AthaMap

For complete usage of AthaMap please enable JavaScript in the settings of your browser!

Documentation

AthaMap displays potential transcription factor binding sites in the genome of Arabidopsis thaliana. Binding sites were determined either by matrix-based or pattern-based screenings. All transcription factors annotated to AthaMap, additional information, links, and references are given below. Furthermore, pre-calculated combinatorial elements calculated from annotated colocalizing transcription factor binding sites are listed. AthaMap also displays target sites of small RNAs.

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. Accession to the TRANSFAC^Ž database requires a license.

Factor	Family	Species	Max. Score	Threshold	No. of Matches	TRANSFAC Acc. No.*	Reference
CBF	- other	several species	7.24	3.98	52,245	-	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	15,955	-	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	4,634	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	139,340	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	12,830	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	11,955	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	465,699	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	310,764	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	229,983	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	602,300	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	6,811	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	173,685	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	12.425	7.742	9,323	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	53,494	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	142,072	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	1,840,355	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	156,641	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	16.4	9.98	887	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	153,308	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	108,199	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	755,289	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	495,484	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	526,877	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	546,159	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	66,460	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	7,115	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	90,825	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	46,240	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	108,045	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	262,900	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	55,389	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	73,298	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	17,836	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	17.81	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	11,574	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	315,722	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	8,529	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	7,638	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	210,035	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	25,828	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	30,835	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	74,680	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	146,721	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	17.618	7.975	5,124	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	37,373	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	14,090	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	1,439,744	-	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	4,302	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

* Accession numbers given in the table refer to the TRANSFAC ^Ž database (license required).

Total Numbers:
Factors:	51
Families:	21
Binding sites:	9,881,343

Transcription factors with binding sites determined by pattern-based screenings
Binding sequences from the transcription factors listed below were used for genomic screenings. Accession to the TRANSFAC^Ž database requires a license.

