Standard name
Human Ortholog
Description Ubiquitin-conjugating enzyme (E2); key E2 partner with Ubc1p for the anaphase-promoting complex (APC); mediates degradation of abnormal or excess proteins, including calmodulin and histone H3; regulates levels of DNA Polymerase-{alpha} to promote efficient and accurate DNA replication; interacts with many SCF ubiquitin protein ligases; component of the cellular stress response; UBC4 has a paralog, UBC5, that arose from the whole genome duplication
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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 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 0.05 0 0.09 – 0.08 0.08 0.1 0.07 0 0 0 0 0 0 0 0 0 0 0 0
Cytoplasm 0.98 1.0 0.95 0.87 0.91 0.84 0.85 – 0.84 0.74 0.68 0.66 1.0 0.99 0.99 0.98 0.94 0.99 0.97 0.95 0.91 0.98 0.97 0.93
Endoplasmic Reticulum 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0.05 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 0 – 0 0.08 0.14 0.1 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 0.1 0 0.12 0.08 – 0.08 0.11 0.12 0.24 0 0 0 0 0.06 0 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 1 0 0 1 – 3 3 3 3 0 0 0 0 0 0 0 0 0 0 0 0
Bud 0 0 0 0 1 0 2 – 1 1 6 3 0 1 2 0 0 0 1 0 0 0 1 7
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 1 3 1 4 12 4 25 – 12 14 21 14 3 6 10 3 3 4 0 0 0 0 0 0
Cytoplasm 183 225 138 182 208 161 248 – 132 137 142 135 289 584 508 228 118 137 170 217 134 237 433 429
Endoplasmic Reticulum 3 0 1 7 7 2 8 – 2 6 5 7 0 2 2 5 1 7 0 0 0 0 2 4
Endosome 0 0 0 0 0 0 1 – 0 0 0 0 0 0 0 0 0 0 2 0 2 0 0 3
Golgi 1 0 0 0 1 0 0 – 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0
Mitochondria 0 0 0 0 1 2 2 – 7 15 30 21 0 0 1 0 1 0 0 0 0 0 0 0
Nucleus 0 0 2 1 4 4 3 – 1 5 1 5 0 1 0 0 0 1 0 3 1 0 3 2
Nuclear Periphery 0 0 0 0 0 0 0 – 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1
Nucleolus 0 0 0 0 0 1 0 – 2 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 2 1 6 21 9 23 23 – 12 20 26 49 1 1 0 3 7 2 0 0 2 0 1 5
Unique Cell Count 186 226 145 210 228 192 293 158 185 210 205 290 588 512 233 125 139 176 228 148 243 448 464
Labelled Cell Count 190 229 148 216 243 197 313 172 202 234 237 293 595 523 239 131 151 176 228 148 243 448 464


Cytoplasm, Nucleus

(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) 33.7 41.1 30.8 27.9 27.6 16.0 17.0 – 12.7 11.6 11.6 11.8 39.2 44.7 45.2 44.5 42.8 41.7 34.1 38.4 40.4
Std Deviation (1e-4) 6.9 8.8 8.8 5.6 6.5 4.5 4.3 – 3.1 2.5 2.5 2.7 8.6 9.4 10.7 13.5 13.8 12.6 7.0 8.2 12.1
Intensity Change (Log2) – – – -0.14 -0.16 -0.94 -0.86 – -1.27 -1.41 -1.41 -1.38 0.35 0.54 0.55 0.53 0.47 0.44 0.15 0.32 0.39


