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Transcription factors with binding sites determined by matrix-based screenings
Genomic screenings with the matrices from transcription factors listed below were performed using the thresholds stated in the table.
Factor Family Species Max. Score Threshold No. of Matches AGI Reference
CBF
(Target genes) 
- other several species 7.24 3.98 52,737 - Shahmuradov IA, Gammerman AJ, Hancock JM, Bramley PM, Solovyev VV. 2003 PlantProm: a database of plant promoter sequences. Nucleic Acids Res 31: 114-7. PubMed 
TBP
(Target genes) 
- other several species 10.98 5.16 16,229 - Shahmuradov IA, Gammerman AJ, Hancock JM, Bramley PM, Solovyev VV. 2003 PlantProm: a database of plant promoter sequences. Nucleic Acids Res 31: 114-7. PubMed 
ARF1
(Target genes) 
ABI3/VP1 Arabidopsis thaliana 14.23 9.05 4,633 At1g59750 Ulmasov T, Hagen G, Guilfoyle TJ. 1997. ARF1, a transcription factor that binds to auxin response elements. Science 276: 1865-8. PubMed 
AtLEC2
(Target genes) 
ABI3/VP1 Arabidopsis thaliana 10.73 5.41 139,281 At1g28300 Braybrook SA, Stone SL, Park S, Bui AQ, Le BH, Fischer RL, Goldberg RB, Harada JJ. 2006. Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis. Proc Natl Acad Sci U S A 103: 3468-73. PubMed 
REM1(1)
(Target genes) 
ABI3/VP1 Arabidopsis thaliana 10.63 5.52 87,514 At4g31610 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
REM1(2)
(Target genes) 
ABI3/VP1 Arabidopsis thaliana 12.31 6.11 42,733 At4g31610 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ABI4(1)
(Target genes) 
AP2/EREBP Zea mays 13.83 8.83 12,816 - Niu X, Helentjaris T, Bate NJ. 2002 Maize ABI4 binds coupling element1 in abscisic acid and sugar response genes. Plant Cell 14: 2565-75. PubMed 
ABI4(2)
(Target genes) 
AP2/EREBP Zea mays 12.9 8.03 11,948 - Niu X, Helentjaris T, Bate NJ. 2002 Maize ABI4 binds coupling element1 in abscisic acid and sugar response genes. Plant Cell 14: 2565-75. PubMed 
ANT
(Target genes) 
AP2/EREBP Arabidopsis thaliana 18.39 11.06 294 At4g37750 DNA binding properties of the Arabidopsis floral development protein AINTEGUMENTA. 2000 Erratum in: Nucleic Acids Res 2001 Mar 1;29(5):1261. Nucleic Acids Res 28: 4076-82. PubMed 
At1g77200
(Target genes) 
AP2/EREBP Arabidopsis thaliana 12.98 8.44 6,420 At1g77200 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ATERF1(1)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 12.97 5.42 150,504 At4g17500 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ATERF1(2)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 12.18 6.47 46,025 At4g17500 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
DDF1
(Target genes) 
AP2/EREBP Arabidopsis thaliana 12.65 8.52 4,526 At1g12610 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
DEAR3(1)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 11.84 4.93 246,166 At2g23340 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
DEAR3(2)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 11.86 5.92 65,966 At2g23340 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
DEAR4(1)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 12.88 8.32 5,100 At4g36900 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
DEAR4(2)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 14.1 8.21 14,148 At4g36900 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
DREB2C(1)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 15.95 10.55 1,721 At2g40340 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
DREB2C(2)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 12.45 7.37 21,590 At2g40340 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ERF1
(Target genes) 
AP2/EREBP Arabidopsis thaliana 13.51 8.2 15,180 At3g23240 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
NtERF2
(Target genes) 
AP2/EREBP Nicotiana tabacum 9.73 4.15 465,303 - Hao D, Ohme-Takagi M, Yamasaki K. 2003 A modified sensor chip for surface plasmon resonance enables a rapid determination of sequence specificity of DNA-binding proteins. FEBS Lett 536: 151-6. PubMed 
ORA47(1)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 12.93 8.19 8,264 At1g74930 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ORA47(2)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 13.51 8.02 13,382 At1g74930 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
