Standard name
Human Ortholog
Description Ubiquitin hydrolase; deubiquitinates intralumenal vesicle (ILVs) cargo proteins; required for recycling ubiquitin from proteasome-bound ubiquitinated intermediates, acts at the late endosome/prevacuolar compartment to recover ubiquitin from ubiquitinated membrane proteins destined for the vacuole; DOA4 has a paralog, UBP5, that arose from the whole genome duplication

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 0.05 0 0 0 0 0 0 0 0 0 0 0 0 0 0.08 0.05 0.06 0 0 0 0 0 0
Bud 0 0 0.09 0.05 0.08 0.1 0.14 0.12 0.13 0.11 0.1 0 0 0.09 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 0 0 0 0 0 0 0 0
Cytoplasm 0.32 0.61 0.25 0.11 0.12 0.2 0.17 0.19 0.19 0.13 0.15 0.49 0.4 0.64 0.54 0.46 0.48 0.09 0.2 0.26 0.39 0.14 0.08
Endoplasmic Reticulum 0.07 0.13 0.09 0 0 0 0 0 0 0 0 0 0 0 0.06 0 0.06 0 0 0 0 0 0
Endosome 0.54 0 0.09 0.31 0.09 0.15 0.14 0.05 0 0 0 0.44 0.55 0.22 0.3 0.38 0.37 0.65 0.44 0.39 0.32 0.53 0.64
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 0.26 0.46 0.3 0.59 0.42 0.41 0.65 0.63 0.71 0.7 0 0 0.08 0 0 0 0.1 0.15 0.14 0.06 0.08 0.08
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 0.05 0.07 0 0.11 0.07 0.05 0.06 0 0 0 0 0 0 0 0 0 0 0 0 0 0
SpindlePole 0.15 0.05 0.23 0.35 0.22 0.27 0.31 0.18 0.24 0.2 0.19 0.07 0.06 0 0.12 0.18 0.13 0 0 0.05 0 0.05 0
Vac/Vac Membrane 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.08 0.05 0 0.11 0.09 0.12 0.09 0.08
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 9 1 4 0 2 2 2 0 2 0 1 1 3 3 31 14 28 4 0 3 1 6 7
Bud 2 4 15 12 21 41 64 33 53 29 34 2 10 26 3 1 7 0 0 0 0 1 3
Bud Neck 0 2 0 6 1 3 6 3 3 1 1 0 0 0 1 0 2 1 0 1 1 2 1
Bud Site 0 0 0 0 0 0 8 5 9 5 8 0 0 0 0 0 0
Cell Periphery 0 0 0 0 0 1 1 0 1 0 0 0 0 0 4 1 1 0 0 0 0 0 0
Cytoplasm 63 83 42 29 31 78 77 52 78 35 55 67 106 189 213 124 212 21 6 47 55 40 27
Endoplasmic Reticulum 13 17 15 2 11 6 1 2 3 2 4 2 7 6 24 10 28 2 1 1 1 3 4
Endosome 107 0 15 81 22 61 63 14 16 7 15 61 144 66 120 104 165 166 13 71 44 151 221
Golgi 2 0 0 1 0 0 0 0 0 0 0 0 1 0 1 1 0 6 0 0 0 2 5
Mitochondria 6 35 79 80 151 164 182 173 265 186 249 2 1 24 7 6 6 26 4 26 8 22 27
Nucleus 0 1 0 1 1 1 2 0 0 1 0 0 2 0 0 1 1 0 0 0 0 0 0
Nuclear Periphery 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 1 2
Nucleolus 0 0 0 2 5 3 3 2 0 0 0 1 1 1 0 0 0 0 0 0 0 2 0
Peroxisomes 0 0 8 18 9 45 29 13 27 8 11 1 4 1 0 8 0 2 0 0 0 1 2
SpindlePole 30 7 39 94 57 107 139 47 101 52 67 9 16 5 46 48 59 11 0 9 6 13 9
Vac/Vac Membrane 3 0 1 7 4 8 4 3 3 5 7 6 6 10 15 23 20 9 3 16 16 24 28
Unique Cell Count 199 135 170 265 255 395 442 267 418 263 357 138 262 294 396 272 444 258 31 184 140 283 347
Labelled Cell Count 235 150 218 333 315 520 581 347 562 331 452 152 301 331 465 341 530 258 31 184 140 283 347


