S.ScerTFYeast transcription factor database Aaron Spivak
← All factors / TF RECORD

RTG3

YBL103C

View at SGD ↗

Basic helix-loop-helix-leucine zipper (bHLH/Zip) transcription factor that forms a complex with another bHLH/Zip protein, Rtg1p, to activate the retrograde (RTG) and TOR pathways

01 / RECOMMENDED MATRIX

Best-performing DNA-binding model.

RecommendedSource: Macisaac et. al
Fisher’s P-value6.88e-07
Information content10.36
Max PWM score8.68
Recommended cutoff7.94
View and copy the recommended matrices ↘
Position frequency matrix (PFM)
A | 0.620 0.001 0.001 0.997 0.001 0.103 0.224 0.448 
C | 0.052 0.001 0.001 0.001 0.997 0.069 0.758 0.121 
G | 0.259 0.001 0.997 0.001 0.001 0.310 0.001 0.190 
T | 0.069 0.997 0.001 0.001 0.001 0.518 0.017 0.241
Position count matrix (PCM)
A |  62   0   0  99   0  10  22  44 
C |   5   0   0   0  99   6  75  12 
G |  25   0  99   0   0  31   0  19 
T |   6  99   0   0   0  51   1  24
Position weight matrix (PWM)
A |  0.66 -5.77 -5.77  1.14 -5.77 -1.13 -0.36  0.34 
C | -1.24 -5.19 -5.19 -5.19  1.71 -0.96  1.44 -0.40 
G |  0.36 -5.19  1.71 -5.19 -5.19  0.54 -5.19  0.05 
T | -1.53  1.14 -5.77 -5.77 -5.77  0.48 -2.94 -0.28
02 / COMPARATIVE BENCHMARKS

Alternative candidate matrices 11

Historical matrix candidates from the original ScerTF database. Expand a source to inspect its original logo, scores, and matrix values.

