| Matrix_130 | TCP16 | Not available | Upstream | -1403 |
| Matrix_144 | AT5G08330;AT5G23280 | Not available | Upstream | -1403 |
| Matrix_196 | TCP20;AT5G41030 | Not available | Upstream | -1518 |
| | | Upstream | -1401 |
| Matrix_216 | TCP16 | Not available | Upstream | -1403 |
| Matrix_232 | TCP23 | Not available | Upstream | -1522 |
| | | Upstream | -1519 |
| Matrix_266 | TCP16 | Determinants of the DNA binding specificity of class I and class II TCP transcription factors | Upstream | -1403 |
| Matrix_278 | AtbZIP44 | Not available | Upstream | -1264 |
| Matrix_294 | MEE35 | Not available | Upstream | -1403 |
| Matrix_297 | TCP15 | Not available | Upstream | -1522 |
| | | Upstream | -1519 |
| Matrix_348 | AT5G51910 | Not available | Upstream | -1521 |
| | | Upstream | -1520 |
| | | Upstream | -1403 |
| Matrix_40 | TCP2 | Not available | Upstream | -1403 |
| Matrix_42 | AT2G45680 | Not available | Upstream | -1521 |
| | | Upstream | -1520 |
| | | Upstream | -1403 |
| Matrix_48 | PI | Not available | Upstream | -296 |
| Matrix_488 | ABF1 | Not available | Upstream | -1504 |
| Matrix_507 | TCP3 | Not available | Upstream | -1519 |
| Matrix_82 | TCP17 | Not available | Upstream | -1403 |
| Matrix_94 | TCP5 | Not available | Upstream | -1403 |
| Motif_104 | CAREOSREP1 | CAREs (CAACTC regulatory elements) found in the promoter region of a cystein proteinase (REP-1) gene in rice | Downstream | 10119 |
| 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 | -1281 |
| Motif_145 | MYCATERD1 | MYC recognition sequence (from -466 to -461) necessary for expression of erd1 (early responsive to dehydration) in dehydrated Arabidopsis; NAC protein bound specifically to the CATGTG motif; NAC protein bound specifically to the CATGTG motif | Upstream | -1501 |
| 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 | -1781 |
| | | Downstream | 10100 |
| 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 | 10124 |
| 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 | 10124 |
| 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 | 10124 |
| Motif_223 | LTRE1HVBLT49 | LTRE-1 (low-temperature-responsive element) in barley (H.v.) blt4.9 gene promoter; A new LTRE; A previously known LTRE is CCGAC | Upstream | -1268 |
| 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 | Upstream | -1863 |
| 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 | -1272 |
| Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Downstream | 10124 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -1282 |
| 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 | -1273 |
| Motif_357 | NTBBF1ARROLB | NtBBF1(Dof protein from tobacco) binding site in Agrobacterium rhizogenes rolB gene; Found in regulatory domain B (-341 to -306); Required for tissue-specific expression and auxin induction | Upstream | -1407 |
| Motif_375 | ERELEE4 | ERE (ethylene responsive element) of tomato E4 and carnation GST1 genes; GST1 is related to senescence; Found in the 5'-LTR region of TLC1.1 retrotransposon family in Lycopersicon chilense; ERE motifs mediate ethylene-induced activation of the U3 promoter region | Upstream | -1748 |
| Motif_447 | AtMYC2 BS in RD22;PIF4 | Binding site for MYC (rd22BP1) in Arabidopsis dehydration-resposive gene, rd22; MYC binding site in rd22 gene of Arabidopsis thaliana; ABA-induction; Located at ca. -200 of rd22 gene; Also MYB at ca. -141 of rd22 gene; See also MYBATRD22; Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -1501 |
| Motif_48 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -1280 |
| 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 | 10118 |
| Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -1496 |
| 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 | -1281 |
| Motif_626 | ACGTTBOX | T-box according to the nomenclature of ACGT elements; One of ACGT elements; See also ACGTABOX,ACGTCBOX, and CACGTGMOTIF | Upstream | -1390 |
| 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 | -1496 |
| Motif_641 | LRENPCABE | LRE; A positive light regulatory element in tobacco CAB (cab-E) gene; Located at -241 | Upstream | -1497 |
| 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 | -1270 |
| Motif_683 | AtMYB2 BS in RD22 | Binding site for MYB (ATMYB2) in dehydration-responsive gene, rd22; MYB binding site in rd22 gene of Arabidopsis thaliana; ABA-induction; Located at ca. -141 of rd22 gene; Also MYC at ca. -200 of rd22 gene; Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression | Upstream | -1607 |
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