| Matrix_119 | RRTF1 | Not available | Upstream | -797 |
| Matrix_224 | ERF1 | Not available | Upstream | -797 |
| Matrix_234 | RAP2.3 | Not available | Upstream | -796 |
| Matrix_295 | ERF1 | Not available | Upstream | -798 |
| Matrix_355 | ERF10;ERF11 | Not available | Upstream | -797 |
| Matrix_360 | ORA59 | Not available | Upstream | -798 |
| Matrix_378 | ATERF1 | Not available | Upstream | -796 |
| Matrix_386 | AGL1 | DNA binding properties of two Arabidopsis MADS domain proteins: binding consensus and dimer formation | Upstream | -638 |
| Matrix_406 | ATERF-7 | Not available | Upstream | -798 |
| Matrix_426 | CRF1;CRF2 | Not available | Upstream | -797 |
| Matrix_43 | AG | Not available | Upstream | -638 |
| Matrix_445 | AG | Not available | Upstream | -638 |
| Matrix_45 | DRN | Not available | Upstream | -798 |
| Matrix_473 | RRTF1 | Not available | Upstream | -796 |
| Matrix_484 | ATERF13 | Not available | Upstream | -798 |
| Matrix_493 | AT1G22985;AT1G71130 | Not available | Upstream | -797 |
| Matrix_50 | ATERF14;AT5G43410 | Not available | Upstream | -797 |
| Matrix_506 | DRNL;ATERF-4 | Not available | Upstream | -797 |
| Matrix_517 | ERF12 | Not available | Upstream | -798 |
| Matrix_91 | CRF3 | Not available | Upstream | -797 |
| Matrix_98 | AG | Isolation and characterization of the binding sequences for the product of the Arabidopsis floral homeotic gene AGAMOUS | Upstream | -638 |
| 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 | -636 |
| 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 | -645 |
| 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 | -635 |
| 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 | -652 |
| 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 | Upstream | -646 |
| Motif_288 | NONAMERMOTIFTAH3H4 | Nonamer motif found in promoter of wheat histone genes H3 and H4 | Upstream | -743 |
| Motif_297 | Bellringer/replumless/pennywise BS1 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | Upstream | -886 |
| 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 | -798 |
| 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 | -705 |
| Motif_351 | GARE1OSREP1 | Gibberellin-responsive element (GARE) found in the promoter region of a cystein proteinase (REP-1) gene in rice | Upstream | -652 |
| 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 | -713 |
| Motif_395 | RHE_element | Functional Conservation of a Root Hair Cell-Specific cis-Element in Angiosperms with Different Root Hair Distribution Patterns | Upstream | -636 |
| Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | Upstream | -646 |
| Motif_520 | AMYBOX1 | amylase box; Conserved sequence found in 5'-upstream region of alpha-amylase gene of rice, wheat, barley | Upstream | -652 |
| 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 | -628 |
| Motif_567 | T/GBOXATPIN2 | T/G-box found in tomato proteinase inhibitor II (pin2) and leucine aminopeptidase (LAP) genes; Involved in jasmonate (JA) induction of these genes; bHLH-Leu zipper JAMYC2 and JAMYC10 proteins specifically recognize this motif | Upstream | -635 |
| 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 | -636 |
| 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 | -666 |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Upstream | -437 |
| 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 | -663 |
| | | Upstream | -708 |
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