 1 1 0 1 0 0 0
SpindlePole 6 0 21 11 25 20 34 27 – 45 29 41 3 11 15 12 20 30 0 1 3 3 2 3
Vac/Vac Membrane 31 42 22 18 23 6 30 27 – 33 30 21 6 21 26 20 42 31 20 56 34 22 22 22
Unique Cell Count 113 147 197 250 313 228 388 433 414 335 404 55 129 115 102 155 175 130 182 210 179 214 234
Labelled Cell Count 160 193 269 320 429 290 501 542 533 432 516 71 160 156 163 232 260 130 182 210 179 214 234


Endosome

(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) 8.3 9.0 6.1 5.8 5.5 5.0 4.7 5.2 – 4.9 5.1 5.1 8.0 8.8 9.1 10.6 10.7 11.7 9.5 10.0 9.8
Std Deviation (1e-4) 1.3 1.5 1.4 1.3 1.4 1.3 1.1 1.2 – 1.2 1.2 1.2 1.4 1.4 1.4 2.1 2.8 2.3 1.9 1.8 1.6
Intensity Change (Log2) – – – -0.08 -0.15 -0.28 -0.37 -0.25 – -0.33 -0.26 -0.25 0.38 0.52 0.57 0.8 0.81 0.93 0.63 0.71 0.68


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
Bud -0.6 1.5 0.6 0 0.5 – 0 1.3 1.6 0 -0.4 -1.2 0.1 -0.7 -2.3
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 1.5 2.1 4.3 3.2 2.9 – 2.9 2.4 2.1 0 1.1 1.9 -0.8 0.7 0.2
Endoplasmic Reticulum 0 0 1.7 0 0 – 0 0 0 0 0 0 0 0 0
Endosome -2.0 -1.8 -6.2 0 -6.4 – 0 -5.6 -5.9 3.4 4.1 4.3 4.4 4.4 5.3
Golgi 0 0 0 0 0 – 0 0 0 0 3.5 3.5 4.8 4.3 5.0
Mitochondria 2.4 1.9 1.5 0 2.7 – 0 2.4 2.2 -5.1 -9.5 -8.5 -6.9 -8.5 -8.5
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 -2.4 -1.3 -1.9 0 -0.7 – 0 -1.0 -0.5 0 -0.2 0 1.8 1.2 1.7
Peroxisomes 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0
SpindlePole -2.5 -1.0 -0.7 0 -1.9 – 0 -0.8 -0.2 -1.2 -0.6 0.6 0.3 0.7 1.8
Vacuole -1.5 -1.5 -3.5 -1.4 -2.1 – -1.3 -0.8 -2.7 -0.1 1.3 2.7 2.0 3.8 1.8

