Standard name
Human Ortholog
Description Component of a Cdc48p-complex involved in protein quality control; exhibits cytosolic and ER-membrane localization, with Cdc48p, during normal growth, and contributes to ER-associated degradation (ERAD) of specific substrates at a step after their ubiquitination; forms a mitochondrially-associated complex with Cdc48p and Npl4p under oxidative stress that is required for ubiquitin-mediated mitochondria-associated protein degradation (MAD); conserved in C. elegans and humans
DOWNLOAD

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
Bud 0 0 0 0 0 0 0 – 0 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 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 0.1 0.12 0.12 0 0 0 0 0 0
Cytoplasm 0.98 0.99 1.0 0.99 0.99 0.93 0.93 – 0.83 0.78 0.64 0.63 0.99 0.99 1.0 0.95 0.91 0.91 0.98 0.96 0.87 0.94 0.94 0.94
Endoplasmic Reticulum 0 0 0 0 0 0 0 – 0 0 0 0.06 0 0 0 0 0 0 0 0 0 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
Golgi 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 0 0 0.06 0.07 – 0.28 0.21 0.47 0.38 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
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 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
SpindlePole 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 0 0 0 0 0 0 0.08 0.05 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 0 0 0 0 0 1 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Bud 0 0 0 1 0 0 0 – 0 1 2 0 1 1 0 0 0 1 0 0 1 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 2 4 1 1 2 2 0 – 1 0 2 2 1 4 3 26 32 24 0 0 0 0 0 0
Cytoplasm 176 186 51 77 111 110 128 – 48 121 82 77 112 113 199 246 249 190 174 173 70 99 183 173
Endoplasmic Reticulum 0 1 1 0 1 3 1 – 1 4 3 7 1 1 0 10 11 6 0 1 2 0 1 0
Endosome 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 1 1 0 0 1 0 0 1 0
Golgi 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 2 4 0 1 0 0 0 0
Mitochondria 1 0 0 2 0 7 9 – 16 32 60 47 0 0 0 1 4 3 0 0 1 0 0 1
Nucleus 1 1 0 2 0 3 4 – 2 2 4 0 0 1 2 3 4 1 0 0 1 0 1 1
Nuclear Periphery 0 0 0 0 0 0 0 – 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0
Nucleolus 1 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 1 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
Vac/Vac Membrane 1 1 0 0 1 0 2 – 0 0 2 1 0 0 0 11 23 10 0 0 1 0 0 0
Unique Cell Count 179 188 51 78 112 118 138 58 155 129 123 113 114 200 259 274 208 178 181 81 105 195 184
Labelled Cell Count 182 193 53 83 115 126 144 68 160 156 134 115 120 204 299 327 239 178 181 81 105 195 184


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) 7.4 9.3 8.5 7.4 8.4 6.4 6.3 – 5.4 5.3 4.9 5.1 8.3 8.0 8.2 11.0 11.5 10.6 7.6 8.1 8.4
Std Deviation (1e-4) 0.8 1.0 1.3 1.6 1.5 1.1 1.4 – 1.4 0.7 0.7 0.7 1.0 0.8 1.5 1.8 2.4 1.7 1.4 1.1 1.0
Intensity Change (Log2) – – – -0.2 -0.02 -0.42 -0.43 – -0.67 -0.68 -0.78 -0.74 -0.04 -0.09 -0.04 0.37 0.44 0.31 -0.16 -0.07 -0.01


