| Matrix_104 | PI | Not available | Upstream | -201 |
| Matrix_108 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -201 |
| Matrix_109 | GBF3 | Not available | Upstream | -201 |
| Matrix_113 | ABI5 | Not available | Upstream | -201 |
| Matrix_118 | PIF3_2 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -203 |
| Matrix_120 | BEE2 | Not available | Upstream | -200 |
| Matrix_122 | ABF1;AREB2 | Not available | Upstream | -201 |
| Matrix_129 | ABF1 | Not available | Upstream | -200 |
| Matrix_14 | ZCW32;AT5G62610 | Not available | Upstream | -200 |
| | | Upstream | -199 |
| Matrix_150 | UNE10;PIF7 | Not available | Upstream | -199 |
| Matrix_153 | AP2 | Not available | Upstream | -201 |
| Matrix_156 | POC1 | Not available | Upstream | -201 |
| | | Upstream | -199 |
| Matrix_158 | AT1G03040;LRL1;UNE12;LRL2;LRL3 | Not available | Upstream | -200 |
| Matrix_186 | FHY3 | Not available | Upstream | -202 |
| Matrix_19 | PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling | Upstream | -200 |
| Matrix_200 | PIL5;AT4G28790;AT4G28800;AT4G28811;AT4G28815 | Not available | Upstream | -200 |
| Matrix_233 | MYC3 | Not available | Upstream | -199 |
| Matrix_247 | PIF3 | Not available | Upstream | -200 |
| Matrix_264 | ATAREB1 | Not available | Upstream | -203 |
| Matrix_269 | FHY3/FAR1 | Not available | Upstream | -86 |
| | | Upstream | -83 |
| Matrix_27 | ATAIB;ATNIG1 | Not available | Upstream | -199 |
| Matrix_305 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -269 |
| Matrix_320 | MYC4 | Not available | Upstream | -199 |
| Matrix_323 | BIM3 | Not available | Upstream | -200 |
| Matrix_330 | MYC2;TT8 | Not available | Upstream | -200 |
| Matrix_331 | GBF1 | Not available | Upstream | -201 |
| Matrix_332 | SPT;ALC | Not available | Upstream | -200 |
| | | Upstream | -199 |
| Matrix_339 | bHLH104 | Not available | Upstream | -200 |
| Matrix_345 | POC1 | Not available | Upstream | -203 |
| Matrix_365 | AT1G10120;AT1G25330;CIB5;AT1G68920;AT3G23690;CIB1 | Not available | Upstream | -199 |
| Matrix_369 | AT2G18300 | Not available | Upstream | -202 |
| | | Upstream | -200 |
| Matrix_389 | ILR3 | Not available | Upstream | -200 |
| Matrix_403 | BZR1 | Not available | Upstream | -202 |
| Matrix_437 | MYC2 | Not available | Upstream | -199 |
| Matrix_449 | BIM2 | Not available | Upstream | -200 |
| Matrix_465 | MYC4 | Not available | Upstream | -200 |
| Matrix_476 | bHLH115;bHLH34 | Not available | Upstream | -199 |
| Matrix_480 | BES1 | Not available | Upstream | -201 |
| | | Upstream | -200 |
| Matrix_53 | MYC3 | Not available | Upstream | -202 |
| | | Upstream | -198 |
| Matrix_55 | PIF3 | Not available | Upstream | -201 |
| Matrix_60 | AT1G01260;AT5G57150 | Not available | Upstream | -199 |
| Matrix_64 | PIF5 | Not available | Upstream | -199 |
| Matrix_65 | POC1;PIL1 | Not available | Upstream | -198 |
| Matrix_7 | PIF4 | Not available | Upstream | -200 |
| | | Upstream | -198 |
| Matrix_77 | PRR5 | Not available | Upstream | -202 |
| Matrix_80 | BIM1 | Not available | Upstream | -201 |
| Motif_139 | RHERPATEXPA7 | Right part of RHEs (Root Hair-specific cis-Elements) conserved among the Arabidopsis thaliana A7 (AtEXPA7) orthologous (and paralogous) genes from diverse angiosperm species with different hair distribution patterns | Upstream | -199 |