RAP2.3(1)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 13.19 6.71 49,378 At3g16770 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
RAP2.3(2)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 12.79 7.21 27,883 At3g16770 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
RAP2.3(3)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 12.95 7.09 27,181 At3g16770 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
RAP2.6(1)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 15.21 9.85 5,157 At1g43160 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
RAP2.6(2)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 11.29 5.77 79,299 At1g43160 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
RAP2.6(3)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 11.89 6.05 46,204 At1g43160 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
RAV1(1)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 10.65 5.01 310,650 At1g13260 Kagaya Y, Ohmiya K, Hattori T. 1999 RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Res 27: 470-8. PubMed 
RAV1(2)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 11.21 4.98 229,818 At1g13260 Kagaya Y, Ohmiya K, Hattori T. 1999 RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants. Nucleic Acids Res 27: 470-8. PubMed 
RRTF1(1)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 14.3 8.74 9,998 At4g34410 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
RRTF1(2)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 13.46 8.76 8,542 At4g34410 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
RRTF1(3)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 14.22 8.65 8,358 At4g34410 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
TEIL
(Target genes) 
AP2/EREBP Nicotiana tabacum 8.38 3.81 602,109 - Kosugi S, Ohashi Y. 2000 Cloning and DNA-binding properties of a tobacco Ethylene-Insensitive3 (EIN3) homolog. Nucleic Acids Res 28: 960-7. PubMed 
TOE1(1)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 12.39 7.11 15,303 At2g28550 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
TOE1(2)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 10.99 4.96 129,702 At2g28550 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
TOE1(3)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 10.25 4.73 203,237 At2g28550 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
TOE2(1)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 12.23 7.38 9,985 At5g60120 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
TOE2(2)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 11.05 5.56 64,050 At5g60120 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
TOE2(3)
(Target genes) 
AP2/EREBP Arabidopsis thaliana 9.14 3.51 696,630 At5g60120 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
WRI1
(Target genes) 
AP2/EREBP Arabidopsis thaliana 19.35 6.03 39,795 At3g54320 Maeo K, Tokuda T, Ayame A, Mitsui N, Kawai T, Tsukagoshi H, Ishiguro S,Nakamura K. 2009. An AP2-type transcription factor, WRINKLED1, of Arabidopsis thaliana binds to the AW-box sequence conserved among proximal upstream regions of genes involved in fatty acid synthesis. Plant J. 60:476-87. PubMed 
ETT(1)
(Target genes) 
ARF Arabidopsis thaliana 11.25 6.77 24,918 At2g33860 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ETT(2)
(Target genes) 
ARF Arabidopsis thaliana 11.71 5.73 61,629 At2g33860 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
AHL12(1)
(Target genes) 
AT-Hook Arabidopsis thaliana 6.5 1.96 1,015,578 At1g63480 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
AHL12(2)
(Target genes) 
AT-Hook Arabidopsis thaliana 7.44 2.06 1,052,969 At1g63480 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
AHL12(3)
(Target genes) 
AT-Hook Arabidopsis thaliana 6.16 1.76 1,055,502 At1g63480 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
AHL20(1)
(Target genes) 
AT-Hook Arabidopsis thaliana 8.89 4.22 467,577 At4g14465 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
AHL20(2)
(Target genes) 
AT-Hook Arabidopsis thaliana 8.2 2.76 2,080,516 At4g14465 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
AHL20(3)
(Target genes) 
AT-Hook Arabidopsis thaliana 6.75 1.95 1,013,106 At4g14465 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