RTG3_AFoat et. al.P = 2.23e-05View matrix ↘
Sequence logo for RTG3_A
Fisher’s P-value2.23e-05
Information content13.55
Max PWM score13.82
Recommended cutoff10.82
Position frequency matrix (PFM)
A | 0.10 0.08 0.49 0.12 0.80 0.04 0.68 0.01 0.97 0.04 0.08 0.10 
C | 0.03 0.27 0.05 0.79 0.15 0.94 0.01 0.94 0.01 0.61 0.01 0.50 
G | 0.04 0.01 0.39 0.09 0.01 0.01 0.21 0.04 0.01 0.01 0.90 0.04 
T | 0.83 0.64 0.07 0.01 0.04 0.01 0.11 0.01 0.01 0.35 0.01 0.36
Position count matrix (PCM)
A |  10   8  49  12  80   4  68   1  97   4   8  10 
C |   3  27   5  79  15  94   1  94   1  61   1  50 
G |   4   1  39   9   1   1  21   4   1   1  90   4 
T |  83  64   7   1   4   1  11   1   1  35   1  36
Position weight matrix (PWM)
A | -1.16 -1.39  0.43 -0.98  0.92 -2.08  0.75 -3.47  1.11 -2.08 -1.39 -1.16 
C | -1.79  0.41 -1.28  1.48 -0.18  1.65 -2.89  1.65 -2.89  1.22 -2.89  1.02 
G | -1.50 -2.89  0.77 -0.69 -2.89 -2.89  0.15 -1.50 -2.89 -2.89  1.61 -1.50 
T |  0.95  0.69 -1.52 -3.47 -2.08 -3.47 -1.07 -3.47 -3.47  0.09 -3.47  0.12
Foat et. al.
RTG3_BFoat et. al.P = 0.001619View matrix ↘
Sequence logo for RTG3_B
Fisher’s P-value0.001619
Information content7.808
Max PWM score7.03
Recommended cutoff6.07
Position frequency matrix (PFM)
A | 0.29 0.50 0.01 0.01 0.97 0.01 
C | 0.49 0.16 0.01 0.01 0.01 0.82 
G | 0.22 0.33 0.01 0.97 0.01 0.01 
T | 0.01 0.01 0.97 0.01 0.01 0.16
Position count matrix (PCM)
A |  28  50   1   1  97   1 
C |  49  16   1   1   1  82 
G |  22  33   1  97   1   1 
T |   1   1  97   1   1  16
Position weight matrix (PWM)
A | -0.10  0.45 -3.47 -3.47  1.11 -3.47 
C |  1.00 -0.12 -2.89 -2.89 -2.89  1.52 
G |  0.20  0.61 -2.89  1.68 -2.89 -2.89 
T | -3.47 -3.47  1.11 -3.47 -3.47 -0.69
Foat et. al.
RTG3_CFoat et. al.P = 4.65e-06View matrix ↘
Sequence logo for RTG3_C
Fisher’s P-value4.65e-06
Information content8.718
Max PWM score8.27
Recommended cutoff6.92
Position frequency matrix (PFM)
A | 0.11 0.27 0.58 0.01 0.01 0.97 0.01 
C | 0.03 0.50 0.11 0.01 0.01 0.01 0.88 
G | 0.58 0.20 0.31 0.01 0.97 0.01 0.01 
T | 0.28 0.02 0.01 0.97 0.01 0.01 0.11
Position count matrix (PCM)
A |  11  27  57   1   1  97   1 
C |   3  50  11   1   1   1  88 
G |  57  20  31   1  97   1   1 
T |  28   2   1  97   1   1  11
Position weight matrix (PWM)
A | -1.07 -0.17  0.59 -3.47 -3.47  1.11 -3.47 
C | -1.79  1.02 -0.49 -2.89 -2.89 -2.89  1.59 
G |  1.17  0.11  0.54 -2.89  1.68 -2.89 -2.89 
T | -0.13 -2.77 -3.47  1.11 -3.47 -3.47 -1.07
Foat et. al.
RTG3_DFoat et. al.P = 0.1912View matrix ↘