Factor	Family	Species	No. of Matches	TRANSFAC Acc. No.*	Reference
ABI3	ABI3/VP1	Arabidopsis thaliana	912	T04393	Reidt W, Wohlfarth T, Ellerstrom M, Czihal A, Tewes A, Ezcurra I, Rask L, Baumlein H. 2000. Gene regulation during late embryogenesis: the RY motif of maturation-specific gene promoters is a direct target of the FUS3 gene product. Plant J. 21:401-8. PubMed
FUS3	ABI3/VP1	Arabidopsis thaliana	1,163	T04719	Reidt W, Wohlfarth T, Ellerstrom M, Czihal A, Tewes A, Ezcurra I, Rask L, Baumlein H. 2000. Gene regulation during late embryogenesis: the RY motif of maturation-specific gene promoters is a direct target of the FUS3 gene product. Plant J. 21:401-8. PubMed
AtERF-1	AP2/EREBP	Arabidopsis thaliana	649	T04633	Fujimoto SY, Ohta M, Usui A, Shinshi H, Ohme-Takagi M. 2000. Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell. 12:393-404. PubMed
AtERF-2	AP2/EREBP	Arabidopsis thaliana	649	T04634	Fujimoto SY, Ohta M, Usui A, Shinshi H, Ohme-Takagi M. 2000. Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell. 12:393-404. PubMed
AtERF-3	AP2/EREBP	Arabidopsis thaliana	1,809	T04635	Fujimoto SY, Ohta M, Usui A, Shinshi H, Ohme-Takagi M. 2000. Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell. 12:393-404. PubMed
AtERF-4	AP2/EREBP	Arabidopsis thaliana	1,983	T04636	Fujimoto SY, Ohta M, Usui A, Shinshi H, Ohme-Takagi M. 2000. Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell. 12:393-404. PubMed
AtERF-5	AP2/EREBP	Arabidopsis thaliana	649	T04637	Fujimoto SY, Ohta M, Usui A, Shinshi H, Ohme-Takagi M. 2000. Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box-mediated gene expression. Plant Cell. 12:393-404. PubMed
AtERF7	AP2/EREBP	Arabidopsis thaliana	344	T05483	Song CP, Agarwal M, Ohta M, Guo Y, Halfter U, Wang P, Zhu JK. 2005. Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses. Plant Cell 17: 2384-96. PubMed
AtTINY2	AP2/EREBP	Arabidopsis thaliana	659	T07771	Wei G, Pan Y, Lei J, Zhu YX. 2005. Molecular cloning, phylogenetic analysis, expressional profiling and in vitro studies of TINY2 from Arabidopsis thaliana. J Biochem Mol Biol 38: 440-6. PubMed
DREB1A	AP2/EREBP	Arabidopsis thaliana	552	T02643	Maruyama K, Sakuma Y, Kasuga M, Ito Y, Seki M, Goda H, Shimada Y, Yoshida S, Shinozaki K, Yamaguchi-Shinozaki K. 2004. Identification of cold-inducible downstream genes of the Arabidopsis DREB1A/CBF3 transcriptional factor using two microarray systems. : Plant J. 38:982-93. PubMed Narusaka Y, Nakashima K, Shinwari ZK, Sakuma Y, Furihata T, Abe H, Narusaka M, Shinozaki K, Yamaguchi-Shinozaki K. 2003. Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J. 34:137-48. PubMed Gilmour SJ, Zarka DG, Stockinger EJ, Salazar MP, Houghton JM, Thomashow MF. 1998. Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J. 16:433-42. PubMed Sakuma Y, Maruyama K, Osakabe Y, Qin F, Seki M, Shinozaki K, Yamaguchi-Shinozaki K. 2006. Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell 18: 1292-309. PubMed
DREB1B	AP2/EREBP	Arabidopsis thaliana	150	T02636	Stockinger EJ, Gilmour SJ, Thomashow MF. 1997. Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc Natl Acad Sci U S A. 94:1035-40. PubMed Gilmour SJ, Zarka DG, Stockinger EJ, Salazar MP, Houghton JM, Thomashow MF. 1998. Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J. 16:433-42. PubMed
DREB1C	AP2/EREBP	Arabidopsis thaliana	150	T04824	Gilmour SJ, Zarka DG, Stockinger EJ, Salazar MP, Houghton JM, Thomashow MF. 1998. Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J. 16:433-42. PubMed
DREB2A	AP2/EREBP	Arabidopsis thaliana	473	T02646	Narusaka Y, Nakashima K, Shinwari ZK, Sakuma Y, Furihata T, Abe H, Narusaka M, Shinozaki K, Yamaguchi-Shinozaki K. 2003. Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J. 34:137-48. PubMed Sakuma Y, Maruyama K, Osakabe Y, Qin F, Seki M, Shinozaki K, Yamaguchi-Shinozaki K. 2006. Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell 18: 1292-309. PubMed
RAP2.2	AP2/EREBP	Arabidopsis thaliana	7,030	-	Welsch R, Maass D, Voegel T, Dellapenna D, Beyer P. 2007. Transcription factor RAP2.2 and its interacting partner SINAT2: stable elements in the carotenogenesis of Arabidopsis leaves. Plant Physiol 145: 1073-85. PubMed
AtMYC2	bHLH	Arabidopsis thaliana	662	T05620	Yadav V, Mallappa C, Gangappa SN, Bhatia S, Chattopadhyay S. 2005. A basic helix-loop-helix transcription factor in Arabidopsis, MYC2, acts as a repressor of blue light-mediated photomorphogenic growth. Plant Cell 17: 1953-66. PubMed