AHL25(1)
(Target genes) 
AT-Hook Arabidopsis thaliana 7.53 2.56 1,073,462 At4g35390 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
AHL25(2)
(Target genes) 
AT-Hook Arabidopsis thaliana 6.86 2 1,067,197 At4g35390 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
AHL25(3)
(Target genes) 
AT-Hook Arabidopsis thaliana 6.51 1.85 1,038,322 At4g35390 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
DYT1
(Target genes) 
bHLH Arabidopsis thaliana 16.25 9.86 1,378 At4g21330 Feng B, Lu D, Ma X, Peng Y, Sun Y, Ning G, Ma H. 2012 Regulation of the Arabidopsis anther transcriptome by DYT1 for pollen development. Plant J. doi:10.1111/j.1365-313X.2012.05104.x. PubMed 
MYC2
(Target genes) 
bHLH Arabidopsis thaliana 10.97 5.76 73,002 At1g32640 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
MYC3
(Target genes) 
bHLH Arabidopsis thaliana 10.11 5.27 146,162 At5g46760 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
MYC4
(Target genes) 
bHLH Arabidopsis thaliana 11.04 7.04 24,551 At4g17880 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
OsbHLH66
(Target genes) 
bHLH Oryza sativa 14.81 8.24 6,806 - Xue GP. 2005. A CELD-fusion method for rapid determination of the DNA-binding sequence specificity of novel plant DNA-binding proteins. Plant J 41: 638-49. PubMed 
PIF3(1)
(Target genes) 
bHLH Arabidopsis thaliana 19.88 10.89 1,154 At1g09530 Martinez-Garcia JF, Huq E, Quail PH. 2000 Direct targeting of light signals to a promoter element-bound transcription factor. Science 288: 859-63. PubMed 
PIF3(2)
(Target genes) 
bHLH Arabidopsis thaliana 18.37 11.18 951 At1g09530 Martinez-Garcia JF, Huq E, Quail PH. 2000 Direct targeting of light signals to a promoter element-bound transcription factor. Science 288: 859-63. PubMed 
PIF3(3)
(Target genes) 
bHLH Arabidopsis thaliana 13.87 9.62 2,972 At1g09530 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
PIF4
(Target genes) 
bHLH Arabidopsis thaliana 11.78 7.82 12,754 At2g43010 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
PIF5
(Target genes) 
bHLH Arabidopsis thaliana 11.33 6.41 53,648 At3g59060 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ABF1
(Target genes) 
bZIP Arabidopsis thaliana 13.16 10.94 2,419 At1g49720 Choi H, Hong J, Ha J, Kang J, Kim SY. 2000 ABFs, a family of ABA-responsive element binding factors. J Biol Chem 275: 1723-30. PubMed 
bZIP60(1)
(Target genes) 
bZIP Arabidopsis thaliana 12.03 5.33 97,448 At1g42990 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
bZIP60(2)
(Target genes) 
bZIP Arabidopsis thaliana 12.68 5.82 64,220 At1g42990 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
bZIP910(1)
(Target genes) 
bZIP Antirrhinum majus 16.68 12.86 345 - Martinez-Garcia JF, Moyano E, Alcocer MJ, Martin C. 1998 Two bZIP proteins from Antirrhinum flowers preferentially bind a hybrid C-box/G-box motif and help to define a new sub-family of bZIP transcription factors. Plant J 13: 489-505. PubMed 
bZIP910(2)
(Target genes) 
bZIP Antirrhinum majus 16.08 10.94 470 - Martinez-Garcia JF, Moyano E, Alcocer MJ, Martin C. 1998 Two bZIP proteins from Antirrhinum flowers preferentially bind a hybrid C-box/G-box motif and help to define a new sub-family of bZIP transcription factors. Plant J 13: 489-505. PubMed 
bZIP911(1)
(Target genes) 
bZIP Antirrhinum majus 17.54 14.19 123 - Martinez-Garcia JF, Moyano E, Alcocer MJ, Martin C. 1998 Two bZIP proteins from Antirrhinum flowers preferentially bind a hybrid C-box/G-box motif and help to define a new sub-family of bZIP transcription factors. Plant J 13: 489-505. PubMed 
bZIP911(2)
(Target genes) 
bZIP Antirrhinum majus 15.73 12.1 145 - Martinez-Garcia JF, Moyano E, Alcocer MJ, Martin C. 1998 Two bZIP proteins from Antirrhinum flowers preferentially bind a hybrid C-box/G-box motif and help to define a new sub-family of bZIP transcription factors. Plant J 13: 489-505. PubMed 
O2
(Target genes) 
bZIP Zea mays 10.35 4.83 173,637 - Izawa T, Foster R, Chua NH. 1993 Plant bZIP protein DNA binding specificity. J Mol Biol 230: 1131-44. PubMed 
STF1
(Target genes) 
bZIP Glycine max 12.43 7.74 9,318 - Song YH, Yoo CM, Hong AP, Kim SH, Jeong HJ, Shin SY, Kim HJ, Yun DJ, Lim CO, Bahk JD, Lee SY, Nagao RT, Key JL, Hong JC. 2008. DNA Binding Study Identifies C-box and Hybrid C/G-box or C/A-box Motifs as High-Affinity Binding Sites for STF1 and HY5 Proteins. Plant Physiol :(Epub ahead of print). PubMed 
