| Matrix_104 | PI | Not available | Upstream | -1710 |
| Matrix_108 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -1776 |
| Matrix_113 | ABI5 | Not available | Upstream | -1708 |
| Matrix_118 | PIF3_2 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -1778 |
| | | Upstream | -1713 |
| Matrix_120 | BEE2 | Not available | Upstream | -1775 |
| Matrix_122 | ABF1;AREB2 | Not available | Upstream | -1710 |
| | | Upstream | -1709 |
| Matrix_129 | ABF1 | Not available | Upstream | -1709 |
| Matrix_134 | ABF1 | Not available | Upstream | -1709 |
| Matrix_145 | GBF4;AT5G44080 | Not available | Upstream | -1708 |
| Matrix_15 | PIF3_1 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -1779 |
| | | Upstream | -1713 |
| Matrix_153 | AP2 | Not available | Upstream | -1776 |
| Matrix_156 | POC1 | Not available | Upstream | -1776 |
| | | Upstream | -1710 |
| Matrix_191 | PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling | Upstream | -1778 |
| Matrix_192 | FHY3/FAR1 | Not available | Upstream | -1708 |
| Matrix_194 | HYH;HY5 | Not available | Upstream | -1712 |
| Matrix_214 | AP1 | Not available | Upstream | -1711 |
| Matrix_24 | POC1 | Not available | Upstream | -1779 |
| | | Upstream | -1713 |
| Matrix_251 | PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling | Upstream | -1712 |
| Matrix_264 | ATAREB1 | Not available | Upstream | -1712 |
| | | Upstream | -1709 |
| Matrix_27 | ATAIB;ATNIG1 | Not available | Upstream | -1774 |
| Matrix_296 | GBF2 | Not available | Upstream | -1708 |
| Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -1708 |
| Matrix_320 | MYC4 | Not available | Upstream | -1774 |
| Matrix_323 | BIM3 | Not available | Upstream | -1775 |
| Matrix_338 | AP2 | Not available | Upstream | -1712 |
| Matrix_345 | POC1 | Not available | Upstream | -1778 |
| | | Upstream | -1713 |
| Matrix_359 | FLC | Not available | Upstream | -1711 |
| Matrix_365 | AT1G10120;AT1G25330;CIB5;AT1G68920;AT3G23690;CIB1 | Not available | Upstream | -1774 |
| Matrix_369 | AT2G18300 | Not available | Upstream | -1777 |
| Matrix_403 | BZR1 | Not available | Upstream | -1711 |
| Matrix_443 | AGL15 | Not available | Upstream | -1711 |
| Matrix_449 | BIM2 | Not available | Upstream | -1775 |
| Matrix_53 | MYC3 | Not available | Upstream | -1777 |
| Matrix_55 | PIF3 | Not available | Upstream | -1710 |
| Matrix_60 | AT1G01260;AT5G57150 | Not available | Upstream | -1708 |
| Matrix_64 | PIF5 | Not available | Upstream | -1774 |
| Matrix_65 | POC1;PIL1 | Not available | Upstream | -1708 |
| Matrix_7 | PIF4 | Not available | Upstream | -1775 |
| | | Upstream | -1707 |
| Matrix_77 | PRR5 | Not available | Upstream | -1777 |
| | | Upstream | -1710 |
| Matrix_80 | BIM1 | Not available | Upstream | -1776 |
| Motif_104 | CAREOSREP1 | CAREs (CAACTC regulatory elements) found in the promoter region of a cystein proteinase (REP-1) gene in rice | Upstream | -556 |
| 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 | -1774 |
| | | Upstream | -1772 |
| Motif_16 | -300ELEMENT | Present upstream of the promoter from the B-hordein gene of barley and the alpha-gliadin, gamma-gliadin, and low molecular weight glutenin genes of wheat; See S000001 -300CORE; See S000002 -300MOTIF | Upstream | -1769 |
| 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 | -1773 |
| | | Upstream | -1707 |
| Motif_182 | MYB2CONSENSUSAT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis; see MYB2 and MYBATRD22 | Upstream | -1666 |
| Motif_189 | CMSRE1IBSPOA | CMSRE-1 (Carbohydrate Metabolite Signal Responsive Element 1) found in the promoter of sweet potato sporamin A gene | Upstream | -1712 |
| 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 | -1773 |
| | | Upstream | -1707 |
| 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 | -1774 |
| | | Upstream | -1708 |
| | | Upstream | -1707 |
| Motif_221 | MYBCORE | Binding site for all animal MYB and at least two plant MYB proteins ATMYB1 and ATMYB2, both isolated from Arabidopsis; ATMYB2 is involved in regulation of genes that are responsive to water stress in Arabidopsis; A petunia MYB protein (MYB.Ph3) is involved in regulation of flavonoid biosynthesis | Upstream | -1666 |