Sequence logo for RTG3_D
Fisher’s P-value0.1912
Information content11.51
Max PWM score12.34
Recommended cutoff9.41
Position frequency matrix (PFM)
A | 0.01 0.20 0.01 0.97 0.01 0.32 0.48 0.31 0.01 0.97 0.17 0.21 0.01 0.57 
C | 0.62 0.01 0.01 0.01 0.01 0.01 0.01 0.13 0.49 0.01 0.01 0.18 0.01 0.01 
G | 0.29 0.51 0.01 0.01 0.01 0.13 0.14 0.49 0.01 0.01 0.07 0.17 0.18 0.01 
T | 0.08 0.28 0.97 0.01 0.97 0.54 0.37 0.06 0.50 0.01 0.75 0.45 0.80 0.41
Position count matrix (PCM)
A |   1  20   1  97   1  32  48  31   1  97  17  21   1  56 
C |  62   1   1   1   1   1   1  13  49   1   1  18   1   1 
G |  28  51   1   1   1  13  14  49   1   1   7  17  18   1 
T |   8  28  97   1  97  54  37   6  50   1  75  45  80  41
Position weight matrix (PWM)
A | -3.47 -0.47 -3.47  1.11 -3.47  0.00  0.41 -0.03 -3.47  1.11 -0.63 -0.42 -3.47  0.58 
C |  1.24 -2.89 -2.89 -2.89 -2.89 -2.89 -2.89 -0.33  1.00 -2.89 -2.89  0.00 -2.89 -2.89 
G |  0.48  1.04 -2.89 -2.89 -2.89 -0.33 -0.25  1.00 -2.89 -2.89 -0.94 -0.06  0.00 -2.89 
T | -1.39 -0.13  1.11 -3.47  1.11  0.52  0.15 -1.67  0.45 -3.47  0.85  0.34  0.92  0.25
Foat et. al.
RTG3_EFoat et. al.P = 2.74e-07View matrix ↘
Sequence logo for RTG3_E
Fisher’s P-value2.74e-07
Information content16.58
Max PWM score18.64
Recommended cutoff9.48
Position frequency matrix (PFM)
A | 0.05 0.06 0.43 0.01 0.84 0.01 0.01 0.12 0.03 0.57 0.13 0.32 0.01 0.01 0.95 0.48 0.23 0.18 
C | 0.34 0.21 0.30 0.16 0.02 0.01 0.03 0.66 0.18 0.01 0.03 0.67 0.07 0.02 0.01 0.01 0.01 0.44 
G | 0.13 0.06 0.07 0.82 0.13 0.01 0.15 0.14 0.67 0.05 0.47 0.01 0.01 0.96 0.03 0.49 0.52 0.01 
T | 0.49 0.67 0.21 0.01 0.01 0.97 0.81 0.08 0.12 0.37 0.37 0.01 0.91 0.01 0.01 0.02 0.24 0.37
Position count matrix (PCM)
A |   5   6  43   1  84   1   1  12   3  56  13  32   1   1  95  48  23  18 
C |  34  21  30  16   2   1   3  66  18   1   3  67   7   2   1   1   1  44 
G |  13   6   7  82  13   1  15  14  67   5  47   1   1  96   3  49  52   1 
T |  49  67  21   1   1  97  81   8  12  37  37   1  91   1   1   2  24  37
Position weight matrix (PWM)
A | -1.86 -1.67  0.30 -3.47  0.97 -3.47 -3.47 -0.98 -2.37  0.58 -0.90  0.00 -3.47 -3.47  1.09  0.41 -0.33 -0.58 
C |  0.64  0.15  0.51 -0.12 -2.20 -2.89 -1.79  1.30  0.00 -2.89 -1.79  1.31 -0.94 -2.20 -2.89 -2.89 -2.89  0.89 
G | -0.33 -1.10 -0.94  1.52 -0.33 -2.89 -0.18 -0.25  1.31 -1.28  0.96 -2.89 -2.89  1.67 -1.79  1.00  1.06 -2.89 
T |  0.43  0.74 -0.42 -3.47 -3.47  1.11  0.93 -1.39 -0.98  0.15  0.15 -3.47  1.05 -3.47 -3.47 -2.77 -0.29  0.15
Foat et. al.