TGA1
(Target genes) 
bZIP Arabidopsis thaliana 10.84 5.81 53,463 At5g65210 Schindler U, Beckmann H, Cashmore AR. 1992 TGA1 and G-box binding factors: two distinct classes of Arabidopsis leucine zipper proteins compete for the G-box-like element TGACGTGG. Plant Cell 4: 1309-19. PubMed 
TGA1a
(Target genes) 
bZIP Nicotiana tabacum 10.45 5.21 142,030 - Izawa T, Foster R, Chua NH. 1993 Plant bZIP protein DNA binding specificity. J Mol Biol 230: 1131-44. PubMed 
TGA2(1)
(Target genes) 
bZIP Arabidopsis thaliana 12.08 6.91 16,655 At5g06950 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
TGA2(2)
(Target genes) 
bZIP Arabidopsis thaliana 11.69 7.23 11,943 At5g06950 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
DAG2
(Target genes) 
C2C2(Zn) Dof Arabidopsis thaliana 9.6 4.65 323,510 At2g46590 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
DOF2
(Target genes) 
C2C2(Zn) Dof Zea mays 8.49 2.72 1,839,875 - Yanagisawa S, Schmidt RJ. 1999 Diversity and similarity among recognition sequences of Dof transcription factors. Plant J 17: 209-14. PubMed 
DOF5.7(1)
(Target genes) 
C2C2(Zn) Dof Arabidopsis thaliana 8.026 4.15 1,014,887 At5g65590 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
DOF5.7(2)
(Target genes) 
C2C2(Zn) Dof Arabidopsis thaliana 10.88 5.44 61,646 At5g65590 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
GATA12
(Target genes) 
C2C2(Zn) GATA Arabidopsis thaliana 7.91 3.88 1,052,732 At5g25830 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
YAB1
(Target genes) 
C2C2(Zn)YABBY Arabidopsis thaliana 8.86 2.48 2,119,161 At2g45190 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
YAB5
(Target genes) 
C2C2(Zn)YABBY Arabidopsis thaliana 7.16 3.45 1,083,987 At2g26580 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
At4g35610
(Target genes) 
C2H2(Zn) Arabidopsis thaliana 10.27 3.23 1,256,980 At4g35610 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ID1
(Target genes) 
C2H2(Zn) Zea mays 11.02 5.71 156,606 - Kozaki A, Hake S, Colasanti J. 2004 The maize ID1 flowering time regulator is a zinc finger protein with novel DNA binding properties. Nucleic Acids Res 32: 1710-20. PubMed 
ZAT14
(Target genes) 
C2H2(Zn) Arabidopsis thaliana 10.73 3.85 451,507 At5g03510 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ZAT18
(Target genes) 
C2H2(Zn) Arabidopsis thaliana 10.5 3.93 334,543 At3g53600 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ZAT2
(Target genes) 
C2H2(Zn) Arabidopsis thaliana 11.52 4.69 354,120 At2g17180 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ZAT6
(Target genes) 
C2H2(Zn) Arabidopsis thaliana 10.01 4.45 208,136 At5g04340 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
OsCBT
(Target genes) 
CAMTA Oryza sativa 16.34 9.98 886 - Choi MS, Kim MC, Yoo JH, Moon BC, Koo SC, Park BO, Lee JH, Koo YD, Han HJ, Lee SY, Chung WS, Lim CO, Cho MJ. 2005. Isolation of a calmodulin-binding transcription factor from rice (Oryza sativa L.). J Biol Chem 280: 40820-31. PubMed 
ARR10
(Target genes) 
GARP Arabidopsis thaliana 12.04 5.23 153,271 At4g31920 Hosoda K, Imamura A, Katoh E, Hatta T, Tachiki M, Yamada H, Mizuno T, Yamazaki T. 2002 Molecular structure of the GARP family of plant Myb-related DNA binding motifs of the Arabidopsis response regulators. Plant Cell 14: 2015-29. PubMed 
GLK1(1)
(Target genes) 
GARP Arabidopsis thaliana 10.43 4.34 357,978 At2g20570 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
GLK1(2)
(Target genes) 
GARP Arabidopsis thaliana 10.4 4.26 448,908 At2g20570 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
KAN1
(Target genes) 
GARP Arabidopsis thaliana 7.95 3.31 1,085,925 At5g16560 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
KAN4(1)
(Target genes) 
GARP Arabidopsis thaliana 11.11 6.3 31,168 At5g42630 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
KAN4(2)
(Target genes) 
GARP Arabidopsis thaliana 11.18 5.83 51,683 At5g42630 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ARR11(1)
(Target genes) 
GARP/ARR-B Arabidopsis thaliana 11.16 6.11 48,623 At1g67710 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ARR11(2)
(Target genes) 