ABI5	bZIP	Arabidopsis thaliana	686	T04543	Bensmihen S, Rippa S, Lambert G, Jublot D, Pautot V, Granier F, Giraudat J, Parcy F. 2002. The homologous ABI5 and EEL transcription factors function antagonistically to fine-tune gene expression during late embryogenesis. Plant Cell. 14:1391-403. PubMed Carles C, Bies-Etheve N, Aspart L, Leon-Kloosterziel KM, Koornneef M, Echeverria M, Delseny M. 2002. Regulation of Arabidopsis thaliana Em genes: role of ABI5. : Plant J. 30:373-83. PubMed
AREB1	bZIP	Arabidopsis thaliana	82	T03823	Narusaka Y, Nakashima K, Shinwari ZK, Sakuma Y, Furihata T, Abe H, Narusaka M, Shinozaki K, Yamaguchi-Shinozaki K. 2003. Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J. 34:137-48. PubMed
AREB2	bZIP	Arabidopsis thaliana	82	T03825	Narusaka Y, Nakashima K, Shinwari ZK, Sakuma Y, Furihata T, Abe H, Narusaka M, Shinozaki K, Yamaguchi-Shinozaki K. 2003. Interaction between two cis-acting elements, ABRE and DRE, in ABA-dependent expression of Arabidopsis rd29A gene in response to dehydration and high-salinity stresses. Plant J. 34:137-48. PubMed
BZIP12	bZIP	Arabidopsis thaliana	181	T05618	Bensmihen S, Rippa S, Lambert G, Jublot D, Pautot V, Granier F, Giraudat J, Parcy F. 2002. The homologous ABI5 and EEL transcription factors function antagonistically to fine-tune gene expression during late embryogenesis. Plant Cell. 14:1391-403. PubMed
HY5	bZIP	Arabidopsis thaliana	2,468	T10638	Chattopadhyay S, Ang LH, Puente P, Deng XW, Wei N. 1998. Arabidopsis bZIP protein HY5 directly interacts with light-responsive promoters in mediating light control of gene expression. Plant Cell. 10:673-83. PubMed Cluis CP, Mouchel CF, Hardtke CS. 2004. The Arabidopsis transcription factor HY5 integrates light and hormone signaling pathways. Plant J. 38:332-47. PubMed 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
GATA-1	C2C2(Zn) GATA	Arabidopsis thaliana	9,894	T05705	Teakle GR, Manfield IW, Graham JF, Gilmartin PM. 2002. Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics. Plant Mol Biol. 50:43-57. PubMed
GATA-2	C2C2(Zn) GATA	Arabidopsis thaliana	4,290	T05706	Teakle GR, Manfield IW, Graham JF, Gilmartin PM. 2002. Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics. Plant Mol Biol. 50:43-57. PubMed
GATA-3	C2C2(Zn) GATA	Arabidopsis thaliana	4,290	T05707	Teakle GR, Manfield IW, Graham JF, Gilmartin PM. 2002. Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics. Plant Mol Biol. 50:43-57. PubMed
GATA-4	C2C2(Zn) GATA	Arabidopsis thaliana	4,290	T05708	Teakle GR, Manfield IW, Graham JF, Gilmartin PM. 2002. Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics. Plant Mol Biol. 50:43-57. PubMed
SUP	C2H2(Zn)	Arabidopsis thaliana	501	T02275	Dathan N, Zaccaro L, Esposito S, Isernia C, Omichinski JG, Riccio A, Pedone C, Di Blasio B, Fattorusso R, Pedone PV. 2002. The Arabidopsis SUPERMAN protein is able to specifically bind DNA through its single Cys2-His2 zinc finger motif. Nucleic Acids Res. 30:4945-51. PubMed
TAC1	C2H2(Zn)	Arabidopsis thaliana	2,315	T10627	Ren S, Mandadi KK, Boedeker AL, Rathore KS, McKnight TD. 2007. Regulation of telomerase in Arabidopsis by BT2, an apparent target of TELOMERASE ACTIVATOR1. Plant Cell 19: 23-31. PubMed
AtSR1	CAMTA	Arabidopsis thaliana	427	-	Yang T, Poovaiah BW. 2002. A calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signaling pathways in plants. J Biol Chem 277: 45049-58. PubMed
E2Fa	E2F/DP	Arabidopsis thaliana	2,302	T06392	Mariconti L, Pellegrini B, Cantoni R, Stevens R, Bergounioux C, Cella R, Albani D. 2002. The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants. J Biol Chem. 277:9911-9. PubMed Egelkrout EM, Mariconti L, Settlage SB, Cella R, Robertson D, Hanley-Bowdoin L. 2002. Two E2F elements regulate the proliferating cell nuclear antigen promoter differently during leaf development. Plant Cell. 14:3225-36. PubMed Ramirez-Parra E, Gutierrez C. 2007. E2F regulates FASCIATA1, a chromatin assembly gene whose loss switches on the endocycle and activates gene expression by changing the epigenetic status. Plant Physiol 144: 105-20. PubMed
E2Fb	E2F/DP	Arabidopsis thaliana	605	T06393	de Jager SM, Menges M, Bauer UM, Murra JA. 2001. Arabidopsis E2F1 binds a sequence present in the promoter of S-phase-regulated gene AtCDC6 and is a member of a multigene family with differential activities. Plant Mol Biol. 47:555-68. PubMed Mariconti L, Pellegrini B, Cantoni R, Stevens R, Bergounioux C, Cella R, Albani D. 2002. The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants. J Biol Chem. 277:9911-9. PubMed Egelkrout EM, Mariconti L, Settlage SB, Cella R, Robertson D, Hanley-Bowdoin L. 2002. Two E2F elements regulate the proliferating cell nuclear antigen promoter differently during leaf development. Plant Cell. 14:3225-36. PubMed