RTG3Harbison et. al.P = 0.02126View matrix ↘
Sequence logo for RTG3
Fisher’s P-value0.02126
Information content11.47
Max PWM score8.92
Recommended cutoff4.53
Position frequency matrix (PFM)
A | 0.012 0.012 0.012 0.012 0.965 0.012 
C | 0.012 0.012 0.012 0.964 0.012 0.964 
G | 0.964 0.964 0.012 0.012 0.012 0.012 
T | 0.012 0.012 0.965 0.012 0.012 0.012
Position count matrix (PCM)
A |   1   1   1   1  96   1 
C |   1   1   1  96   1  96 
G |  96  96   1   1   1   1 
T |   1   1  96   1   1   1
Position weight matrix (PWM)
A | -3.28 -3.28 -3.28 -3.28  1.10 -3.28 
C | -2.71 -2.71 -2.71  1.68 -2.71  1.68 
G |  1.68  1.68 -2.71 -2.71 -2.71 -2.71 
T | -3.28 -3.28  1.10 -3.28 -3.28 -3.28
Harbison et. al.
RTG3_AMorozov et. al.P = 0.0006008View matrix ↘
Sequence logo for RTG3_A
Fisher’s P-value0.0006008
Information content7.213
Max PWM score8.53
Recommended cutoff5.67
Position frequency matrix (PFM)
A | 0.105 0.098 0.021 0.049 0.070 0.722 0.039 
C | 0.491 0.107 0.099 0.172 0.822 0.147 0.823 
G | 0.331 0.705 0.821 0.071 0.086 0.079 0.085 
T | 0.073 0.090 0.059 0.708 0.022 0.052 0.053
Position count matrix (PCM)
A |  10   9   2   4   7  72   3 
C |  49  10   9  17  82  14  82 
G |  33  70  82   7   8   7   8 
T |   7   9   5  70   2   5   5
Position weight matrix (PWM)
A | -1.11 -1.18 -2.72 -1.88 -1.52  0.81 -2.10 
C |  1.00 -0.52 -0.60 -0.05  1.52 -0.20  1.52 
G |  0.61  1.37  1.52 -0.93 -0.74 -0.82 -0.75 
T | -1.48 -1.27 -1.69  0.79 -2.68 -1.82 -1.80
Morozov et. al.
RTG3_BMorozov et. al.P = 1.64e-05View matrix ↘
Sequence logo for RTG3_B
Fisher’s P-value1.64e-05
Information content7.599
Max PWM score8.72
Recommended cutoff6.94
Position frequency matrix (PFM)
A | 0.535 0.033 0.047 0.810 0.005 0.040 0.055 0.525 0.021 
C | 0.090 0.039 0.219 0.093 0.969 0.067 0.780 0.102 0.275 
G | 0.247 0.040 0.584 0.040 0.003 0.156 0.102 0.159 0.123 
T | 0.128 0.888 0.149 0.058 0.022 0.737 0.063 0.214 0.581
Position count matrix (PCM)
A |  53   3   4  81   0   4   5  52   2 
C |   9   3  21   9  96   6  78  10  27 
G |  24   4  58   4   0  15  10  15  12 
T |  12  88  14   5   2  73   6  21  58
Position weight matrix (PWM)
A |  0.51 -2.27 -1.92  0.93 -4.16 -2.08 -1.76  0.50 -2.72 
C | -0.69 -1.53  0.20 -0.66  1.68 -0.99  1.47 -0.57  0.42 
G |  0.32 -1.50  1.18 -1.50 -4.09 -0.14 -0.57 -0.12 -0.38 
T | -0.92  1.02 -0.76 -1.71 -2.68  0.83 -1.63 -0.40  0.60
Morozov et. al.
RTG3Pachkov et alP = 0.0007004View matrix ↘
Sequence logo for RTG3
Fisher’s P-value0.0007004
Information content10.94
Max PWM score8.2