GARP/ARR-B Arabidopsis thaliana 10.04 2.12 1,098,901 At1g67710 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ARR11(3)
(Target genes) 
GARP/ARR-B Arabidopsis thaliana 9.14 3.08 1,366,503 At1g67710 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ARR14(1)
(Target genes) 
GARP/ARR-B Arabidopsis thaliana 10.99 6.35 29,511 At2g01760 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ARR14(2)
(Target genes) 
GARP/ARR-B Arabidopsis thaliana 10.87 3.06 1,326,246 At2g01760 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ARR14(3)
(Target genes) 
GARP/ARR-B Arabidopsis thaliana 11.2 6.15 70,886 At2g01760 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
AGP1
(Target genes) 
GATA Nicotiana tabacum 10.11 5.45 108,176 - Sugimoto K, Takeda S, Hirochika H. 2003 Transcriptional activation mediated by binding of a plant GATA-type zinc finger protein AGP1 to the AG-motif (AGATCCAA) of the wound-inducible Myb gene NtMyb2. Plant J 36: 550-64. PubMed 
WOX13(1)
(Target genes) 
HD-HOX Arabidopsis thaliana 9.3 4.73 255,250 At4g35550 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
WOX13(2)
(Target genes) 
HD-HOX Arabidopsis thaliana 6.98 3.35 1,031,589 At4g35550 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ZmHOX2a(1)
(Target genes) 
HD-HOX Zea mays 7.33 4.29 755,085 - Kirch T, Bitter S, Kisters-Woike B, Werr W. 1998. The two homeodomains of the ZmHox2a gene from maize originated as an internal gene duplication and have evolved different target site specificities. Nucleic Acids Res 26: 4714-20. PubMed 
ZmHOX2a(2)
(Target genes) 
HD-HOX Zea mays 7.77 4.44 495,363 - Kirch T, Bitter S, Kisters-Woike B, Werr W. 1998. The two homeodomains of the ZmHox2a gene from maize originated as an internal gene duplication and have evolved different target site specificities. Nucleic Acids Res 26: 4714-20. PubMed 
HVH21
(Target genes) 
HD-KNOTTED Hordeum vulgare 10.69 3.82 526,536 - Krusell L, Rasmussen I, Gausing K. 1997 DNA binding sites recognised in vitro by a knotted class 1 homeodomain protein encoded by the hooded gene, k, in barley (Hordeum vulgare). FEBS Lett 408: 25-9. PubMed 
ALFIN1
(Target genes) 
HD-PHD Medicago sativa 11.23 4.16 545,903 - Bastola DR, Pethe VV, Winicov I. 1998 Alfin1, a novel zinc-finger protein in alfalfa roots that binds to promoter elements in the salt-inducible MsPRP2 gene. Plant Mol Biol 38: 1123-35. PubMed 
ATHB1
(Target genes) 
HD-ZIP Arabidopsis thaliana 9.98 5.77 66,445 At3g01470 Sessa G, Morelli G, Ruberti I. 1993 The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities. EMBO J 12: 3507-17. PubMed 
ATHB12
(Target genes) 
HD-ZIP Arabidopsis thaliana 9.8 3.91 559,739 At3g61890 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ATHB5
(Target genes) 
HD-ZIP Arabidopsis thaliana 13.59 7.99 7,114 At5g65310 Johannesson H, Wang Y, Engstrom P. 2001. DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro. Plant Mol Biol. 45:63-73. PubMed 
ATHB51
(Target genes) 
HD-ZIP Arabidopsis thaliana 9.54 5.06 139,348 At5g03790 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ATHB9
(Target genes) 
HD-ZIP Arabidopsis thaliana 17.83 10.8 303 At1g30490 Sessa G, Steindler C, Morelli G, Ruberti I. 1998 The Arabidopsis Athb-8, -9 and -14 genes are members of a small gene family coding for highly related HD-ZIP proteins. Plant Mol Biol 38: 609-22. PubMed 
HAHB4
(Target genes) 
HD-ZIP Helianthus anuus 9.64 5.32 90,813 - Palena CM, Gonzalez DH, Chan RL. 1999 A monomer-dimer equilibrium modulates the interaction of the sunflower homeodomain leucine-zipper protein Hahb-4 with DNA. Biochem J 341: 81-7. PubMed 
ICU4
(Target genes) 
HD-ZIP Arabidopsis thaliana 9.09 3.32 823,995 At1g52150 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
HSFB2a(1)
(Target genes) 
HSF Arabidopsis thaliana 10.67 5.24 144,389 At5g62020 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
HSFB2a(2)
(Target genes) 
HSF Arabidopsis thaliana 9.7 4.2 441,163 At5g62020 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
HSFC1(1)
(Target genes) 
HSF Arabidopsis thaliana 10.92 6.6 39,964 At3g24520 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
HSFC1(2)
(Target genes) 
HSF Arabidopsis thaliana 11.41 5.57 138,544 At3g24520 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
LBD16
(Target genes) 