Ambiguous, 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) 5.3 3.6 3.7 3.9 3.6 3.4 3.6 3.3 3.3 3.3 3.1 5.5 5.5 4.8 6.6 7.3 7.6 5.1 5.0 5.6
Std Deviation (1e-4) 0.6 0.4 1.2 0.9 0.7 0.7 0.7 0.9 1.0 0.9 0.9 1.4 1.3 1.0 0.9 1.5 1.3 1.5 1.7 1.5
Intensity Change (Log2) 0.04 0.1 -0.01 -0.07 -0.02 -0.14 -0.15 -0.12 -0.2 0.6 0.61 0.42 0.86 1.01 1.08 0.5 0.47 0.64


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 3.0 0 2.6
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 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Cytoplasm -6.5 -10.6 -10.2 -9.1 -10.0 -8.4 -9.5 -10.0 -10.2 -2.1 -4.0 0.6 -1.6 -3.0 -2.8
Endoplasmic Reticulum 0 0 0 0 0 0 0 0 0 -3.6 -3.9 0 -2.5 -3.4 -2.4
Endosome 0 0 0 0 0 0 0 0 0 8.8 10.8 0 7.3 8.3 8.4
Golgi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Mitochondria 0 0 0 0 0 0 0 0 0 -5.9 -8.4 0 -9.0 -7.5 -9.7
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 0.5 0.4 0 2.2 3.5 2.6
Vacuole 0 0 0 0 0 0 0 0 0 0 0 0 0 3.5 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 1.5571 1.6804 1.1872 1.1345 1.2107 1.2133 1.146 1.9058 1.6271 1.6328 1.557 1.5821 -0.2337 0.287 0.2592 0.3331 0.152 0.1785
Actin 0.0381 0.005 0.0085 0.0017 0.0289 0.0016 0.0229 0.0011 0.022 0.0134 0.03 0.0076 0.0044 0.0003 0.0045 0.0001 0.0074 0.0014
Bud 0.0075 0.0082 0.0004 0.0002 0.0008 0.0007 0.0009 0.0001 0.0009 0.0003 0.0009 0.0003 0.0001 0.0003 0.0007 0.0001 0.0001 0.0001
Bud Neck 0.0042 0.0004 0.001 0.0005 0.0017 0.0037 0.006 0.0002 0.0004 0.0002 0.0008 0.001 0.0003 0.0005 0.0004 0.0001 0.0006 0.0005
Bud Periphery 0.0043 0.0047 0.0005 0.0002 0.0015 0.0012 0.0016 0.0001 0.0012 0.0002 0.002 0.0003 0.0001 0.0003 0.0028 0.0001 0.0001 0.0002
Bud Site 0.0171 0.0161 0.0022 0.0006 0.0027 0.0007 0.0091 0.0006 0.0031 0.0004 0.0022 0.0004 0.0006 0.0046 0.0012 0.0004 0.0009 0.0001
Cell Periphery 0.0016 0.0007 0.0005 0.0002 0.0005 0.0002 0.0009 0.0001 0.0001 0 0.0002 0.0001 0.0002 0.0005 0.0004 0.0001 0 0.0002
Cytoplasm 0.1604 0.26 0.2311 0.1084 0.1901 0.2421 0.201 0.37 0.3298 0.1999 0.2764 0.2627 0.2206 0.1931 0.2055 0.1873 0.356 0.2292
Cytoplasmic Foci 0.1957 0.2143 0.1907 0.2413 0.1752 0.2843 0.1752 0.1749 0.1783 0.1995 0.2203 0.2615 0.1585 0.2862 0.1464 0.2402 0.1202 0.2017
Eisosomes 0.0014 0.0001 0.0002 0.0001 0.0004 0.0001 0.0004 0 0.0001 0 0.0006 0 0.0002 0.0001 0.0004 0 0.0001 0.0001
Endoplasmic Reticulum 0.0116 0.0055 0.0085 0.0019 0.0069 0.0056 0.0076 0.0037 0.0051 0.0028 0.0031 0.006 0.0056 0.0032 0.0034 0.0038 0.0017 0.0038
Endosome 0.2277 0.2934 0.2477 0.4636 0.3149 0.275 0.2439 0.2214 0.2715 0.3904 0.2719 0.3342 0.1823 0.1661 0.1333 0.3319 0.1749 0.2322
