Standard name
Human Ortholog
Description Part of a Vps34p phosphatidylinositol 3-kinase complex; functions in carboxypeptidase Y (CPY) sorting; binds Vps30p and Vps34p to promote production of phosphatidylinositol 3-phosphate (PtdIns3P) which stimulates kinase activity; required for overflow degradation of misfolded proteins when ERAD is saturated
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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
Bud 0 0 0 0 0 0.05 0 0.06 – 0.09 0.12 0.09 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
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 0 0 0 0 0 0
Cytoplasm 0 0.05 0.05 0.07 0.06 0.1 0.07 0.08 – 0.09 0.13 0.08 0.05 0.05 0.05 – – 0.09 0 0 0 0 0 0
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 – – 0.05 0 0 0 0 0 0
Endosome 0.58 0.21 0.56 0.51 0.67 0.37 0.34 0.23 – 0.05 0.05 0.08 0.61 0.65 0.59 – – 0.66 0.81 0.77 0.82 0.83 0.85 0.84
Golgi 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 – – 0 0 0 0 0 0 0
Mitochondria 0.36 0.65 0.33 0.34 0.26 0.48 0.46 0.48 – 0.74 0.71 0.7 0 0 0 – – 0.12 0 0.05 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
Nuclear Periphery 0 0 0 0 0 0 0 0 – 0 0 0 0 0 0 – – 0 0 0 0 0 0 0
Nucleolus 0.08 0.05 0.07 0 0 0 0 0.05 – 0 0 0 0 0 0 – – 0.05 0 0 0 0 0 0
Peroxisomes 0 0 0.06 0.15 0.21 0.17 0.22 0.15 – 0.09 0.08 0.1 0 0 0 – – 0 0 0 0 0 0 0
SpindlePole 0.29 0.09 0.3 0.29 0.27 0.26 0.3 0.29 – 0.2 0.26 0.26 0.41 0.4 0.28 – – 0.32 0 0.06 0.06 0.06 0 0
Vac/Vac Membrane 0.15 0.12 0.08 0 0.07 0 0 0 – 0 0 0 0.14 0.14 0.33 – – 0.2 0 0.05 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 1 1 0 0 0 0 1 1 – 0 0 1 2 1 0 – – 0 1 1 3 0 1 3
Bud 7 5 6 16 19 32 32 55 – 49 54 43 1 1 0 – – 2 0 1 2 1 0 1
Bud Neck 0 0 0 2 1 0 1 2 – 0 0 0 2 1 2 – – 0 0 0 0 0 2 1
Bud Site 1 2 0 1 0 0 1 1 – 9 7 7 0 0 0 – – 0 – – – – – –
Cell Periphery 0 0 0 0 0 0 0 0 – 1 0 0 1 1 0 – – 0 0 0 0 0 0 0
Cytoplasm 5 10 20 32 34 56 55 66 – 53 56 36 14 14 14 – – 20 2 1 3 0 3 1
Endoplasmic Reticulum 1 8 2 4 1 1 0 2 – 1 0 0 2 5 2 – – 12 0 0 1 1 3 2
Endosome 99 42 249 238 368 215 265 198 – 29 22 36 182 195 159 – – 151 172 184 412 234 502 465
Golgi 0 1 0 0 0 0 0 0 – 0 0 0 0 0 0 – – 1 2 2 1 1 7 11
Mitochondria 61 127 145 157 144 283 354 411 – 424 307 317 1 1 3 – – 28 8 11 14 7 14 17
Nucleus 0 0 0 1 4 4 2 5 – 2 4 0 2 2 6 – – 1 0 0 0 0 0 0
Nuclear Periphery 3 4 4 3 0 0 0 0 – 0 1 1 2 2 1 – – 2 1 2 3 1 2 3
Nucleolus 13 10 30 16 13 16 19 39 – 12 7 4 10 10 2 – – 11 1 2 1 1 1 1
Peroxisomes 6 1 26 71 118 100 169 128 – 54 36 47 9 11 3 – – 2 6 2 14 4 10 11
SpindlePole 50 18 135 137 146 151 229 245 – 115 111 116 123 119 76 – – 74 7 13 28 16 20 14
Vac/Vac Membrane 25 24 34 18 37 24 30 17 – 7 3 11 43 43 88 – – 45 4 13 12 6 12 14
Unique Cell Count 170 196 444 465 550 589 774 848 570 432 453 297 301 269 229 212 241 503 282 588 556
Labelled Cell Count 272 253 651 696 885 882 1158 1170 756 608 619 394 406 356 349 212 241 503 282 588 556