LOB/AS2 Arabidopsis thaliana 9.02 3.48 748,929 At2g42430 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
AG
(Target genes) 
MADS Arabidopsis thaliana 14.56 6.32 46,217 At4g18960 Huang H, Mizukami Y, Hu Y, Ma H. 1993 Isolation and characterization of the binding sequences for the product of the Arabidopsis floral homeotic gene AGAMOUS. Nucleic Acids Res 21: 4769-76. PubMed 
AGL1
(Target genes) 
MADS Arabidopsis thaliana 14.15 5.44 107,987 At3g58780 Huang H, Tudor M, Su T, Zhang Y, Hu Y, Ma H. 1996. DNA binding properties of two Arabidopsis MADS domain proteins: binding consensus and dimer formation. Plant Cell 8: 81-94. PubMed 
AGL15
(Target genes) 
MADS Arabidopsis thaliana 12.09 4.48 262,825 At5g13790 Tang W, Perry SE. 2003 Binding site selection for the plant MADS domain protein AGL15: an in vitro and in vivo study. J Biol Chem 278: 28154-9. PubMed 
AGL2
(Target genes) 
MADS Arabidopsis thaliana 13.9 6.18 55,361 At5g15800 Huang H, Tudor M, Su T, Zhang Y, Hu Y, Ma H. 1996. DNA binding properties of two Arabidopsis MADS domain proteins: binding consensus and dimer formation. Plant Cell 8: 81-94. PubMed 
AGL3
(Target genes) 
MADS Arabidopsis thaliana 13.32 5.79 73,285 At2g03710 Huang H, Tudor M, Weiss CA, Hu Y, Ma H. 1995 The Arabidopsis MADS-box gene AGL3 is widely expressed and encodes a sequence-specific DNA-binding protein. Plant Mol Biol 28: 549-67. PubMed 
AtMYB15
(Target genes) 
MYB Arabidopsis thaliana 17.49 11.85 209 At3g23250 Romero I, Fuertes A, Benito MJ, Malpica JM, Leyva A, Paz-Ares J. 1998 More than 80R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana. Plant J 14: 273-84. PubMed 
AtMYB61
(Target genes) 
MYB Arabidopsis thaliana 11.85 5.65 216,623 At1g09540 Prouse MB, Campbell MM. 2013. Interactions between the R2R3-MYB Transcription Factor, AtMYB61, and Target DNA Binding Sites. PLoS One. 8(5):e65132. PubMed 
AtMYB77
(Target genes) 
MYB Arabidopsis thaliana 13.11 7.25 17,825 At3g50060 Romero I, Fuertes A, Benito MJ, Malpica JM, Leyva A, Paz-Ares J. 1998 More than 80R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana. Plant J 14: 273-84. PubMed 
AtMYB84
(Target genes) 
MYB Arabidopsis thaliana 17.8 12.43 231 At3g49690 Romero I, Fuertes A, Benito MJ, Malpica JM, Leyva A, Paz-Ares J. 1998 More than 80R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana. Plant J 14: 273-84. PubMed 
CCA1(1)
(Target genes) 
MYB Arabidopsis thaliana 10.46 6.44 39,020 At2g46830 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
CCA1(2)
(Target genes) 
MYB Arabidopsis thaliana 9.09 4.09 332,599 At2g46830 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
CDC5
(Target genes) 
MYB Arabidopsis thaliana 13.93 7.47 11,561 At1g09770 Hirayama T, Shinozaki K. 1996. A cdc5+ homolog of a higher plant, Arabidopsis thaliana. Proc Natl Acad Sci U S A. 93:13371-6. PubMed 
GAMYB
(Target genes) 
MYB Hordeum vulgare 9.62 4.64 315,583 - Gubler F, Raventos D, Keys M, Watts R, Mundy J, Jacobsen JV. 1999. Target genes and regulatory domains of the GAMYB transcriptional activator in cereal aleurone. Plant J. 17:1-9. PubMed 
MYB.PH3(1)
(Target genes) 
MYB Petunia hybrida 13.34 7.65 8,525 - Solano R, Nieto C, Avila J, Canas L, Diaz I, Paz-Ares J. 1995. Dual DNA binding specificity of a petal epidermis-specific MYB transcription factor (MYB.Ph3) from Petunia hybrida. EMBO J. 14:1773-84. PubMed 
MYB.PH3(2)
(Target genes) 
MYB Petunia hybrida 12.96 8 7,633 - Solano R, Nieto C, Avila J, Canas L, Diaz I, Paz-Ares J. 1995 Dual DNA binding specificity of a petal epidermis-specific MYB transcription factor (MYB.Ph3) from Petunia hybrida. EMBO J 14: 1773-84. PubMed 
MYB111(1)
(Target genes) 
MYB Arabidopsis thaliana 11.35 5.95 59,274 At5g49330 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
MYB111(2)
(Target genes) 
MYB Arabidopsis thaliana 12.23 6.67 42,572 At5g49330 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
MYB46(1)
(Target genes) 
MYB Arabidopsis thaliana 7.66 3.98 379,287 At5g12870 Zhong R, Ye ZH. 2012. MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes. Plant Cell Physiol. 53:368-80. PubMed 
MYB46(2)
(Target genes) 
MYB Arabidopsis thaliana 10.58 6.15 53,232 At1g12870 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
MYB46(3)
(Target genes) 
