| Matrix_101 | ERF5 | Not available | Upstream | -1390 |
| | | Upstream | -1961 |
| Matrix_109 | GBF3 | Not available | Upstream | -1266 |
| | | Upstream | -1980 |
| Matrix_224 | ERF1 | Not available | Upstream | -1391 |
| Matrix_242 | AT2G25820;AT3G16280;AT4G32800;TINY2;tny | Not available | Upstream | -359 |
| Matrix_244 | DREB2C | Not available | Upstream | -358 |
| | | Upstream | -1718 |
| Matrix_261 | ATERF-1 | Not available | Upstream | -1391 |
| Matrix_305 | PIF4 | Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -215 |
| Matrix_326 | AT5G07310;Rap2.6L;AT5G61890 | Not available | Upstream | -1391 |
| Matrix_334 | AT3G23230 | Not available | Upstream | -1391 |
| Matrix_363 | RAP2.3 | Not available | Upstream | -1391 |
| Matrix_374 | AT5G07580;AT5G61590 | Not available | Upstream | -1960 |
| Matrix_377 | AT1G75490;DREB2C;AT2G40350;AT5G18450 | Not available | Upstream | -1391 |
| | | Upstream | -1719 |
| Matrix_385 | DEAR4 | Not available | Upstream | -358 |
| Matrix_394 | DREB_U | Not available | Upstream | -358 |
| Matrix_406 | ATERF-7 | Not available | Upstream | -1392 |
| | | Upstream | -1959 |
| Matrix_426 | CRF1;CRF2 | Not available | Upstream | -1391 |
| Matrix_478 | AT1G01250 | Not available | Upstream | -359 |
| Matrix_493 | AT1G22985;AT1G71130 | Not available | Upstream | -1391 |
| Matrix_73 | DEAR3;RAP2.9;RAP2.10 | Not available | Upstream | -359 |
| Matrix_86 | CRF5;CRF6;CRF4 | Not available | Upstream | -1391 |
| Matrix_91 | CRF3 | Not available | Upstream | -1391 |
| Matrix_92 | AT1G33760 | Not available | Upstream | -358 |
| Motif_125 | BOXIINTPATPB | Box II found in the tobacco plastid atpB gene promoter; Conserved in several NCII (nonconsensus type II) promoters of plastid genes; Important for the activity of this NCII promoter | Upstream | -332 |
| Motif_129 | GAGAGMGSA1 | GAGA element found in the promoter of the heme and chlorophyll synthesis gene Gsa1 in soybean; GAGA binding protein (GBP) binds to (GA)n/(CT)n DNA | Upstream | -8 |
| | | Upstream | -10 |
| | | Upstream | -12 |
| | | Upstream | -14 |
| | | Upstream | -16 |
| | | Upstream | -18 |
| Motif_168 | IBOX | I box; I-box; Conserved sequence upstream of light-regulated genes; Sequence found in the promoter region of rbcS of tomato and Arabidopsis; I box; Binding site of LeMYB1, that is a member of a novel class of myb-like proteins; LeMYBI act as a transcriptional activator; An evolutionarily conserved protein binding sequence upstream of a plant light-regulated gene | Downstream | 1123 |
| Motif_181 | IBOXCORENT | I-box core motif in the CAMs (conserved DNA modular arrays) associated with light-responsive promoter regions | Downstream | 1124 |
| 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 | -203 |
| Motif_195 | TATABOX4 | TATA box; TATA box found in the 5'upstream region of sweet potato sporamin A gene; TATA box found in beta-phaseolin promoter; sequence and spacing of TATA box elements are critical for accurate initiation | Upstream | -958 |
| Motif_254 | MYB46;MYB83 | MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes | Downstream | 1137 |
| Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Downstream | 1103 |
| Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Downstream | 1122 |
| Motif_313 | ERF1 BS in AtCHI-B | Core of GCC-box found in many pathogen-responsive genes such as PDF1.2, Thi2.1, and PR4; Has been shown to function as ethylene-responsive element; Appears to play important roles in regulating jasmonate-responsive gene expression; Tomato Pti4 (ERF) regulates defence-related gene expression via GCC box and non-GCC box cis elements (Myb1 (GTTAGTT) and G-box(CACGTG)); Nuclear events in ethylene signaling: a transcriptional cascade mediated by ETHYLENE-INSENSITIVE3 and ETHYLENE-RESPONSE-FACTOR1;Molecular responses to dehydration and low temperature | Upstream | -1392 |
