| Matrix_160 | RVE1 | Not Available | | 96.33% |
| Motif_408 | EVENINGAT | Evening element found 46 times in the promoters of 31 cycling genes in Arabidopsis thaliana; Required for circadian control of gene expression; EE (evening element) motif; Also found in the promoter of the Solanum melongena gene encoding cysteine protease, and identified as cis-element for its circadian regulation;Orchestrated transcription of key pathways in Arabidopsis by the circadian clock | | 83.79% |
| Matrix_114 | EPR1; AT3G10113 | Not Available | | 76.49% |
| Matrix_157 | LHY; RVE2 | Not Available | | 75.91% |
| Matrix_89 | SOC1 | Genome-wide identification of SOC1 and SVP targets during the floral transition in Arabidopsis | | 74.55% |
| Matrix_276 | AT1G01520; AT3G09600; AT4G01280; LCL1; AT5G52660 | Not Available | | 72.33% |
| Matrix_4 | ARR14 | Not Available | | 69.81% |
| Motif_43 | CCA1 binding site motif | CCA1 binding site; CCA1 protein (myb-related transcription factor) interact with two imperfect repeats of AAMAATCT in Lhcb1*3 gene of Arabidopsis thaliana; Related to regulation by phytochrome;A myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene | | 69.75% |
| Matrix_391 | AHL20 | Not Available | | 69.70% |
| Matrix_210 | ARR1 | Not Available | | 69.67% |
| Motif_540 | CCA1 motif1 BS in CAB1 | A myb-related transcription factor is involved in the phytochrome regulation of an Arabidopsis Lhcb gene | | 67.69% |
| Matrix_236 | CCA1 | Not Available | | 67.01% |
| Matrix_88 | AHL12 | Not Available | | 66.94% |
| Matrix_125 | AHL12 | Not Available | | 66.84% |
| Motif_579 | WRECSAA01 | Wound-responsive element (WRE) found in the promoter region of cucumber ascorbate oxidase gene, CsAAO1; Binding site of proteins in tobacco nuclear extracts | | 66.03% |
| Matrix_103 | ATHB1 | The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities | | 65.46% |
| Matrix_421 | GLK1 | Not Available | | 65.35% |
| Matrix_324 | AT2G01060 | Not Available | | 64.13% |
| Matrix_429 | KAN4 | Not Available | | 63.66% |
| Matrix_444 | AT1G19485; AT4G17950 | Not Available | | 63.61% |
| Matrix_9 | AT5G04760 | Not Available | | 63.51% |
| Matrix_284 | KAN2; KAN3; KAN; KAN4 | Not Available | | 63.31% |
| Matrix_361 | AT1G25550 | Not Available | | 62.76% |
| Matrix_16 | AT3G04450; PHL1 | Not Available | | 62.67% |
| Matrix_32 | AHL25 | Not Available | | 62.57% |
| Matrix_434 | ARR11 | Not Available | | 62.38% |
| Motif_624 | ATHB6 binding site motif | Consensus binding sequence for Arabidopsis homeodomain-leucine zipper protein, ATHB6; ATHB6 is a target of the protein phosphatase ABI1 and regulates hormone responses; Homeodomain protein ATHB6 is a target of the protein phosphatase ABI1 and regulates hormone responses in Arabidopsis | | 62.31% |
| Matrix_67 | GLK1 | Not Available | | 62.25% |
| Matrix_491 | AT1G68670; AT3G25790 | Not Available | | 61.92% |
| Matrix_97 | APRR2 | Not Available | | 61.48% |
| Motif_561 | GATA-2; GATA-4; GATA-3; GATA-1 | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | | 61.40% |
| Matrix_442 | AT5G62260 | Not Available | | 60.75% |
| Matrix_366 | ARR14 | Not Available | | 60.68% |
| Motif_34 | LECPLEACS2 | Core element in LeCp (tomato Cys protease) binding cis-element (from -715 to -675) in LeAcs2 gene | | 60.59% |
| Matrix_185 | AHL25 | Not Available | | 60.52% |
| Matrix_62 | HAT5 | Not Available | | 60.30% |
| Matrix_168 | AHL25 | Not Available | | 60.08% |
| Matrix_336 | AT5G08520 | Not Available | | 60.07% |
| Matrix_522 | GATA11; GATA13 | Not Available | | 59.85% |
| Matrix_255 | cdf3 | Not Available | | 59.61% |