E2Fc	E2F/DP	Arabidopsis thaliana	2,752	T05360	Mariconti L, Pellegrini B, Cantoni R, Stevens R, Bergounioux C, Cella R, Albani D. 2002. The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants. J Biol Chem. 277:9911-9. PubMed Egelkrout EM, Mariconti L, Settlage SB, Cella R, Robertson D, Hanley-Bowdoin L. 2002. Two E2F elements regulate the proliferating cell nuclear antigen promoter differently during leaf development. Plant Cell. 14:3225-36. PubMed Stevens R, Mariconti L, Rossignol P, Perennes C, Cella R, Bergounioux C. 2002. Two E2F sites in the Arabidopsis MCM3 promoter have different roles in cell cycle activation and meristematic expression. J Biol Chem. 277:32978-84. PubMed
E2Fd	E2F/DP	Arabidopsis thaliana	2,754	T06407	Mariconti L, Pellegrini B, Cantoni R, Stevens R, Bergounioux C, Cella R, Albani D. 2002. The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants. J Biol Chem. 277:9911-9. PubMed Egelkrout EM, Mariconti L, Settlage SB, Cella R, Robertson D, Hanley-Bowdoin L. 2002. Two E2F elements regulate the proliferating cell nuclear antigen promoter differently during leaf development. Plant Cell. 14:3225-36. PubMed Stevens R, Mariconti L, Rossignol P, Perennes C, Cella R, Bergounioux C. 2002. Two E2F sites in the Arabidopsis MCM3 promoter have different roles in cell cycle activation and meristematic expression. J Biol Chem. 277:32978-84. PubMed
E2Fe	E2F/DP	Arabidopsis thaliana	396	T07424	Mariconti L, Pellegrini B, Cantoni R, Stevens R, Bergounioux C, Cella R, Albani D. 2002. The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants. J Biol Chem. 277:9911-9. PubMed Egelkrout EM, Mariconti L, Settlage SB, Cella R, Robertson D, Hanley-Bowdoin L. 2002. Two E2F elements regulate the proliferating cell nuclear antigen promoter differently during leaf development. Plant Cell. 14:3225-36. PubMed
E2Ff	E2F/DP	Arabidopsis thaliana	114	T07257	Mariconti L, Pellegrini B, Cantoni R, Stevens R, Bergounioux C, Cella R, Albani D. 2002. The E2F family of transcription factors from Arabidopsis thaliana. Novel and conserved components of the retinoblastoma/E2F pathway in plants. J Biol Chem. 277:9911-9. PubMed
ARR1	GARP/ARR-B	Arabidopsis thaliana	8,752	T04729	Sakai H, Aoyama T, Oka A. 2000. Arabidopsis ARR1 and ARR2 response regulators operate as transcriptional activators. Plant J. 24:703-11. PubMed
ARR2	GARP/ARR-B	Arabidopsis thaliana	13,767	T04730	Sakai H, Aoyama T, Oka A. 2000. Arabidopsis ARR1 and ARR2 response regulators operate as transcriptional activators. Plant J. 24:703-11. PubMed Lohrmann J, Sweere U, Zabaleta E, Baurle I, Keitel C, Kozma-Bognar L, Brennicke A, Schafer E, Kudla J, Harter K. 2001. The response regulator ARR2: a pollen-specific transcription factor involved in the expression of nuclear genes for components of mitochondrial complex I in Arabidopsis. Mol Genet Genomics. 265:2-13.PubMed
ATML1	HD-ZIP	Arabidopsis thaliana	130	T04097	Abe M, Takahashi T, Komeda Y. 2001. Identification of a cis-regulatory element for L1 layer-specific gene expression, which is targeted by an L1-specific homeodomain protein. Plant J. 26:487-94. PubMed
PDF2	HD-ZIP	Arabidopsis thaliana	130	T06614	Abe M, Katsumata H, Komeda Y, Takahashi T. 2003. Regulation of shoot epidermal cell differentiation by a pair of homeodomain proteins in Arabidopsis. Development. 130:635-43. PubMed
AtCCA1	MYB	Arabidopsis thaliana	309	T08583	Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA. 2005. LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proc Natl Acad Sci U S A 102: 10387-92. PubMed
AtLHY	MYB	Arabidopsis thaliana	309	T08584	Hazen SP, Schultz TF, Pruneda-Paz JL, Borevitz JO, Ecker JR, Kay SA. 2005. LUX ARRHYTHMO encodes a Myb domain protein essential for circadian rhythms. Proc Natl Acad Sci U S A 102: 10387-92. PubMed
AtMYB44	MYB	Arabidopsis thaliana	485	T02559	Kirik V, Kolle K, Misera S, Baumlein H. 1998. Two novel MYB homologues with changed expression in late embryogenesis-defective Arabidopsis mutants. Plant Mol Biol. 37:819-27. PubMed
AtWER	MYB	Arabidopsis thaliana	877	T02580	Koshino-Kimura Y, Wada T, Tachibana T, Tsugeki R, Ishiguro S, Okada K. 2005. Regulation of CAPRICE transcription by MYB proteins for root epidermis differentiation in Arabidopsis. Plant Cell Physiol 46: 817-26. PubMed
MYB1	MYB	Arabidopsis thaliana	962	T02535	Urao T, Yamaguchi-Shinozaki K, Urao S, Shinozaki K. 1993. An Arabidopsis myb homolog is induced by dehydration stress and its gene product binds to the conserved MYB recognition sequence. Plant Cell. 5:1529-39. PubMed