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 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
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 2.1 0
Cytoplasm -0.8 -0.7 -1.9 -2.0 – -3.1 -3.7 -5.0 -5.1 -0.7 -0.7 -0.5 -1.6 -2.2 -2.2
Endoplasmic Reticulum 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0
Endosome 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
Mitochondria 0 0 0 0 – 4.1 3.5 6.0 5.2 0 0 0 0 0 0
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 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
SpindlePole 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0
Vacuole 0 0 0 0 – 0 0 0 0 0 0 0 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 1.4649 2.6537 2.1654 1.6553 1.4613 2.1106 1.904 3.4035 3.0906 2.3567 2.4594 2.9945 2.0478 3.0833 2.7043 2.3836 2.3312 2.776
Actin 0.0093 0.001 0.0047 0.0022 0.0078 0.0055 0.0343 0.0017 0.0079 0.0286 0.0029 0.0027 0.0332 0.001 0.0511 0.0006 0.0183 0.0222
Bud 0.0014 0.0073 0.008 0.0003 0.003 0.0008 0.0007 0.0006 0.0003 0.0007 0.0006 0.0001 0.001 0.0012 0.0007 0.0065 0.0014 0.0006
Bud Neck 0.0023 0.0003 0.0008 0.0007 0.0011 0.0012 0.0014 0.0003 0.0006 0.0004 0.0005 0.0005 0.0022 0.0002 0.0008 0.0002 0.0044 0.0014
Bud Periphery 0.0017 0.0029 0.0027 0.0001 0.0056 0.0004 0.0009 0.0008 0.0002 0.0016 0.0006 0.0005 0.0012 0.0004 0.0011 0.0012 0.0015 0.001
Bud Site 0.0041 0.0139 0.0081 0.0007 0.0059 0.0001 0.0034 0.0014 0.003 0.0008 0.0017 0.0001 0.0031 0.0068 0.0023 0.0008 0.0163 0.0003
Cell Periphery 0.0003 0.0002 0.0004 0.0001 0.0004 0 0.0003 0.0002 0.0001 0.0003 0.0002 0.0001 0.0002 0.0001 0.0001 0.0004 0.0003 0.0001
Cytoplasm 0.7549 0.9307 0.8574 0.8332 0.8437 0.9255 0.7571 0.904 0.8121 0.7779 0.4946 0.9081 0.7916 0.9146 0.8412 0.9473 0.6661 0.8466
Cytoplasmic Foci 0.033 0.0045 0.0175 0.0201 0.0145 0.0123 0.0178 0.0057 0.0183 0.0127 0.0728 0.0196 0.0113 0.0118 0.0123 0.006 0.0395 0.0209
Eisosomes 0.0001 0 0.0001 0 0.0002 0 0.0002 0 0.0001 0.0007 0.0001 0.0002 0.0005 0 0.0002 0 0.0001 0.0001
Endoplasmic Reticulum 0.0056 0.0047 0.0028 0.0051 0.002 0.0015 0.005 0.0025 0.0067 0.007 0.0024 0.0028 0.0097 0.0037 0.0068 0.0096 0.0029 0.0092
Endosome 0.0455 0.005 0.0147 0.0263 0.0187 0.0094 0.0238 0.0088 0.0202 0.0183 0.1221 0.0064 0.0281 0.0028 0.0061 0.0066 0.0365 0.0254
Golgi 0.0151 0.0002 0.0058 0.014 0.0191 0.0034 0.0092 0.0016 0.0108 0.0077 0.0406 0.0027 0.0073 0.0006 0.0027 0.0003 0.0154 0.0032
Lipid Particles 0.012 0.0001 0.003 0.001 0.0085 0.0002 0.0148 0.0017 0.0097 0.0009 0.1361 0.0137 0.0077 0.0003 0.0024 0.0002 0.037 0.0016
Mitochondria 0.0175 0.0002 0.0153 0.0011 0.039 0.0102 0.0123 0.0114 0.0044 0.0108 0.0172 0.0203 0.0069 0.0002 0.0009 0.0003 0.0025 0.0019
None 0.0652 0.0227 0.0478 0.0849 0.0176 0.0237 0.0715 0.0489 0.084 0.1174 0.0042 0.0117 0.0628 0.0511 0.0588 0.0131 0.0784 0.0374
Nuclear Periphery 0.0059 0.0015 0.001 0.0022 0.0013 0.0006 0.0107 0.0012 0.0049 0.0034 0.0017 0.0018 0.0121 0.0008 0.0014 0.0018 0.0071 0.0126
Nucleolus 0.0004 0 0.0004 0.0001 0.0002 0 0.0007 0.0012 0.0002 0.0001 0.0009 0.0001 0.0003 0 0.0003 0.0001 0.0048 0.0002
Nucleus 0.0027 0.0017 0.0023 0.0033 0.0029 0.002 0.0141 0.0012 0.0011 0.0036 0.0009 0.0013 0.0052 0.0011 0.0014 0.002 0.0044 0.0039
Peroxisomes 0.0149 0 0.0035 0.0017 0.0043 0.0012 0.011 0.0019 0.0114 0.0003 0.0867 0.005 0.0068 0.0009 0.0023 0 0.0259 0.0011
Punctate Nuclear 0.0028 0.0004 0.0014 0.001 0.0008 0.0007 0.0021 0.0004 0.0019 0.0007 0.0017 0.0007 0.0033 0.0012 0.0057 0.0005 0.0322 0.0056
Vacuole 0.0037 0.0022 0.0019 0.0015 0.0028 0.0009 0.0063 0.0036 0.0015 0.0048 0.0071 0.0008 0.0035 0.001 0.0011 0.002 0.0041 0.0027
Vacuole Periphery 0.0016 0.0003 0.0004 0.0004 0.0007 0.0002 0.0023 0.0009 0.0005 0.0014 0.0046 0.0007 0.0019 0.0001 0.0002 0.0005 0.0009 0.0019

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 13.6546 16.6214 16.5735 15.269 15.067 7.5494 19.4318 15.5964 16.93 16.2179
Translational Efficiency 1.2414 1.4308 1.131 1.1571 1.1416 1.9931 0.8565 0.9439 0.9671 0.9869

Hit Data

Dataset Hit
Protein Concentration ✘
Protein Localization ✘
Gene Expression ✘
Translational Efficiency ✘
Standard name
Human Ortholog
Description Component of a Cdc48p-complex involved in protein quality control; exhibits cytosolic and ER-membrane localization, with Cdc48p, during normal growth, and contributes to ER-associated degradation (ERAD) of specific substrates at a step after their ubiquitination; forms a mitochondrially-associated complex with Cdc48p and Npl4p under oxidative stress that is required for ubiquitin-mediated mitochondria-associated protein degradation (MAD); conserved in C. elegans and humans
Localization
Cell Percentages cytoplasm (98%)
Cell Cycle Regulation No
Subcompartmental Group cytoplasm-9

Vms1

Vms1


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 (Vms1-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