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 2.8657 4.1337 3.7021 3.3148 2.8929 3.7134 4.9494 6.0482 5.7454 5.4766 5.2738 5.5523 3.1482 4.1199 3.6142 3.301 3.0628 3.6607
Actin 0.0016 0.002 0.0121 0.0001 0.0011 0.0001 0.019 0.0001 0.0018 0.0011 0.0005 0.0021 0.0001 0.0001 0.0001 0.0056 0.0002 0.004
Bud 0.0002 0.0049 0.0014 0.0001 0.0001 0.0003 0.0001 0.0001 0.0005 0.0001 0.0001 0.0001 0.0001 0.0001 0.0001 0.0005 0.0001 0.0002
Bud Neck 0.0002 0.0005 0.0004 0.0001 0.0002 0.0003 0.0001 0.0002 0.0002 0.0002 0.0001 0.0005 0.0001 0.0002 0.0001 0.0002 0.0001 0.0002
Bud Periphery 0.0003 0.0021 0.0011 0.0001 0.0001 0.0006 0.0002 0.0002 0.001 0.0001 0.0001 0.0002 0.0001 0.0001 0.0001 0.0008 0.0002 0.0009
Bud Site 0.0004 0.0062 0.0024 0.0002 0.0002 0.0001 0.0002 0.0004 0.0004 0.0003 0.0001 0.0001 0.0001 0.0002 0.0001 0.0007 0.0001 0.0001
Cell Periphery 0.0001 0.0002 0.0001 0 0.0001 0.0001 0.0001 0.0001 0.0001 0 0 0.0001 0 0.0001 0 0.0002 0 0.0001
Cytoplasm 0.0039 0.0109 0.0064 0.0054 0.0057 0.0063 0.004 0.005 0.0036 0.0058 0.0044 0.0026 0.0024 0.0091 0.004 0.0018 0.0054 0.0025
Cytoplasmic Foci 0.1023 0.1255 0.0747 0.0762 0.0969 0.0768 0.0843 0.0559 0.0788 0.1127 0.0766 0.0514 0.0525 0.0836 0.0803 0.0205 0.0666 0.0578
Eisosomes 0 0 0.0001 0 0.0003 0 0 0 0.0002 0 0 0 0 0 0 0.0001 0 0.0002
Endoplasmic Reticulum 0.0037 0.0017 0.0022 0.0007 0.0014 0.0012 0.0015 0.0017 0.001 0.0017 0.0014 0.0021 0.0009 0.0021 0.0012 0.0075 0.0027 0.0018
Endosome 0.5993 0.6055 0.6998 0.7832 0.6758 0.7158 0.6693 0.6894 0.6797 0.6813 0.7309 0.709 0.6881 0.6875 0.6954 0.7073 0.6455 0.7163
Golgi 0.047 0.0554 0.0796 0.0519 0.0931 0.0672 0.0533 0.0736 0.1023 0.0501 0.0714 0.1106 0.064 0.0694 0.0872 0.0739 0.0727 0.0904
Lipid Particles 0.061 0.0262 0.0181 0.0107 0.0116 0.0228 0.0512 0.0265 0.0338 0.0373 0.0032 0.0256 0.0388 0.0294 0.0341 0.0044 0.0312 0.0198
Mitochondria 0.0269 0.0031 0.0085 0.015 0.0067 0.0062 0.0033 0.0236 0.0136 0.0094 0.0547 0.0109 0.0015 0.0014 0.0047 0.0097 0.0072 0.0116
None 0.0006 0.0012 0.0003 0.0002 0.0078 0.0003 0.0002 0.0001 0.0107 0.0004 0.0001 0.0008 0.0001 0.0002 0.0008 0.0004 0.0001 0.0004
Nuclear Periphery 0.0045 0.0031 0.0022 0.0015 0.0086 0.0038 0.0032 0.0068 0.0012 0.001 0.0009 0.0045 0.0014 0.004 0.0012 0.0116 0.0145 0.0044
Nucleolus 0.0003 0.0022 0.0003 0.0001 0.0013 0.0005 0.0002 0.0001 0.0003 0.0001 0 0.0003 0.0001 0.0003 0.0002 0.0001 0.0001 0.0001
Nucleus 0.0004 0.0025 0.0007 0.0002 0.002 0.0015 0.0002 0.0003 0.0003 0.0001 0.0001 0.0008 0.0002 0.0005 0.0003 0.0006 0.0003 0.0003
Peroxisomes 0.0369 0.0105 0.0112 0.0038 0.0296 0.0053 0.0163 0.0024 0.0137 0.0081 0.0106 0.0027 0.0031 0.0041 0.0022 0.0008 0.0011 0.002
Punctate Nuclear 0.0023 0.0013 0.0008 0.0002 0.004 0.0011 0.0006 0.0002 0.0004 0.0069 0.0001 0.0032 0.0001 0.0003 0.0006 0.0002 0.0003 0.0015
Vacuole 0.0575 0.0875 0.0437 0.0326 0.0281 0.0417 0.048 0.0646 0.03 0.0315 0.0193 0.0307 0.0778 0.0465 0.0461 0.0603 0.0529 0.0412
Vacuole Periphery 0.0508 0.0478 0.0338 0.0177 0.0253 0.0478 0.0447 0.0486 0.0263 0.0518 0.0253 0.0418 0.0686 0.061 0.0408 0.0928 0.0987 0.0443

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 18.3901 16.4396 14.7671 20.4349 10.6668 19.3473 22.3086 17.7139 19.8799 21.5096
Translational Efficiency 1.2823 1.5813 1.4763 1.1016 2.1359 1.638 1.1895 1.717 1.4672 1.3686

Hit Data

Dataset Hit
Protein Concentration ✘
Protein Localization ✘
Gene Expression ✘
Translational Efficiency ✘
Standard name
Human Ortholog
Description Vacuolar protein component of the retromer; forms part of the multimeric membrane-associated retromer complex involved in vacuolar protein sorting along with Vps35p, Vps29p, Vps17p, and Vps5p; essential for endosome-to-Golgi retrograde protein transport; interacts with Ypt7p; protein abundance increases in response to DNA replication stress
Localization
Cell Percentages endosome (33%), vacuolar membrane (9%), mixed (37%)
Cell Cycle Regulation No
Subcompartmental Group N/A

Pep8

Pep8


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 (Pep8-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