| Matrix_110 | ATABI4;AT3G57600 | Not available | Upstream | -358 |
| | | Upstream | -361 |
| Matrix_118 | PIF3_2 | Direct targeting of light signals to a promoter element-bound transcription factor | Upstream | -369 |
| Matrix_179 | AtMYB84;MYB36;MYB68;O49746_ARATH | Not available | Upstream | -428 |
| | | Upstream | -568 |
| Matrix_192 | FHY3/FAR1 | Not available | Upstream | -314 |
| Matrix_196 | TCP20;AT5G41030 | Not available | Upstream | -535 |
| Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -314 |
| Matrix_237 | MYB55 | Not available | Upstream | -460 |
| Matrix_301 | PIL5 | Not available | Upstream | -308 |
| Matrix_34 | RAV1_2 | RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants | Upstream | -363 |
| Matrix_356 | PRR5 | Not available | Upstream | -306 |
| Matrix_467 | RAV1 | Not available | Upstream | -363 |
| Matrix_47 | AtMYB77 | Not available | Downstream | 9060 |
| Matrix_477 | RAV1 | Not available | Upstream | -363 |
| Matrix_48 | PI | Not available | Upstream | -431 |
| Matrix_482 | AT2G25650;AT4G00270 | Not available | Upstream | -376 |
| Matrix_488 | ABF1 | Not available | Upstream | -363 |
| | | Upstream | -364 |
| Matrix_498 | AT2G28710;AT3G46070;AT3G46080;ZAT7 | Not available | Upstream | -537 |
| Matrix_510 | AtMYB84 | More than 80 R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana | Upstream | -568 |
| Matrix_68 | AtMYB77 | More than 80 R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana. Plant J 14: 273-84 | Downstream | 9060 |
| Motif_1 | GT1CORE | Critical for GT-1 binding to box II of rbcS; Transcriptional activation by Arabidopsis GT-1 may be through interaction with TFIIA-TBP-TATA complex | Downstream | 9067 |
| 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 | -2 |
| Motif_171 | TCP binding consensus | found enriched in peaks in chip-seq data for SEP3 | Downstream | 9022 |
| | | Upstream | -171 |
| 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 | Downstream | 9059 |
| Motif_193 | GLK1 | GLK transcription factors coordinate expression of the photosynthetic apparatus in Arabidopsis | Upstream | -556 |
| | | Upstream | -614 |
| 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 | Downstream | 9059 |
| 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 | -103 |
| 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 | Downstream | 9059 |
| | | Upstream | -179 |
| Motif_244 | ABRE-like binding site motif | Not available | Upstream | -314 |
| 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 | -539 |
| Motif_274 | MYB1 binding site motif | Isolation and characterization of a fourth Arabidopsis thaliana G-box-binding factor, which has similarities to Fos oncoprotein | Upstream | -462 |
| Motif_292 | MYBPZM | Core of consensus maize P (myb homolog) binding site; 6 bp core; Maize P gene specifies red pigmentation of kernel pericarp, cob, and other floral organs; P binds to A1 gene, but not Bz1 gene; Maize C1 (myb homolog) activates both A1 and Bz1 genes | Downstream | 9026 |
| | | Upstream | -462 |
| Motif_318 | CGCGBOXAT | CGCG box recognized by AtSR1-6 (Arabidopsis thaliana signal-responsive genes); Multiple CGCG elements are found in promoters of many genes; Ca2+/calmodulin binds to all AtSRs | Upstream | -423 |
| Motif_321 | TATABOX5 | TATA box; TATA box found in the 5'upstream region of pea (Pisum sativum) glutamine synthetase gene; a functional TATA element by in vivo analysis | Upstream | -182 |
| Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Downstream | 9059 |
| Motif_370 | TATABOX2 | TATA box; TATA box found in the 5'upstream region of pea legA gene; sporamin A of sweet potato; TATA box found in beta-phaseolin promoter; sequence and spacing of TATA box elements are critical for accurate initiation | Upstream | -105 |
| | | Upstream | -111 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -2 |
| | | Upstream | -4 |
| 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 | -103 |
| 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 | Downstream | 9041 |
| Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -315 |
| Motif_603 | SITEIIATCYTC | Site II element found in the promoter regions of cytochrome genes (Cytc-1, Cytc-2) in Arabidopsis; Located between -147 and -156 from the translational starts sites;Overrepresented in the promoters of nuclear genes encoding components of the oxidative phosphorylation (OxPhos) machinery from both Arabidopsis and rice | Upstream | -536 |
| Motif_606 | NAPINMOTIFBN | Sequence found in 5' upstream region (-6, -95, -188) of napin (2S albumin) gene in Brassica napus; Interact with a protein present in crude nuclear extracts from developing B. napus seeds | Downstream | 8903 |
| Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Downstream | 9066 |
| 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 | -315 |
| Motif_631 | MARARS | ARS element; Motif found in SAR (MAR) | Upstream | -107 |
| Motif_638 | ABRE binding site motif | Not available | Upstream | -314 |
| 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 | Downstream | 8897 |
| Motif_667 | TATABOXOSPAL | Binding site for OsTBP2, found in the promoter of rice pal gene encoding phenylalanine ammonia-lyase; OsTFIIB stimulated the DNA binding and bending activities of OsTBP2 and synergistically enhanced OsTBP2-mediated transcription from the pal promoter | Upstream | -183 |
| 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 | Downstream | 8897 |
| Motif_689 | ANAC092 | NAC Transcription Factor ORE1 and Senescence-Induced BIFUNCTIONAL NUCLEASE1 (BFN1) Constitute a Regulatory Cascade in Arabidopsis | Upstream | -564 |
| 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 | -2 |
| | | Upstream | -4 |
| | | Upstream | -6 |
| | | Upstream | -8 |
| | | Upstream | -10 |
| | | Upstream | -53 |
| | | Upstream | -154 |
| Motif_79 | UPRMOTIFIIAT | Motif II in the conserved UPR (unfolded protein response) cis-acting element in Arabidopsis genes coding for SAR1B, HSP-90, SBR-like, Ca-ATPase 4, CNX1, PDI, etc | Upstream | -353 |
| Motif_98 | SEF3MOTIFGM | SEF3 binding site; Soybean consensus sequence found in the 5' upstream region of beta-conglycinin (7S globulin) gene; AACCCA(-27bp-)AACCCA; SEF=soybean embryo factor; SEF2; SEF3; SEF4 | Upstream | -808 |
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