| Motif_244 | ABRE-like binding site motif | Not available | Upstream | -1709 |
| | | Upstream | -1707 |
| Motif_249 | DPBF1&2 binding site motif | A novel class of bZIP transcription factors, DPBF-1 and 2 (Dc3 promoter-binding factor-1 and 2) binding core sequence; Found in the carrot Dc3 gene promoter; Dc3 expression is normally embryo-specific, and also can be induced by ABA; The Arabidopsis abscisic acid response gene ABI5 encodes a bZIP transcription factor; abi5 mutant have a pleiotropic defects in ABA response; ABI5 regulates a subset of late embryogenesis-abundant genes; GIA1 (growth-insensitivity to ABA) is identical to ABI5; Isolation of a novel class of bZIP transcription factors that interact with ABA-responsive and embryo-specification elements in the Dc3 promoter using a modified yeast one-hybrid system | Upstream | -1707 |
| Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Upstream | -1666 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -1773 |
| | | Upstream | -1707 |
| Motif_365 | ARF1 binding site motif | ARF (auxin response factor) binding site found in the promoters of primary/early auxin response genes of Arabidopsis thaliana; AuxRE;Binding site of Arabidopsis ARF1 (Auxin response factor1); Sequence found in NDE element in Soybean SAUR (Small Auxin-Up RNA) 15A gene promoter;Found in D1 or D4 element in Soybean GH3 promoter; This element was enriched in the 5'-flanking region of genes up-regulated by both IAA and BL;Dimerization and DNA binding of auxin response factors | Upstream | -1703 |
| Motif_392 | PALBOXAPC | Box A; Consensus; One of three putative cis-acting elements (boxes P, A, and L) of phenylalanine ammonia-lyase (PAL; EC 4.3.1.5) genes in parsley (P.c.); None of these elements (boxes P, A, and L) alone, or the promoter region containing all of them together, conferred elicitor or light responsiveness. These elements appear to be necessary but not sufficient for elicitor- or light-mediated PAL gene activation; See also Box P, Box L | Upstream | -1712 |
| Motif_448 | IRO2OS | OsIRO2-binding core sequence; G-box plus G; Transcription factor OsIRO2 is induced exclusively by Fe deficiency | Upstream | -1708 |
| Motif_469 | QELEMENTZMZM13 | Q(quantitative)-element in maize ZM13 gene promoter; Found at -107 to -102; Involved in expression enhancing activity; ZM13 is a maize homolog of tomato LAT52 gene; ZM13 is a pollen-specific maize gene | Upstream | -1764 |
| Motif_498 | SGBFGMGMAUX28 | bZIP proteins SGBF-1 and SGBF-2 binding site in soybean GmAux28 gene promoter | Upstream | -1709 |
| 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 | -557 |
| | | Upstream | -547 |
| Motif_563 | PYRIMIDINEBOXOSRAMY1A | Pyrimidine box found in rice alpha-amylase (RAmy1A) gene; Gibberellin-respons cis-element of GARE and pyrimidine box are partially involved in sugar repression; Found in the promoter of barley alpha-amylase (Amy2/32b) gene which is induced in the aleurone layers in response to GA; BPBF protein binds specifically to this site | Upstream | -1767 |
| | | Upstream | -1661 |
| 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 | -1776 |
| Motif_627 | ACGTABREMOTIFA2OSEM | Experimentally determined sequence requirement of ACGT-core of motif A in ABRE of the rice gene, OSEM; DRE and ABRE are interdependent in the ABA-responsive expression of the rd29A in Arabidopsis | Upstream | -1706 |
| Motif_630 | WBOXNTCHN48 | W box identified in the region between -125 and -69 of a tobacco class I basic chitinase gene CHN48; NtWRKY1, NtWRKY2 and NtWRKY4 bound to W box; NtWRKYs possibly involved in elicitor-respsonsive transcription of defense genes in tobacco | Upstream | -1763 |
| Motif_72 | GADOWNAT | Sequence present in 24 genes in the GA-down regulated d1 cluster (106 genes) found in Arabidopsis seed germination; This motif is similar to ABRE | Upstream | -1706 |
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