MYB2	MYB	Arabidopsis thaliana	5,400	T02536	Hoeren FU, Dolferus R, Wu Y, Peacock WJ, Dennis ES. 1998. Evidence for a role for AtMYB2 in the induction of the Arabidopsis alcohol dehydrogenase gene (ADH1) by low oxygen. Genetics. 149:479-90. PubMed Urao T, Yamaguchi-Shinozaki K, Urao S, Shinozaki K. 1993. An Arabidopsis myb homolog is induced by dehydration stress and its gene product binds to the conserved MYB recognition sequence. Plant Cell. 5:1529-39. PubMed
MYB98	MYB	Arabidopsis thaliana	10,303	T04708	Punwani JA, Rabiger DS, Drews GN. 2007. MYB98 positively regulates a battery of synergid-expressed genes encoding filiform apparatus localized proteins. Plant Cell 19: 2557-68. PubMed
ANAC019	NAC	Arabidopsis thaliana	104	T06866	Tran LS, Nakashima K, Sakuma Y, Simpson SD, Fujita Y, Maruyama K, Fujita M, Seki M, Shinozaki K, Yamaguchi-Shinozaki K. 2004. Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. Plant Cell. 16:2481-98. PubMed
ANAC055	NAC	Arabidopsis thaliana	104	T07333	Tran LS, Nakashima K, Sakuma Y, Simpson SD, Fujita Y, Maruyama K, Fujita M, Seki M, Shinozaki K, Yamaguchi-Shinozaki K. 2004. Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. Plant Cell. 16:2481-98. PubMed
ANAC072	NAC	Arabidopsis thaliana	104	T07624	Tran LS, Nakashima K, Sakuma Y, Simpson SD, Fujita Y, Maruyama K, Fujita M, Seki M, Shinozaki K, Yamaguchi-Shinozaki K. 2004. Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. Plant Cell. 16:2481-98. PubMed
NAM	NAC	Arabidopsis thaliana	982	T05781	Duval M, Hsieh TF, Kim SY, Thomas TL. 2002. Molecular characterization of AtNAM: a member of the Arabidopsis NAC domain superfamily. Plant Mol Biol. 50:237-48. PubMed
SPL1	SBP	Arabidopsis thaliana	382	T05275	Cardon G, Hohmann S, Klein J, Nettesheim K, Saedler H, Huijser P. 1999. Molecular characterisation of the Arabidopsis SBP-box genes. Gene. 237:91-104. PubMed
SPL4	SBP	Arabidopsis thaliana	717	T05277	Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Nunokawa E, Ishizuka Y, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S. 2004. A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. : J Mol Biol. 337:49-63. PubMed Cardon G, Hohmann S, Klein J, Nettesheim K, Saedler H, Huijser P. 1999. Molecular characterisation of the Arabidopsis SBP-box genes. Gene. 237:91-104. PubMed
SPL5	SBP	Arabidopsis thaliana	382	T05278	Cardon G, Hohmann S, Klein J, Nettesheim K, Saedler H, Huijser P. 1999. Molecular characterisation of the Arabidopsis SBP-box genes. Gene. 237:91-104. PubMed
SPL7	SBP	Arabidopsis thaliana	335	T05280	Yamasaki K, Kigawa T, Inoue M, Tateno M, Yamasaki T, Yabuki T, Aoki M, Seki E, Matsuda T, Nunokawa E, Ishizuka Y, Terada T, Shirouzu M, Osanai T, Tanaka A, Seki M, Shinozaki K, Yokoyama S. 2004. A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. : J Mol Biol. 337:49-63. PubMed
GT-1	Trihelix	Arabidopsis thaliana	3,702	T04454	Hiratsuka K, Wu X, Fukuzawa H, Chua NH. 1994. Molecular dissection of GT-1 from Arabidopsis. Plant Cell. 6:1805-13. PubMed
GT-2	Trihelix	Arabidopsis thaliana	513	T04458	Kuhn RM, Caspar T, Dehesh K, Quail PH. 1993. DNA binding factor GT-2 from Arabidopsis. Plant Mol Biol. 23:337-48. PubMed
GT-3b	Trihelix	Arabidopsis thaliana	4,914	T07188	Park HC, Kim ML, Kang YH, Jeon JM, Yoo JH, Kim MC, Park CY, Jeong JC, Moon BC, Lee JH, Yoon HW, Lee SH, Chung WS, Lim CO, Lee SY, Hong JC, Cho MJ. 2004. Pathogen- and NaCl-induced expression of the SCaM-4 promoter is mediated in part by a GT-1 box that interacts with a GT-1-like transcription factor. Plant Physiol. 135:2150-61. PubMed
WRKY18	WRKY(Zn)	Arabidopsis thaliana	5,704	T04725	Du L, Chen Z. 2000. Identification of genes encoding receptor-like protein kinases as possible targets of pathogen- and salicylic acid-induced WRKY DNA-binding proteins in Arabidopsis. Plant J. 24:837-47. PubMed Yu D, Chen C, Chen Z. 2001. Evidence for an important role of WRKY DNA binding proteins in the regulation of NPR1 gene expression. Plant Cell. 13:1527-40. PubMed Chen C, Chen Z. 2002. Potentiation of developmentally regulated plant defense response by AtWRKY18, a pathogen-induced Arabidopsis transcription factor. Plant Physiol. 129:706-16. PubMed Xu X, Chen C, Fan B, Chen Z. 2006. Physical and functional interactions between pathogen-induced Arabidopsis WRKY18, WRKY40, and WRKY60 transcription factors. Plant Cell 18: 1310-26. PubMed
WRKY40	WRKY(Zn)	Arabidopsis thaliana	641	T07026	Xu X, Chen C, Fan B, Chen Z. 2006. Physical and functional interactions between pathogen-induced Arabidopsis WRKY18, WRKY40, and WRKY60 transcription factors. Plant Cell 18: 1310-26. PubMed
WRKY6	WRKY(Zn)	Arabidopsis thaliana	1,122	T05354	Robatzek S, Somssich IE. 2002. Targets of AtWRKY6 regulation during plant senescence and pathogen defense. Genes Dev. 16:1139-49. PubMed