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 2.3 0 3.3 – 3.0 3.0 3.6 2.8 0 0 0 0 0 0
Cytoplasm -2.6 -1.4 -3.3 -3.2 – -3.2 -5.1 -6.3 -6.5 3.3 3.7 3.4 1.4 -0.3 1.6
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 – 0 3.5 4.8 4.0 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 2.0 -0.1 2.5 1.5 – 1.3 2.2 2.7 5.0 0 0 0 0 0.6 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 16.5948 27.2528 24.3387 22.6463 18.6319 23.6516 24.9426 31.8645 29.8957 26.8903 23.6596 30.8601 24.7563 34.6681 31.3042 31.4456 24.0513 31.7169
Actin 0.0323 0.0001 0.0045 0.0499 0.0274 0.0013 0.0197 0.0003 0.0064 0.0304 0.0194 0.0001 0.0625 0.0011 0.0272 0.0002 0.048 0.001
Bud 0.0023 0 0.0003 0.0005 0.0008 0.0001 0.0006 0.0001 0.0006 0.0003 0.0022 0 0.0007 0.001 0.0004 0.0001 0.0024 0.0001
Bud Neck 0.0021 0.0001 0.0005 0.0023 0.0015 0.0009 0.0013 0.0001 0.0007 0.0006 0.003 0.0005 0.0013 0.0002 0.0005 0.0001 0.003 0.0006
Bud Periphery 0.0035 0 0.0002 0.0007 0.0013 0.0001 0.0006 0.0001 0.0005 0.0003 0.0017 0 0.0006 0.0004 0.0004 0 0.0022 0.0002
Bud Site 0.0042 0 0.0025 0.0011 0.0035 0.0001 0.0032 0.0001 0.002 0.0005 0.012 0 0.0014 0.0012 0.0009 0 0.0028 0.0003
Cell Periphery 0.0012 0 0.0001 0.0001 0.0003 0 0.0002 0 0.0001 0.0002 0.0004 0 0.0002 0.0001 0.0001 0 0.0003 0
Cytoplasm 0.7513 0.9906 0.9228 0.8851 0.7166 0.9308 0.8786 0.9863 0.9285 0.9096 0.8022 0.9807 0.7463 0.9639 0.9081 0.9938 0.7145 0.9737
Cytoplasmic Foci 0.0325 0.0002 0.0108 0.004 0.013 0.0015 0.0141 0.0006 0.0086 0.0031 0.0282 0.0004 0.057 0.0093 0.0087 0.0004 0.0273 0.0024
Eisosomes 0.0005 0 0.0001 0.0002 0.0003 0 0.0003 0 0 0.0006 0.0003 0 0.0004 0 0.0001 0 0.0002 0
Endoplasmic Reticulum 0.0109 0.0003 0.0015 0.0006 0.002 0.0029 0.0034 0.0002 0.0035 0.0057 0.0034 0.0014 0.0104 0.0002 0.003 0.0001 0.0166 0.0004
Endosome 0.0205 0.0001 0.0144 0.0084 0.0525 0.0061 0.012 0.0002 0.0106 0.0077 0.0305 0.0002 0.0191 0.0065 0.0081 0.0001 0.0348 0.0032
Golgi 0.007 0 0.0071 0.0107 0.0331 0.0069 0.003 0 0.0041 0.0042 0.0085 0 0.0047 0.0041 0.0056 0 0.0388 0.004
Lipid Particles 0.0206 0 0.0066 0.0024 0.0459 0.005 0.0102 0.0001 0.0028 0.0028 0.0267 0 0.0053 0.0002 0.0045 0 0.0213 0.0029
Mitochondria 0.0241 0 0.0038 0.0091 0.0696 0.0028 0.0132 0.0048 0.0067 0.0078 0.0103 0.0001 0.0022 0.0013 0.0031 0.0001 0.0324 0.0017
None 0.0115 0.0002 0.0019 0.0003 0.0006 0.0003 0.0021 0.0002 0.0013 0.001 0.0081 0.0002 0.0065 0.0007 0.0023 0.0004 0.0018 0.0003
Nuclear Periphery 0.0168 0.0011 0.0065 0.0031 0.005 0.0097 0.0064 0.0009 0.0033 0.0058 0.0053 0.0031 0.0244 0.0007 0.0082 0.0004 0.0088 0.001
Nucleolus 0.0011 0 0.0003 0.0001 0.0014 0.0001 0.0005 0.0001 0.0014 0.0002 0.0028 0 0.0006 0.0005 0.0002 0 0.0003 0.0001
Nucleus 0.0158 0.007 0.0078 0.0106 0.0056 0.0288 0.0135 0.005 0.0085 0.0149 0.0117 0.0127 0.0231 0.0037 0.006 0.0041 0.0056 0.006
Peroxisomes 0.0187 0 0.0015 0.0088 0.0094 0.0005 0.0056 0.0003 0.0071 0.001 0.0061 0 0.0097 0.0006 0.0064 0 0.0263 0.001
Punctate Nuclear 0.0107 0.0001 0.0007 0.0003 0.0027 0.0005 0.0045 0.0001 0.0012 0.0011 0.0054 0.0002 0.019 0.0005 0.0021 0.0001 0.0048 0.0003
Vacuole 0.0085 0.0001 0.0043 0.0009 0.0045 0.0011 0.0051 0.0003 0.0016 0.0016 0.0092 0.0002 0.0038 0.0028 0.0027 0 0.0051 0.0005
Vacuole Periphery 0.0039 0 0.0018 0.0008 0.0031 0.0005 0.0021 0.0001 0.0006 0.0007 0.0025 0.0001 0.0011 0.0008 0.0013 0 0.0027 0.0002

Sequencing Data

R1 R2
G1 Post-START S/G2 Metaphase Anaphase Telophase G1 Post-START S/G2 Metaphase Anaphase Telophase
Gene Expression 273.9998 333.2054 227.6035 365.4768 300.8446 160.3615 319.6122 350.869 286.517 322.1843
Translational Efficiency 2.5741 2.3712 2.9864 1.2735 2.3443 4.9031 2.6227 2.1857 2.8963 2.4681

Hit Data

Dataset Hit
Protein Concentration ✘
Protein Localization ✘
Gene Expression ✘
Translational Efficiency ✘
Standard name
Human Ortholog
Description Ubiquitin-conjugating enzyme (E2); key E2 partner with Ubc1p for the anaphase-promoting complex (APC); mediates degradation of abnormal or excess proteins, including calmodulin and histone H3; regulates levels of DNA Polymerase-{alpha} to promote efficient and accurate DNA replication; interacts with many SCF ubiquitin protein ligases; component of the cellular stress response; UBC4 has a paralog, UBC5, that arose from the whole genome duplication
Localization
Cell Percentages cytoplasm (97%)
Cell Cycle Regulation No
Subcompartmental Group cytoplasm-7

Ubc4

Ubc4


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 (Ubc4-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