Golgi 0.0264 0.0155 0.0223 0.0259 0.0492 0.0149 0.0177 0.0096 0.0168 0.0311 0.0338 0.0188 0.0074 0.0078 0.0065 0.0121 0.0048 0.0098
Lipid Particles 0.0555 0.0251 0.0176 0.0123 0.0432 0.0297 0.0132 0.003 0.0117 0.0318 0.0629 0.0064 0.0229 0.0043 0.0113 0.0044 0.0109 0.0246
Mitochondria 0.0368 0.0028 0.0157 0.0484 0.0559 0.006 0.023 0.0066 0.0087 0.0045 0.0399 0.0045 0.0015 0.001 0.0032 0.0017 0.0003 0.0076
None 0.1511 0.1224 0.2269 0.0514 0.0919 0.0998 0.2345 0.196 0.1242 0.0976 0.0237 0.0759 0.3575 0.3134 0.4548 0.1991 0.2639 0.271
Nuclear Periphery 0.0114 0.0011 0.0017 0.0015 0.0038 0.0019 0.0032 0.0006 0.0017 0.0017 0.0046 0.002 0.0022 0.0006 0.0009 0.002 0.001 0.0007
Nucleolus 0.0013 0.0003 0.0003 0.0005 0.001 0.0002 0.0016 0.0001 0.0002 0.0001 0.0004 0.0001 0.0005 0.0005 0.0003 0.0002 0.0002 0.0002
Nucleus 0.0048 0.0012 0.0009 0.0013 0.0012 0.001 0.0017 0.0005 0.0009 0.0005 0.0008 0.0007 0.0011 0.0009 0.0007 0.0012 0.0004 0.0004
Peroxisomes 0.0191 0.0048 0.0104 0.0027 0.0104 0.0175 0.021 0.0016 0.0122 0.0151 0.0147 0.0077 0.0198 0.0063 0.014 0.0035 0.0257 0.009
Punctate Nuclear 0.0108 0.0018 0.0018 0.0009 0.0055 0.0028 0.0033 0.0005 0.0014 0.0009 0.0017 0.0012 0.0061 0.0019 0.003 0.001 0.0269 0.0012
Vacuole 0.0103 0.0146 0.0091 0.0301 0.0106 0.0092 0.0092 0.0081 0.0077 0.007 0.0054 0.0066 0.0071 0.0074 0.0054 0.0088 0.0033 0.0048
Vacuole Periphery 0.0027 0.002 0.0019 0.0062 0.0037 0.002 0.0022 0.001 0.0019 0.0024 0.0037 0.0019 0.0011 0.0008 0.001 0.002 0.0006 0.0012

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 8.3321 7.803 5.2638 11.0502 6.6875 6.7413 10.669 13.0704 11.1816 12.3189
Translational Efficiency 0.5244 0.4976 0.7183 0.3956 0.6557 0.9738 0.6503 0.4658 0.6307 0.5602

Hit Data

Dataset Hit
Protein Concentration
Protein Localization
Gene Expression
Translational Efficiency
Standard name
Human Ortholog
Description Ubiquitin hydrolase; deubiquitinates intralumenal vesicle (ILVs) cargo proteins; required for recycling ubiquitin from proteasome-bound ubiquitinated intermediates, acts at the late endosome/prevacuolar compartment to recover ubiquitin from ubiquitinated membrane proteins destined for the vacuole; DOA4 has a paralog, UBP5, that arose from the whole genome duplication
Localization
Cell Percentages endosome (25%), cytoplasm (17%), mixed (23%)
Cell Cycle Regulation No
Subcompartmental Group N/A

Doa4

Doa4


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 (Doa4-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