| Motif_371 | DRE-like promoter motif | The Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses | Upstream | -359 |
| | | Upstream | -1486 |
| Motif_419 | MYB4 binding site motif | Not available | Downstream | 1137 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -8 |
| | | Upstream | -10 |
| | | Upstream | -12 |
| | | Upstream | -14 |
| | | Upstream | -16 |
| | | Upstream | -18 |
| | | Upstream | -20 |
| Motif_454 | DRECRTCOREAT | Core motif of DRE/CRT (dehydration-responsive element/C-repeat) cis-acting element found in many genes in Arabidopsis and in rice; Os DREB1A bound to GCCGAC more preferentially than to ACCGAC whereas At DREB1A bound to both GCCGAC and ACCGAC efficiently; Maize ZmDREB1A bound to DRE; HaDREB2 in Helianthus annuus (sunflower) | Upstream | -359 |
| | | Upstream | -1487 |
| Motif_49 | TATAPVTRNALEU | TATA-like motif; A TATA-like sequence found in Phaseolus vulgaris tRNALeu gene promoter; Frequently observed upstream of plant tRNA genes; Found in maize glycolytic glyceraldehyde-3-phospate dehydrogenase 4 (GapC4) gene promoter; Binding site of TATA binding protein (TBP) | Upstream | -957 |
| Motif_495 | TRANSINITMONOCOTS | Context sequence of translational initiation codon in monocots | Downstream | 1038 |
| Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | Downstream | 1138 |
| Motif_54 | LTREATLTI78 | Putative low temperature responsive element (LTRE); Found in Arabidopsis thaliana low-temperature-induced (lti) genes, lti78 and lti65; Repeated four times in lti78 which is also known as cor78 and rd29A; Found also in barley low temperature responsive genes, blt4.2, blt4.6, blt4.9 (lipid transfer genes); cold inducible; See LTRECORE; Also present in rab18, kin1, and kin2; Differential expression of two related, low-temperature-induced genes in Arabidopsis thaliana | Upstream | -359 |
| 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 | -386 |
| | | Upstream | -511 |
| Motif_591 | CBFHV | Binding site of barley CBF1, and also of barley CBF2; CBF = C-repeat (CRT) binding factors; CBFs are also known as dehydration-responsive element (DRE) binding proteins (DREBs) | Upstream | -359 |
| Motif_643 | DRE2COREZMRAB17 | DRE2 core found in maize rab17 gene promoter; DBF1 and DBF2 bound to DRE2; rab17 is expressed during late embryogenesis, and is induced by ABA | Upstream | -359 |
| 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 | -329 |
| | | Upstream | -336 |
| Motif_682 | GT1GMSCAM4 | GT-1 motif found in the promoter of soybean CaM isoform, SCaM-4; Plays a role in pathogen- and salt-induced SCaM-4 gene expression | Upstream | -329 |
| Motif_69 | CTRMCAMV35S | CT-rich motif (inverted GAGA) found in a 60-nucleotide region (S1) downstream of the transcription start site of the CaMV 35S RNA; Can enhance gene expression; Inverted GAGA | Upstream | -8 |
| | | Upstream | -10 |
| | | Upstream | -12 |
| | | Upstream | -14 |
| | | Upstream | -16 |
| | | Upstream | -18 |
| | | Upstream | -20 |
| | | Upstream | -22 |
| | | Upstream | -24 |
| | | Upstream | -26 |
| | | Upstream | -92 |
| | | Upstream | -94 |
| Motif_76 | SURE1STPAT21 | Sucrose Responsive Element (SURE); A motif conserved among genes regulated by sucrose; See also SURE2STPAT21; Found between -184 and -156 bp in the patatin (a major tuber protein) gene promoter of potato | Upstream | -330 |
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