MYB Arabidopsis thaliana 10.94 4.14 583,790 At5g12670 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
MYB52(1)
(Target genes) 
MYB Arabidopsis thaliana 10.12 3.7 495,867 At1g17950 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
MYB52(2)
(Target genes) 
MYB Arabidopsis thaliana 11.47 5.2 127,344 At1g17950 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
MYB55(1)
(Target genes) 
MYB Arabidopsis thaliana 12.1 6.96 22,537 At4g01680 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
MYB55(2)
(Target genes) 
MYB Arabidopsis thaliana 12.9 6.36 71,146 At4g01680 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
MYB59
(Target genes) 
MYB Arabidopsis thaliana 10.18 4.74 179,807 At5g59780 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
MYB83
(Target genes) 
MYB Arabidopsis thaliana 7.66 3.98 379,287 At3g08500 Zhong R, Ye ZH. 2012. MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes. Plant Cell Physiol. 53:368-80. PubMed 
P
(Target genes) 
MYB Zea mays 10.19 4.94 209,954 - Grotewold E, Drummond BJ, Bowen B, Peterson T. 1994. The myb-homologous P gene controls phlobaphene pigmentation in maize floral organs by directly activating a flavonoid biosynthetic gene subset. Cell. 76:543-53. PubMed 
RVE1(1)
(Target genes) 
MYB Arabidopsis thaliana 10.28 5.95 67,323 At5g17300 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
RVE1(2)
(Target genes) 
MYB Arabidopsis thaliana 7.52 3.74 1,051,672 At5g17300 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
TaMYB80
(Target genes) 
MYB Triticum aestivum 11.99 6.45 25,814 - Xue GP. 2005. A CELD-fusion method for rapid determination of the DNA-binding sequence specificity of novel plant DNA-binding proteins. Plant J 41: 638-49. PubMed 
ANAC46
(Target genes) 
NAC Arabidopsis thaliana 10.26 2.92 1,291,415 At3g04060 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ANAC55(1)
(Target genes) 
NAC Arabidopsis thaliana 10.55 5.25 76,218 At3g15500 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ANAC55(2)
(Target genes) 
NAC Arabidopsis thaliana 9.28 3.52 456,376 At3g15500 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ANAC58
(Target genes) 
NAC Arabidopsis thaliana 9.74 2.9 1,389,524 At3g18400 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ANAC81
(Target genes) 
NAC Arabidopsis thaliana 21.7 9.67 23,681 At5g08790 Wang X, Culver JN. 2012. DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus. BMC Plant Biol. 12:157. PubMed 
TaNAC69(1)
(Target genes) 
NAC Triticum aestivum 21.96 12.53 107 - Xue GP, Bower NI, McIntyre CL, Riding GA, Kazan K, Shorter R. 2006. TaNAC69 from the NAC superfamily of transcription factors is up-regulated by abiotic stresses in wheat and recognises two consensus DNA-binding sequences. Funct Plant Biol 33: 43-57.
TaNAC69(2)
(Target genes) 
NAC Triticum aestivum 19.93 6.05 30,812 - Xue GP, Bower NI, McIntyre CL, Riding GA, Kazan K, Shorter R. 2006. TaNAC69 from the NAC superfamily of transcription factors is up-regulated by abiotic stresses in wheat and recognises two consensus DNA-binding sequences. Funct Plant Biol 33: 43-57.
AtSPL3
(Target genes) 
SBP Arabidopsis thaliana 11.69 5.09 74,660 At2g33810 Birkenbihl RP, Jach G, Saedler H, Huijser P. 2005. Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains. J Mol Biol 352: 585-96. PubMed 
AtSPL8
(Target genes) 
SBP Arabidopsis thaliana 10.26 4.48 146,672 At1g02065 Birkenbihl RP, Jach G, Saedler H, Huijser P. 2005. Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains. J Mol Biol 352: 585-96. PubMed 
SPL1(1)
(Target genes) 
SBP Arabidopsis thaliana 13.18 8.51 2,634 At2g47070 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
SPL1(2)
(Target genes) 
SBP Arabidopsis thaliana 13.34 8.57 2,385 At2g47070 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
SPL14
(Target genes) 
SBP Arabidopsis thaliana 17.62 7.98 5,126 At1g20980 Liang X, Nazarenus TJ, Stone JM. 2008. Identification of a Consensus DNA-Binding Site for the Arabidopsis thaliana SBP Domain Transcription Factor, AtSPL14, and Binding Kinetics by Surface Plasmon Resonance. Biochemistry 47: 3645-53. PubMed 
SPL7(1)
(Target genes) 
SBP Arabidopsis thaliana 11.36 4.61 136,136 At5g18830 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
STY1(1)
(Target genes) 
SRS Arabidopsis thaliana 13.25 8.04 5,681 At3g51060 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
