Factor Family Species Max. Score Threshold No. of Matches TRANSFAC Acc. No. Reference CBF - 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 - 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 ABI3/VP1 Arabidopsis thaliana 14.23 9.05 4,633 T08787 Ulmasov T, Hagen G, Guilfoyle TJ. 1997. ARF1, a transcription factor that binds to auxin response elements. Science 276: 1865-8. PubMed AtLEC2 ABI3/VP1 Arabidopsis thaliana 10.73 5.41 139,281 T08727 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 ABI4(1) AP2/EREBP Zea mays 13.83 8.83 12,816 T05743 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) AP2/EREBP Zea mays 12.9 8.03 11,948 T05743 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 AP2/EREBP Arabidopsis thaliana 18.39 11.06 294 T02639 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 NtERF2 AP2/EREBP Nicotiana tabacum 9.73 4.15 465,303 T02654 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 RAV1(1) AP2/EREBP Arabidopsis thaliana 10.65 5.01 310,650 T02637 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) AP2/EREBP Arabidopsis thaliana 11.21 4.98 229,818 T02637 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 TEIL AP2/EREBP Nicotiana tabacum 8.38 3.81 602,109 T04804 Kosugi S, Ohashi Y. 2000 Cloning and DNA-binding properties of a tobacco Ethylene-Insensitive3 (EIN3) homolog. Nucleic Acids Res 28: 960-7. PubMed OsbHLH66 bHLH Oryza sativa 14.81 8.24 6,806 T06540 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) bHLH Arabidopsis thaliana 19.88 10.89 1,154 T04492 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) bHLH Arabidopsis thaliana 18.37 11.18 951 T04492 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 ABF1 bZIP Arabidopsis thaliana 13.16 10.94 2,419 T03820 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 bZIP910(1) bZIP Antirrhinum majus 16.68 12.86 345 T02789 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) bZIP Antirrhinum majus 16.08 10.94 470 T02789 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) bZIP Antirrhinum majus 17.54 14.19 123 T02790 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) bZIP Antirrhinum majus 15.73 12.1 145 T02790 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 bZIP Zea mays 10.35 4.83 173,637 T00668 Izawa T, Foster R, Chua NH. 1993 Plant bZIP protein DNA binding specificity. J Mol Biol 230: 1131-44. PubMed STF1 bZIP Glycine max 12.43 7.74 9,318 T02969 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 bZIP Arabidopsis thaliana 10.84 5.81 53,463 T02794 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 bZIP Nicotiana tabacum 10.45 5.21 142,030 T00829 Izawa T, Foster R, Chua NH. 1993 Plant bZIP protein DNA binding specificity. J Mol Biol 230: 1131-44. PubMed DOF2 C2C2(Zn) Dof Zea mays 8.49 2.72 1,839,875 T02690 Yanagisawa S, Schmidt RJ. 1999 Diversity and similarity among recognition sequences of Dof transcription factors. Plant J 17: 209-14. PubMed ID1 C2H2(Zn) Zea mays 11.02 5.71 156,606 T03994 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 OsCBT CAMTA Oryza sativa 16.34 9.98 886 T08415 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 GARP Arabidopsis thaliana 12.04 5.23 153,271 T05654 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 AGP1 GATA Nicotiana tabacum 10.11 5.45 108,176 T06043 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 ZmHOX2a(1) HD-HOX Zea mays 7.33 4.29 755,085 T04102 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) HD-HOX Zea mays 7.77 4.44 495,363 T04102 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 HD-KNOTTED Hordeum vulgare 10.69 3.82 526,536 T02063 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 HD-PHD Medicago sativa 11.23 4.16 545,903 T04733 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 HD-ZIP Arabidopsis thaliana 9.98 5.77 66,445 T01474 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 ATHB5 HD-ZIP Arabidopsis thaliana 13.59 7.99 7,114 T04066 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 ATHB9 HD-ZIP Arabidopsis thaliana 17.83 10.8 303 T04001 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 HD-ZIP Helianthus anuus 9.64 5.32 90,813 T04073 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 AG MADS Arabidopsis thaliana 14.56 6.32 46,217 T01007 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 MADS Arabidopsis thaliana 14.15 5.44 107,987 T03022 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 MADS Arabidopsis thaliana 12.09 4.48 262,825 T03018 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 MADS Arabidopsis thaliana 13.9 6.18 55,361 T03024 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 MADS Arabidopsis thaliana 13.32 5.79 73,285 T03025 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 MYB Arabidopsis thaliana 17.49 11.85 209 T02534 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 AtMYB77 MYB Arabidopsis thaliana 13.11 7.25 17,825 T02590 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 MYB Arabidopsis thaliana 17.8 12.43 231 T02597 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 CDC5 MYB Arabidopsis thaliana 13.93 7.47 11,561 T02855 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 MYB Hordeum vulgare 9.62 4.64 315,583 T02679 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) MYB Petunia hybrida 13.34 7.65 8,525 T01568 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) MYB Petunia hybrida 12.96 8 7,633 T01568 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 P MYB Zea mays 10.19 4.94 209,954 T01590 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 TaMYB80 MYB Triticum aestivum 11.99 6.45 25,814 T06533 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 TaNAC69(1) NAC Triticum aestivum 21.96 12.53 107 T06532 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) NAC Triticum aestivum 19.93 6.05 30,812 T06532 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 SBP Arabidopsis thaliana 11.69 5.09 74,660 T05182 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 SBP Arabidopsis thaliana 10.26 4.48 146,672 T08557 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 SPL14 SBP Arabidopsis thaliana 17.62 7.98 5,126 T09195 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 PCF2 TCP Oryza sativa 12.22 6.53 37,322 T05573 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 TCP Oryza sativa 12.26 7.48 14,048 T05738 Kosugi S, Ohashi Y. 2002 DNA binding and dimerization specificity and potential targets for the TCP protein family. Plant J 30: 337-48. PubMed GT1 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 ZAP1 WRKY(Zn) Arabidopsis thaliana 12.26 8.48 4,300 T03722 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