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) 4.7 4.8 4.2 4.3 4.3 3.9 3.6 3.9 – 3.3 3.4 3.4 6.3 6.3 6.3 3.9 4.7 5.6 6.4 6.3 6.7
Std Deviation (1e-4) 0.7 1.0 0.8 1.2 1.5 1.4 0.8 1.0 – 0.9 1.1 0.8 1.1 1.1 0.8 0.9 1.0 1.2 1.9 1.3 1.5
Intensity Change (Log2) – – – 0.03 0.02 -0.14 -0.25 -0.14 – -0.36 -0.31 -0.31 0.56 0.56 0.58 -0.14 0.14 0.41 0.58 0.57 0.65


Localization RAP60 RAP140 RAP220 RAP300 RAP380 RAP460 RAP540 RAP620 RAP700 HU80 HU120 HU160 rpd3Δ_1 rpd3Δ_2 rpd3Δ_3
Actin – – – – – – – – – – – – – – –
Bud – – – – – – – – – – – – – – 0
Bud Neck – – – – – – – – – – – – – – 0
Bud Site – – – – – – – – – – – – – – 0
Cell Periphery – – – – – – – – – – – – – – 0
Cyto – – – – – – – – – – – – – – –
Endoplasmic Reticulum – – – – – – – – – – – – – – 0
Endosome – – – – – – – – – – – – – – 0
Golgi – – – – – – – – – – – – – – 0
Mitochondria – – – – – – – – – – – – – – 0
Nuclear Periphery – – – – – – – – – – – – – – 0
Nuc – – – – – – – – – – – – – – –
Nucleolus – – – – – – – – – – – – – – 0
Peroxisomes – – – – – – – – – – – – – – 0
SpindlePole – – – – – – – – – – – – – – 0
Vac – – – – – – – – – – – – – – –
Cortical Patches – – – – – – – – – – – – – – 0
Cytoplasm – – – – – – – – – – – – – – 0
Nucleus – – – – – – – – – – – – – – 0
Vacuole – – – – – – – – – – – – – – 4.6