* Accession numbers given in the table refer to the TRANSFAC ^Ž database (license required).

Total Numbers:
Factors:	58
Families:	15
Binding sites:	117,393

Combinatorial elements annotated to AthaMap
Combinatorial elements were determined by colocalization analysis with the parameters listed below.

Combinatorial element	Distance between sites	Factor binding sites employed		Number of elements annotated
Combinatorial element	Distance between sites	Element 1	Element 2	Number of elements annotated
bZIP_bZIP	10-15bp	TGA1a	TGA1a	1,037
bZIP_DOF	3-40bp	TGA1a	DOF2	84,389
HOX2a_HOX2a	6-30bp	ZmHOX2a(1)	ZmHOX2a(2)	176,708
MADS_MADS	10-100bp	AG AGL3 AGL15	AG AGL3 AGL15	31,133
MYC_MYB	3-40bp	TGA1a	AtMYB15 AtMAB77 AtMYB84 CDC5 MYB.PH3(1) MYB.PH3(2) P GAMYB	38,065
RAV	3-20bp	RAV1(1)	RAV1(2)	28,535
total number of combinatorial elements:				359,867

Small RNAs annotated to AthaMap
17mer sequence signatures derived from a small RNA transcriptome analysis of Arabidopsis thaliana inflorescence tissue and seedlings (Lu et al., 2005) were used for genomic screenings. The complete lists of screening sequences are available at NCBI's GEO (GSM65747 and GSM65750). Small RNAs from inflorescence tissue (smallRNA(i)) and seedlings (smallRNA(s)) were annotated to AthaMap resulting in a total of 403,173 genomic matches. 5,772 genes were predicted to be post-transcriptionally regulated by small RNAs since their transcribed regions are targets by at least one smallRNA in antisense orientation. The complete list of genes predicted to be down-regulated by small RNAs can be downloaded as text file (73 KB).

printer-friendly version