Recommended cutoff5.28
Position frequency matrix (PFM)
A | 0.001 0.001 0.001 0.001 1.000 0.001 
C | 0.453 0.001 0.001 1.000 0.001 0.726 
G | 0.547 1.000 0.001 0.001 0.001 0.205 
T | 0.001 0.001 1.000 0.001 0.001 0.069
Position count matrix (PCM)
A |   0   0   0   0 100   0 
C |  45   0   0 100   0  72 
G |  54 100   0   0   0  20 
T |   0   0 100   0   0   6
Position weight matrix (PWM)
A | -5.77 -5.77 -5.77 -5.77  1.14 -5.77 
C |  0.92 -5.19 -5.19  1.71 -5.19  1.39 
G |  1.11  1.71 -5.19 -5.19 -5.19  0.13 
T | -5.77 -5.77  1.14 -5.77 -5.77 -1.53
Pachkov et al
RTG3Zhu et. al.P = 0.03116View matrix ↘
Sequence logo for RTG3
Fisher’s P-value0.03116
Information content13.41
Max PWM score13.68
Recommended cutoff6.96
Position frequency matrix (PFM)
A | 0.03 0.02 0.90 0.01 0.03 0.01 0.01 0.28 0.15 0.11 0.40 0.28 0.32 
C | 0.03 0.95 0.01 0.95 0.02 0.08 0.02 0.66 0.33 0.27 0.12 0.26 0.17 
G | 0.66 0.02 0.08 0.02 0.95 0.01 0.95 0.03 0.16 0.19 0.28 0.30 0.03 
T | 0.28 0.01 0.01 0.03 0.01 0.90 0.02 0.03 0.36 0.43 0.20 0.17 0.48
Position count matrix (PCM)
A |   3   2  90   1   3   1   1  28  15  11  40  28  32 
C |   3  95   1  95   2   8   2  66  33  27  12  26  17 
G |  66   2   8   2  95   1  95   3  16  19  28  30   3 
T |  28   1   1   3   1  90   2   3  36  43  20  17  48
Position weight matrix (PWM)
A | -2.37 -2.77  1.03 -3.47 -2.37 -3.47 -3.47 -0.13 -0.76 -1.07  0.22 -0.13  0.00 
C | -1.79  1.66 -2.89  1.66 -2.20 -0.81 -2.20  1.30  0.61  0.41 -0.41  0.37 -0.06 
G |  1.30 -2.20 -0.81 -2.20  1.66 -2.89  1.66 -1.79 -0.12  0.05  0.44  0.51 -1.79 
T | -0.13 -3.47 -3.47 -2.37 -3.47  1.03 -2.77 -2.37  0.12  0.30 -0.47 -0.63  0.41
Zhu et. al.
RTG3Zhao and StormoP = 1View matrix ↘
Sequence logo for RTG3
Fisher’s P-value1
Information content1.525
Max PWM score4.11
Recommended cutoff3.54
Position frequency matrix (PFM)
A | 0.270 0.260 0.248 0.235 0.254 0.250 0.251 0.170 
C | 0.252 0.263 0.276 0.296 0.247 0.271 0.243 0.051 
G | 0.217 0.207 0.203 0.196 0.198 0.189 0.193 0.755 
T | 0.262 0.271 0.274 0.273 0.301 0.290 0.312 0.024
Position count matrix (PCM)
A |  27  26  24  23  25  25  25  17 
C |  25  26  27  29  24  27  24   5 
G |  21  20  20  19  19  18  19  75 
T |  26  27  27  27  30  28  31   2
Position weight matrix (PWM)
A | -0.17 -0.21 -0.25 -0.31 -0.23 -0.25 -0.24 -0.63 
C |  0.34  0.38  0.43  0.50  0.32  0.41  0.30 -1.26 
G |  0.19  0.14  0.12  0.09  0.10  0.05  0.07  1.43 
T | -0.20 -0.17 -0.16 -0.16 -0.06 -0.10 -0.03 -2.59
Zhao and Stormo
03 / EXPERIMENTAL CONTEXT