| Motif_179 | CACGTGMOTIF;BES1;PIF4;PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling;A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana; CACGTG motif; G-box; Binding site of Arabidopsis GBF4; C. roseus G-box binding factor 1 (CrGBF1) and 1 (CrGBF2) can act as transcriptional repressors of the Str promoter via direct interaction with the G-box; Essential for expression of beta-phaseolin gene during embryogenesis in bean, tobacco, Arabidopsis; Tomato Pti4 (ERF) regulates defense-related gene expression via GCC box and non-GCC box cis-element (Myb1 (GTTAGTT) and G-box (CACGTG)); Isolation and characterization of a fourth Arabidopsis thaliana G-box-binding factor, which has similarities to Fos oncoprotein; Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -198 |
| Motif_194 | EBOXBNNAPA | E-box of napA storage-protein gene of Brassica napus;This sequence is also known as RRE (R response element); MYC recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis; Binding site of ATMYC2 (previously known as rd22BP1); see E-box and MYCATRD22; MYC recognition sequence in CBF3 promoter; Binding site of ICE1 (inducer of CBF expression 1) that regulates the transcription of CBF/DREB1 genes in the cold in Arabidopsis; ICE1 | Upstream | -198 |
| Motif_218 | ABRERATCAL | ABRE-related sequence or Repeated sequence motifs identified in the upstream regions of 162 Ca(2+)-responsive upregulated genes; see also ABRE | Upstream | -199 |
| | | Upstream | -198 |
| Motif_248 | L1-box | Arabidopsis DELLA and two HD-ZIP transcription factors regulate GA signaling in the epidermis through the L1 box cis-element | Downstream | 978 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -198 |
| Motif_342 | POLASIG1 | PolyA signal; poly A signal found in legA gene of pea, rice alpha-amylase; -10 to -30 in the case of animal genes. Near upstream elements (NUE) in Arabidopsis | Upstream | -132 |
| Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -198 |
| Motif_495 | TRANSINITMONOCOTS | Context sequence of translational initiation codon in monocots | Upstream | -121 |
| Motif_503 | EECCRCAH1 | EEC; Consensus motif of the two enhancer elements, EE-1 and EE-2, both found in the promoter region of the Chlamydomonas Cah1 (encoding a periplasmic carbonic anhydrase); Binding site of Myb transcription factor LCR1 | Upstream | -181 |
| Motif_549 | TBF1 | The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition | Upstream | -84 |
| Motif_57 | ABREOSRAB21 | ABA responsive element (ABRE) of wheat Em and rice rab21 genes; Proposed consensus sequence for the repeated motif (Em1a and Em1b) of wheat Em gene | Upstream | -201 |
| 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 | Downstream | 978 |
| Motif_658 | GT1CONSENSUS | Consensus GT-1 binding site in many light-regulated genes, e.g., RBCS from many species, PHYA from oat and rice, spinach RCA and PETA, and bean CHS15; GT-1 can stabilize the TFIIA-TBP-DNA (TATA box) complex; The activation mechanism of GT-1 may be achieved through direct interaction between TFIIA and GT-1; Binding of GT-1-like factors to the PR-1a promoter influences the level of SA-inducible gene expression | Upstream | -192 |
| | | Downstream | 982 |
| Motif_668 | TCA1MOTIF | TCA-1 (tobacco nuclear protein 1) binding site; Related to salicylic acid-inducible expression of many genes; Found in barley beta-1,3-glucanase and over 30 different plant genes which are known to be induced by one or more forms of stress; A similar sequence (TCATTTCTT) was found in tobacco Tnt1 retrotransposon promoter | Upstream | -80 |
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