| Matrix_435 | ATHB51 | Not Available | | 59.53% |
| Matrix_69 | AT2G03500 | Not Available | | 59.45% |
| Matrix_162 | AtPHR1 | Not Available | | 59.32% |
| Matrix_54 | AHL20 | Not Available | | 59.23% |
| Matrix_8 | KAN1 | Not Available | | 59.10% |
| Matrix_471 | KAN4 | Not Available | | 59.05% |
| Matrix_318 | ATHB16 | Not Available | | 58.75% |
| Matrix_447 | RVE1 | Not Available | | 58.66% |
| Matrix_508 | APL; AT3G12730; AT3G24120; UNE16 | Not Available | | 58.13% |
| Matrix_327 | ARR11 | Not Available | | 58.11% |
| Matrix_81 | YAB1 | Not Available | | 57.78% |
| Matrix_279 | HRS1 | Not Available | | 57.70% |
| Matrix_441 | ATHB5 | Not Available | | 57.67% |
| Motif_277 | ATHB1 binding site motif | Recognition sequence of Arabidopsis Athb-1 protein; Athb-1 protein has a HD-Zip motif (homeodomain (HD) with a closely linked leucine zipper motif (Zip)); HD-Zip domain binds to DNA as a dimer; The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities | | 57.67% |
| Matrix_72 | CDF2 | Not Available | | 57.64% |
| Matrix_520 | ARR14 | Not Available | | 57.61% |
| Matrix_63 | ARR10 | Not Available | | 57.59% |
| Matrix_143 | GATA14; GATA6; GATA5 | Not Available | | 57.47% |
| Matrix_76 | GATA10 | Not Available | | 57.37% |
| Matrix_161 | MYBC1; AT3G10760; LUX; AT5G05090; AT5G59570 | Not Available | | 57.35% |
| Matrix_483 | ICU4 | Not Available | | 57.21% |
| Matrix_333 | GATA3 | Not Available | | 56.96% |
| Motif_352 | ATHB5 binding site motif | Consensus binding sequence for Arabidopsis class I HDzip (Homeodomein-leucine zipper) protein, ATHB5; ATHB5 protein forms dimers in solution; ATHB5 and ATHB6 exhibit identical DNA binding specificities; ATHB5 forms heterodimers with other class I HDzip proteins; DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro | | 56.49% |
| Matrix_205 | AGL15 | Not Available | | 56.44% |
| Matrix_523 | FUSCA3 | Not Available | | 56.27% |
| Matrix_392 | ARR2 | Not Available | | 55.82% |
| Motif_285 | HDZIP2ATATHB2 | Binding site of the Arabidopsis homeobox gene (ATHB-2) found in its own promoter; Located between -72 and -80; Similar to the HD-ZIP-2 binding consensus sequence; ATHB-2 is regulated by light signals which function as a negative autoregulator of its own gene | | 55.32% |
| Matrix_354 | AHL12 | Not Available | | 55.30% |
| Motif_673 | Bellringer/replumless/pennywise BS2 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | | 55.07% |
| Matrix_431 | ATHB21; HB-3 | Not Available | | 55.07% |
| Matrix_51 | LFY | Not Available | | 54.93% |
| Matrix_393 | REM1 | Not Available | | 54.92% |
| Motif_423 | MYB2 | Evidence for a role for AtMYB2 in the induction of the Arabidopsis alcohol dehydrogenase gene (ADH1) by low oxygen | | 54.65% |
| Matrix_38 | SPL14 | Not Available | | 54.57% |
| Motif_188 | CDA1ATCAB2 | CDA-1 (CAB2 DET1-associated factor 1) binding site in DtRE (dark response element) f of chlorophyll a/b-binding protein2 (CAB2) gene in Arabidopsis | | 54.56% |
| Matrix_283 | GATA15; GATA17; AT4G16141; GATA22; GATA23; GATA16; GNC | Not Available | | 54.55% |
| Motif_677 | AGL22; AGL20; AGL24 | Regulation of floral patterning by flowering time genes | | 54.44% |
| Motif_248 | L1-box | Arabidopsis DELLA and two HD-ZIP transcription factors regulate GA signaling in the epidermis through the L1 box cis-element | | 54.38% |
| Matrix_258 | WOX13 | Not Available | | 54.20% |