Gene-level annotations and interactions.

Genes bound in ChIP-chip experiments 71 genes

YAL028W, YAL029C, YBL097W, YBR167C, YBR168W, YCR018C-A, YCR019W, YCR096C, YDL017W, YDL018C, YDL044C, YDL236W, YDL247W, YDR042C, YDR131C, YDR179C, YDR179W-A, YDR434W, YDR473C, YDR522C, YEL050C, YER002W, YER115C, YER129W, YER138C, YFL011W, YFR023W, YGL001C, YGL178W, YGR071C, YGR072W, YGR273C, YHR011W, YHR043C, YIL036W, YIL037C, YIR005W, YJL203W, YJL204C, YJR088C, YJR089W, YJR108W, YKL071W, YKL177W, YKL179C, YKR004C, YKR009C, YKR061W, YKR089C, YKR090W, YKR103W, YLR105C, YLR125W, YLR276C, YLR316C, YLR318W, YLR322W, YLR363C, YLR364W, YMR049C, YMR098C, YMR193W, YMR258C, YNL009W, YOL144W, YOL145C, YOR058C, YPL124W, YPL208W, YPL209C, YPR197C

Genes affected by TF deletion 245 genes

YER145C, YER178W, YHL016C, YIL116W, YKR039W, YOR225W, YOR227W, YDL131W, YGL009C, YHR146W, YLR027C, YLR029C, YGL231C, YHL047C, YLR217W, YMR009W, YOL016C, YOR220W, YOR226C, YGR120C, YLR089C, YLR061W, YLR435W, YOR036W, YOR382W, YPR138C, YDR342C, YDR098C, YDR100W, YFR003C, YHR053C, YHR055C, YIR034C, YKL016C, YJR149W, YLL034C, YMR105C, YNL147W, YOL136C, YPR184W, YAR064W, YAR068W, YBL027W, YDR339C, YER056C-A, YER030W, YHR208W, YIL052C, YLR154C, YMR284W, YMR314W, YMR316W, YBR061C, YBR129C, YFR004W, YKL011C, YLL002W, YLR304C, YMR072W, YMR074C, YMR135C, YNL142W, YOL139C, YOL109W, YOR086C, YBL026W, YDL191W, YDR279W, YER029C, YGL106W, YKL206C, YLR119W, YML024W, YMR255W, YNL302C, YPL111W, YPL081W, YKR022C, YNL030W, YOR261C, YOR203W, YFR044C, YKL119C, YLR038C, YOR385W, YBL092W, YDR071C, YDR077W, YIL117C, YNL055C, YNL090W, YOR198C, YOR230W, YOR202W, YJR148W, YLR200W, YBR164C, YDL135C, YDL075W, YEL051W, YJL126W, YLR438W, YOR010C, YOR046C, YMR145C, YOL118C, YOL150C, YOR327C, YOR357C, YBR297W, YHR214W, YLR194C, YMR260C, YPL090C, YPL154C, YBR101C, YBR105C, YDL012C, YDR167W, YDR139C, YGR012W, YHR030C, YJR119C, YJR150C, YMR112C, YMR142C, YOL143C, YOL149W, YOR298C-A, YPL273W, YBL028C, YCL025C, YDL201W, YER035W, YGR253C, YHR214W-A, YKL214C, YLR195C, YML063W, YML094W, YML095C-A, YMR321C, YNR001C, YNR003C, YPL117C, YPL091W, YBL103C, YCL074W, YER131W, YHR010W, YIL094C, YKR093W, YML131W, YOL058W, YBR207W, YDL082W, YDR210W, YGR136W, YLR416C, YLR420W, YMR178W, YNL255C, YOR051C, YOR021C, YLR262C, YLR292C, YLR294C, YNL064C, YNL096C, YNL037C, YOL032W, YOR210W, YAR018C, YDR209C, YGR135W, YGR137W, YKL120W, YLR075W, YMR241W, YOR052C, YBR082C, YBR084C-A, YCR097W, YDR112W, YFL028C, YGR019W, YHR071W, YKL030W, YKL001C, YMR120C, YOL126C, YOR333C, YOR383C, YJL167W, YLR136C, YMR300C, YCR096C, YDR111C, YDR481C, YOL119C, YCL031C, YDL241W, YER100W, YKL216W, YLR167W, YNR044W, YPL129W, YDR032C, YLR299W, YOR277C, YPL199C, YBR181C, YDL120W, YDR272W, YEL065W, YFR056C, YGL031C, YGR146C, YGR148C, YMR184W, YOR089C, YCR005C, YOR276W, YDL215C, YBR244W, YFR055W, YLR421C, YPL075W, YFL034C-A, YGR085C, YDL182W, YIL076W, YPL134C, YDR151C, YLR359W, YOR306C, YOR374W, YBR278W, YER073W, YGL098W, YJL200C, YKL160W, YNL007C, YNR050C, YOR184W

Genes supported by both experiments 1 genes

YCR096C

Predicted TF–TF partners 8 genes

ACA1, BAS1, GCN4, MBP1, RSC3, STB5, SWI4, SWI6

Explore 8 original interaction plots →