STY1(2)
(Target genes) 
SRS Arabidopsis thaliana 11.98 6.63 27,311 At3g51060 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
PCF2
(Target genes) 
TCP Oryza sativa 12.22 6.53 37,322 - Kosugi S, Ohashi Y. 2002 DNA binding and dimerization specificity and potential targets for the TCP protein family. Plant J 30: 337-48. PubMed 
PCF5
(Target genes) 
TCP Oryza sativa 12.26 7.48 14,048 - Kosugi S, Ohashi Y. 2002 DNA binding and dimerization specificity and potential targets for the TCP protein family. Plant J 30: 337-48. PubMed 
TCP11(1)
(Target genes) 
TCP Arabidopsis thaliana 14.85 9.16 2,115 At2g37000 Viola IL, Uberti Manassero NG, Ripoll R, Gonzalez DH. 2011. The Arabidopsis class I TCP transcription factor AtTCP11 is a developmental regulator with distinct DNA-binding properties due to the presence of a threonine residue at position 15 of the TCP domain. Biochem J. 435(1):143-55. PubMed 
TCP11(2)
(Target genes) 
TCP Arabidopsis thaliana 14.1 9.78 689 At2g37000 Viola IL, Uberti Manassero NG, Ripoll R, Gonzalez DH. 2011. The Arabidopsis class I TCP transcription factor AtTCP11 is a developmental regulator with distinct DNA-binding properties due to the presence of a threonine residue at position 15 of the TCP domain. Biochem J. 435(1):143-55. PubMed 
TCP15(1)
(Target genes) 
TCP Arabidopsis thaliana 13.25 8.54 4,383 At1g69690 Viola IL, Uberti Manassero NG, Ripoll R, Gonzalez DH. 2011. The Arabidopsis class I TCP transcription factor AtTCP11 is a developmental regulator with distinct DNA-binding properties due to the presence of a threonine residue at position 15 of the TCP domain. Biochem J. 435(1):143-55. PubMed 
TCP15(2)
(Target genes) 
TCP Arabidopsis thaliana 15.1 10.16 1,450 At1g69690 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
TCP16(1)
(Target genes) 
TCP Arabidopsis thaliana 13.31 8.66 3,826 At3g45150 Viola IL, Reinheimer R, Ripoll R, Manassero NG, Gonzalez DH. 2012. Determinants of the DNA binding specificity of class I and class II TCP transcription factors. J Biol Chem. 287:347-56. PubMed 
TCP16(2)
(Target genes) 
TCP Arabidopsis thaliana 13.67 9.37 1,984 At1g69690 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
TCP20
(Target genes) 
TCP Arabidopsis thaliana 13.19 8.28 6,844 At3g27010 Viola IL, Uberti Manassero NG, Ripoll R, Gonzalez DH. 2011. The Arabidopsis class I TCP transcription factor AtTCP11 is a developmental regulator with distinct DNA-binding properties due to the presence of a threonine residue at position 15 of the TCP domain. Biochem J. 435(1):143-55. PubMed 
TCP23
(Target genes) 
TCP Arabidopsis thaliana 15.05 10.23 1,011 At1g35560 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
At5g28300
(Target genes) 
Trihelix Arabidopsis thaliana 10.64 5.11 104,610 At5g28300 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
GT1
(Target genes) 
Trihelix Nicotiana tabacum 8.94 2.72 1,439,344 - Ouwerkerk PB, Trimborn TO, Hilliou F, Memelink J. 1999 Nuclear factors GT-1 and 3AF1 interact with multiple sequences within the promoter of the Tdc gene from Madagascar periwinkle: GT-1 is involved in UV light-induced expression. Mol Gen Genet 261: 610-22. PubMed 
WRKY12
(Target genes) 
WRKY(Zn) Arabidopsis thaliana 12.11 6 63,260 At2g44745 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
WRKY18(1)
(Target genes) 
WRKY(Zn) Arabidopsis thaliana 11.77 6.28 55,907 At4g31800 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
WRKY38(1)
(Target genes) 
WRKY(Zn) Arabidopsis thaliana 11.82 5.93 63,374 At5g22570 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
WRKY45
(Target genes) 
WRKY(Zn) Arabidopsis thaliana 12.3 7.38 15,934 At3g01970 Franco-Zorrilla JM, López-Vidriero I, Carrasco JL, Godoy M, Vera P, Solano R. 2014. DNA-binding specificities of plant transcription factors and their potential to define target genes. Proc Natl Acad Sci U S A 111: 2367-72. PubMed 
ZAP1
(Target genes) 
WRKY(Zn) Arabidopsis thaliana 12.26 8.48 4,300 At2g04880 de Pater S, Greco V, Pham K, Memelink J, Kijne J. 1996 Characterization of a zinc-dependent transcriptional activator from Arabidopsis. Nucleic Acids Res 24: 4624-31. PubMed 
Total Numbers: 
Factors:  126
Families:  29
Binding sites:  48,822,485

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