| Motif_184 | PROXBBNNAPA | prox B (proximal portion of B-box) found in napA gene of Brassica napus; CA-rich sequence; Found between -130 and -124; Required for seed specific expression and ABA responsiveness; dist B ABRE mediated transactivation by ABI3 adn ABI3-dependent response to ABA; a tetramer of the composite RY/G complex mediated only ABA-independent transactivation by ABI3; B2 domain of ABI3 is necessary for ABA-independent and ABA-dependent activation through the dist B ABRE | | 54.10% |
| Motif_424 | GATA-1 | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | | 54.05% |
| Motif_131 | P1BS | PHR1-binding sequence found in the upstream regions of phosphate starvation responsive genes from several plant species; phr1 (phosphate starvation response 1) gene codes for PHR1 protein related to PSR1 gene in C. reinhardtii | | 53.91% |
| Motif_169 | ATHB2 binding site motif | Recognition sequence of Arabidopsis Athb-2 protein; Athb-2 protein has a HD-Zip motif (homeodomain (HD) with a closely linked leucine zipper motif (Zip)); The Athb-1 and -2 HD-Zip domains homodimerize forming complexes of different DNA binding specificities | | 53.87% |
| Motif_231 | EIN3 | Ethylene signaling in Arabidopsis involves feedback regulation via the elaborate control of EBF2 expression by EIN3 | | 53.83% |
| Matrix_237 | MYB55 | Not Available | | 53.77% |
| Motif_637 | SARD1; CBP60g | Control of salicylic acid synthesis and systemic acquired resistance by two members of a plant-specific family of transcription factors | | 53.77% |
| Matrix_93 | YAB5 | Not Available | | 53.73% |
| Motif_420 | SORLREP2AT | one of Sequences Over-Represented in Light-Repressed Promoters (SORLREPs) in Arabidopsis; Computationally identified phyA-repressed motifs; See also all SORLREPs and all SORLIPs; Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data | | 53.64% |
| Matrix_6 | AT1G70000 | Not Available | | 53.35% |
| Motif_115 | HSEs binding site motif | Arabidopsis and the heat stress transcription factor world: how many heat stress transcription factors do we need? | | 53.35% |
| Matrix_178 | HSFB2A | Not Available | | 53.34% |
| Matrix_423 | AT3G04030 | Not Available | | 53.22% |
| Matrix_182 | ATHB6 | Not Available | | 53.01% |
| Motif_20 | HSELIKENTGLN2 | HSE-like sequence in 5' upstream region of beta-1,3-glucanase gene (GLN2) of tobacco | | 53.00% |
| Motif_58 | LREBOXIPCCHS1 | BoxI; Light responsive element (LRE) found in the parsley CHS-1 (chalcone synthase-1) gene promoter; Required for light responsiveness; nuclear protein binding site; MRECHS (MRE=Myb Recognition Element)Recognition site of MYB305 and a novel factor PcMYB1 (Myb1 from P. crispum); PcMYB1 contains only one MYB repeat | | 52.99% |
| Matrix_70 | GATA26 | Not Available | | 52.98% |
| Matrix_203 | GATA9; GATA12 | Not Available | | 52.64% |
| Matrix_408 | GATA12 | Not Available | | 52.41% |
| Matrix_181 | Dof5.7 | Not Available | | 52.24% |
| Matrix_129 | ABF1 | Not Available | | 52.24% |
| Matrix_227 | AT1G64620 | Not Available | | 52.19% |
| Matrix_521 | AHL20 | Not Available | | 52.11% |
| Motif_297 | Bellringer/replumless/pennywise BS1 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | | 52.05% |
| Motif_12 | CEREGLUBOX2PSLEGA | cereal glutenin box in pea legumin gene (legA); sequence homologous to the cereal glutenin gene control element (-300 element) | | 51.93% |
| Matrix_495 | HD-GL2-1; ANL2 | Not Available | | 51.90% |
| Motif_642 | SEF1MOTIF | SEF1 (soybean embryo factor 1) binding motif; sequence found in 5'-upstream region (-640; -765) of soybean beta-conglicinin (7S globulin) gene | | 51.87% |
| Matrix_328 | AT1G76580 | Not Available | | 51.86% |
| Matrix_302 | HAT1; HAT2 | Not Available | | 51.80% |