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 1.1929 1.037 1.2206 0.8191 0.8441 0.9814 0.3274 1.4156 0.999 0.5532 0.6132 1.0833 -0.0031 1.1326 0.4838 0.6534 0.3336 0.3808
Actin 0.0395 0.0006 0.0297 0.0001 0.0013 0.0032 0.0099 0.0281 0.0158 0.0007 0.0499 0.0022 0.0178 0 0.0001 0.002 0.0008 0.0001
Bud 0.0006 0.0014 0.0002 0 0.0011 0.0002 0.0001 0.0001 0.0003 0.0001 0.0001 0.0001 0.0001 0 0.0001 0.0001 0 0
Bud Neck 0.0055 0.0003 0.0004 0.0004 0.0004 0.0009 0.0069 0.0023 0.0017 0.0002 0.0005 0.0007 0.0015 0.0003 0.0003 0.0002 0.0002 0.0002
Bud Periphery 0.0009 0.0009 0.0002 0 0.002 0.0002 0.0001 0.0001 0.0005 0.0001 0.0001 0.0001 0.0002 0 0.0001 0.0002 0 0
Bud Site 0.0088 0.0064 0.0012 0.0002 0.0018 0.0005 0.0008 0.0007 0.0026 0.0006 0.0012 0.0005 0.001 0.0002 0.0005 0.0003 0.0001 0.0001
Cell Periphery 0.0007 0.0003 0.0001 0 0.0002 0.0001 0.0001 0 0.0003 0 0.0001 0 0.0001 0.0001 0.0002 0.0001 0 0
Cytoplasm 0.021 0.0458 0.0056 0.0018 0.0433 0.0112 0.0059 0.0037 0.0065 0.0017 0.0077 0.0022 0.0069 0.0108 0.0035 0.0058 0.0011 0.0024
Cytoplasmic Foci 0.1993 0.1917 0.1816 0.1317 0.142 0.1906 0.2193 0.1898 0.2005 0.1734 0.1756 0.1756 0.1634 0.1949 0.1934 0.1669 0.1748 0.1706
Eisosomes 0.0005 0.0001 0.0001 0 0 0 0.0002 0 0.0007 0 0.0003 0 0.0005 0 0 0.0007 0 0
Endoplasmic Reticulum 0.012 0.0101 0.0249 0.0002 0.0096 0.0012 0.0013 0.0004 0.0009 0.0001 0.0008 0.0005 0.0015 0.0011 0.0007 0.0004 0.0003 0.0002
Endosome 0.3105 0.3694 0.4143 0.6475 0.5727 0.3971 0.3206 0.4177 0.3532 0.4227 0.3237 0.2797 0.3514 0.4234 0.3827 0.4979 0.5447 0.3462
Golgi 0.0273 0.0223 0.0635 0.0535 0.0342 0.0531 0.046 0.0523 0.0651 0.0657 0.0469 0.039 0.0382 0.0375 0.0487 0.0566 0.0749 0.0514
Lipid Particles 0.2107 0.2027 0.1848 0.1274 0.0713 0.2027 0.2426 0.1911 0.1873 0.1665 0.2295 0.3686 0.2739 0.2005 0.2593 0.1492 0.1046 0.355
Mitochondria 0.0096 0.005 0.0138 0.0024 0.0036 0.0039 0.0053 0.0046 0.0183 0.0082 0.0012 0.0031 0.0042 0.001 0.009 0.0041 0.0086 0.0013
None 0.0321 0.0513 0.0005 0.0002 0.007 0.0072 0.0128 0.0009 0.0306 0.0003 0.0417 0.0158 0.0379 0.0382 0.0086 0.0132 0.0001 0.0009
Nuclear Periphery 0.0162 0.0012 0.0006 0.0001 0.0427 0.007 0.0013 0.0004 0.0009 0.0001 0.0003 0.0011 0.0033 0.0009 0.0009 0.0018 0.0002 0.0003
Nucleolus 0.0091 0.0016 0.0003 0.0005 0.0006 0.001 0.0007 0.0005 0.0013 0.0004 0.0002 0.0003 0.0011 0.0005 0.0011 0.0032 0.0002 0.0002
Nucleus 0.0153 0.001 0.0002 0.0001 0.0238 0.0016 0.0006 0.0003 0.0007 0.0001 0.0001 0.0001 0.0014 0.0006 0.0002 0.0017 0 0.0001
Peroxisomes 0.0481 0.0523 0.0566 0.024 0.0208 0.0945 0.1158 0.0924 0.0994 0.1365 0.1152 0.1046 0.0769 0.0493 0.0709 0.0727 0.0825 0.0626
Punctate Nuclear 0.0142 0.0068 0.0039 0.0017 0.0031 0.0105 0.0045 0.0045 0.0038 0.0005 0.0017 0.0015 0.0094 0.0015 0.0075 0.007 0.0005 0.0038
Vacuole 0.0147 0.0252 0.0153 0.0062 0.0137 0.0095 0.004 0.0077 0.0071 0.0201 0.0021 0.0031 0.0076 0.0358 0.0097 0.0124 0.0039 0.0033
Vacuole Periphery 0.0032 0.0035 0.0023 0.0021 0.005 0.0038 0.0012 0.0022 0.0026 0.0021 0.0009 0.0013 0.0018 0.0034 0.0027 0.0034 0.0024 0.0013

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 8.7771 11.2088 8.3174 11.7155 7.5866 3.3418 8.8777 14.0235 11.1798 12.2658
Translational Efficiency 0.4366 0.4647 0.6261 0.4527 0.6006 1.1782 0.8398 0.5584 0.4668 0.5236

Hit Data

Dataset Hit
Protein Concentration ✘
Protein Localization ✔
Gene Expression ✘
Translational Efficiency ✘
Standard name
Human Ortholog
Description Part of a Vps34p phosphatidylinositol 3-kinase complex; functions in carboxypeptidase Y (CPY) sorting; binds Vps30p and Vps34p to promote production of phosphatidylinositol 3-phosphate (PtdIns3P) which stimulates kinase activity; required for overflow degradation of misfolded proteins when ERAD is saturated
Localization
Cell Percentages endosome (30%)
Cell Cycle Regulation No
Subcompartmental Group N/A

Vps38

Vps38


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 (Vps38-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