| Motif_489 | SORLREP3AT | one of Sequences Over-Represented in Light-Repressed Promoters (SORLREPs) in Arabidopsis; Computationally identified phyA-repressed motifs; See also all SORLREPs and also all SORLIPs;Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data | | 51.78% |
| Matrix_461 | ATHB12 | Not Available | | 51.77% |
| Motif_533 | Bellringer/replumless/pennywise BS3 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | | 51.74% |
| Motif_590 | MYB3 binding site motif | Expression profile matrix of Arabidopsis transcription factor genes suggests their putative functions in response to environmental stresses | | 51.62% |
| Matrix_259 | AT1G50680; AT1G51120 | Not Available | | 51.47% |
| Matrix_351 | HAT9; ATHB-4; ATHB2; HAT22; HAT14 | Not Available | | 51.35% |
| Motif_580 | L1BOXATPDF1 | L1 box found in promoter of Arabidopsis thaliana PROTODERMAL FACTOR1 (PDF1) gene; Located between -134 and -127; Involved in L1 layer-specific expression; L1-specific homeodomain protein ATML can bind to the L1 box; Y=C/T; A cotton fiber gene, RD22-like 1 (RDL1), contains a homeodomain binding L1 box and a MYB binding motif ; HDZip IV; Identification of a cis-regulatory element for L1 layer-specific gene expression, which is targeted by an L1-specific homeodomain protein | | 51.29% |
| Matrix_212 | ATHB-12 | Not Available | | 51.26% |
| Matrix_87 | AT1G19000 | Not Available | | 51.22% |
| Matrix_505 | GATA8 | Not Available | | 51.21% |
| Matrix_167 | ZAT6 | Not Available | | 51.20% |
| Motif_258 | -10PEHVPSBD | -10 promoter element found in the barley (H.v.) chloroplast psbD gene promoter; Involved in the expression of the plastid gene psbD which encodes a photosystem II reaction center chlorophyll-binding protein that is activated by blue, white or UV-A light | | 51.13% |
| Motif_25 | GLUTAACAOS | glutelin common motif; AACA motif; Conserved in all member of rice glutelin | | 51.11% |
| Matrix_106 | AT5G47390 | Not Available | | 51.09% |
| Motif_422 | SP8BFIBSP8BIB | One of SPBF binding site (SP8b); Found at -330, -220, and -200 of gSPO-B1 (sporamin) gene, and also at -80 of gB-Amy (beta-amylase) gene; SP8BF recognizes both SP8a and SP8b sequences; See also SP8BFIBSP8AIB; SP8BF activity is also found in tobacco; SP8b found in the 5' upstream region of three differnt genes coding for sporamin and beta-amylase; Binding site of SPF1; SPF1 also binds to the SP8b | | 50.98% |
| Matrix_152 | EIL1; AT5G65100 | Not Available | | 50.95% |
| Motif_358 | UP2ATMSD | Up2 motif found in 193 of the 1184 up-regulated genes after main stem decapitation in Arabidopsis | | 50.94% |
| Motif_649 | 2SSEEDPROTBANAPA | Conserved in many storage-protein gene promoters; May be important for high activity of the napA promoter | | 50.93% |
| Matrix_501 | DAG2 | Not Available | | 50.84% |
| Matrix_357 | WRKY61; WRKY6; WRKY9; WRKY36; WRKY47; WRKY42; WRKY31; WRKY72 | Not Available | | 50.72% |
| Matrix_411 | DOF5.6 | Not Available | | 50.61% |
| Motif_257 | BOX1PSGS2 | Box 1 element in pea glutamine synthetase (GS2) gene; An element in a 33-bp AT-rich sequence (box 1) of the 5' end of a GS2 promoter; Located at -837 to -827 of pea GS2; Multimer of box 1 element was used to isolate a cDNA encoding an AT-rich DNA binding protein (ATBP-1) | | 50.48% |
| Matrix_195 | GATA2; GATA4 | Not Available | | 50.37% |
| Matrix_410 | TOE2 | Not Available | | 50.24% |
| Matrix_22 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | | 50.21% |
| Matrix_228 | TGA2 | Not Available | | 50.18% |
| Matrix_37 | GATA27 | Not Available | | 50.13% |
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