| Matrix_109 | GBF3 | Not available | Upstream | -688 |
| Matrix_144 | AT5G08330;AT5G23280 | Not available | Upstream | -842 |
| Matrix_192 | FHY3/FAR1 | Not available | Upstream | -690 |
| Matrix_196 | TCP20;AT5G41030 | Not available | Upstream | -1465 |
| Matrix_217 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -690 |
| Matrix_229 | CDC5 | A cdc5+ homolog of a higher plant, Arabidopsis thaliana | Upstream | -794 |
| Matrix_232 | TCP23 | Not available | Upstream | -842 |
| Matrix_278 | AtbZIP44 | Not available | Upstream | -688 |
| Matrix_281 | TCP13 | Not available | Upstream | -841 |
| Matrix_294 | MEE35 | Not available | Upstream | -841 |
| Matrix_296 | GBF2 | Not available | Upstream | -687 |
| Matrix_297 | TCP15 | Not available | Upstream | -840 |
| Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -687 |
| Matrix_331 | GBF1 | Not available | Upstream | -688 |
| Matrix_348 | AT5G51910 | Not available | Upstream | -844 |
| | | Upstream | -841 |
| Matrix_41 | anac058 | Not available | Downstream | 9501 |
| Matrix_420 | ANAC58 | Not available | Downstream | 9500 |
| Matrix_438 | AtbZIP63 | Not available | Upstream | -687 |
| Matrix_44 | CUC3;anac046;NAC3;ANAC087;ATNAC6;CUC2 | Not available | Downstream | 9501 |
| Matrix_440 | LFY | Not available | Downstream | 9504 |
| Matrix_456 | bZIP60 | Not available | Upstream | -687 |
| Matrix_496 | ATMYB15 | Not available | Upstream | -1499 |
| Matrix_507 | TCP3 | Not available | Upstream | -842 |
| Matrix_517 | ERF12 | Not available | Upstream | -561 |
| Matrix_56 | BZIP17;BZIP28;BZIP49 | Not available | Upstream | -686 |
| Matrix_82 | TCP17 | Not available | Upstream | -841 |
| Motif_104 | CAREOSREP1 | CAREs (CAACTC regulatory elements) found in the promoter region of a cystein proteinase (REP-1) gene in rice | Upstream | -680 |
| 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 | -631 |
| 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 | -756 |
| 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 | -672 |
| 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 | -672 |
| Motif_235 | C8GCARGAT | Binding site of plant MADS-domain protein AGL15; CArG motif with a longer A/T-rich core;A variant of CArG motif, with a longer A/T-rich core; Binding site for AGL15 (AGAMOUS-like 15) | Upstream | -1287 |
| Motif_244 | ABRE-like binding site motif | Not available | Upstream | -687 |
| Motif_297 | Bellringer/replumless/pennywise BS1 IN AG | Repression of AGAMOUS by BELLRINGER in Floral and Inflorescence Meristems | Upstream | -1286 |
| Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Upstream | -325 |
| Motif_317 | GAREAT | GARE (GA-responsive element); Occurrence of GARE in GA-inducible, GA-responsible, and GA-nonresponsive genes found in Arabidopsis seed germination was 20, 18, and 12%, respectively | Upstream | -710 |
| 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 | -713 |
| Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Upstream | -672 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -685 |
| | | Upstream | -632 |
| 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 | -623 |
| Motif_346 | SND1;VND6;VND7;NST1;NST2 | Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis | Upstream | -315 |
| | | Downstream | 9490 |
| 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 | -756 |
| 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 | -1291 |
| Motif_391 | REALPHALGLHCB21 | REalpha found in Lemna gibba Lhcb21 gene promoter; Located at -134 to -129; Binding site of proteins of whole-cell extracts; The DNA binding activity is high in etiolated plants but much lower in green plants; Required for phytochrome regulation | Downstream | 9482 |
| Motif_399 | UPRMOTIFIAT | Motif I 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 | -686 |
| Motif_437 | ANAERO2CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1) | Downstream | 9513 |
| Motif_440 | TGA1 binding site motif | Hex motif; Binding site of Arabidopsis bZIP protein TGA1 and G box binding factor GBF1; TGA1 and members of the GBF family differ in their DNA binding properties; G-Box-like element;TGA1 and G-box binding factors: two distinct classes of Arabidopsis leucine zipper proteins compete for the G-box-like element TGACGTGG | Upstream | -686 |
| Motif_450 | E2FCONSENSUS | E2F consensus sequence of all different E2F-DP-binding motifs that were experimentally verified in plants | Upstream | -787 |
| Motif_453 | HEXMOTIFTAH3H4 | hexamer motif found in promoter of wheat histone genes H3 and H4; CaMV35S; NOS; Binding with HBP-1A and HBP-1B; Binding site of wheat nuclear protein HBP-1 (histone DNA binding protein-1); HBP-1 has a leucine zipper motif; hexamer motif in type 1 element may play important roles in regulation of replication- dependent but not of replication-independent expression of the wheat histone H3 gene;Rice OBF1-homodimer-binding site | Upstream | -684 |
| Motif_48 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Upstream | -630 |
| 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 | -649 |
| Motif_530 | CPBCSPOR | The sequence critical for Cytokinin-enhanced Protein Binding in vitro, found in -490 to -340 of the promoter of the cucumber POR (NADPH-protochlorophyllide reductase) gene | Upstream | -310 |
| Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -687 |
| Motif_562 | -300CORE | TGTAAAG core motif in -300 elements of alpha-zein genes of maize; -300 element core; prolamin box; P-box; Binds with P-box binding factor (PBF); Binds with BPBF (Barley PBF); PBF is a DNA-binding protein of the DOF class of transcription factors | Upstream | -755 |
| 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 | -631 |
| Motif_570 | POLASIG2 | PolyA signal; poly A signal found in rice alpha-amylase; -10 to -30 in the case of animal genes | Upstream | -1285 |
| Motif_576 | TGACGTVMAMY | TGACGT motif found in the Vigna mungo alpha-Amylase (Amy) gene promoter; Located between -128 and -123; Required for high level expression of alpha-Amylase in the cotyledons of the germinated seeds | Upstream | -684 |
| Motif_604 | EMHVCHORD | Endosperm motif (EM) found in the promoter of barley c-hordein gene; Involved in the nitrogen response of c-hordein promoter | Upstream | -756 |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Upstream | -20 |
| | | Upstream | -19 |
| | | Upstream | -18 |
| | | Upstream | -17 |
| Motif_626 | ACGTTBOX | T-box according to the nomenclature of ACGT elements; One of ACGT elements; See also ACGTABOX,ACGTCBOX, and CACGTGMOTIF | Upstream | -749 |
| 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 | -687 |
| Motif_641 | LRENPCABE | LRE; A positive light regulatory element in tobacco CAB (cab-E) gene; Located at -241 | Upstream | -688 |
| Motif_65 | BS1EGCCR | BS1 (binding site 1) found in E. gunnii Cinnamoyl-CoA reductase (CCR) gene promoter; nuclear protein binding site; Required for vascular expression | Upstream | -789 |
| Motif_652 | AUXRETGA2GMGH3 | TGA-box #2 in putative auxin-resonsive element (AUXRE) E1 of soybean GH3 promoter; Strong binding site for proteins in plant nuclear extracts; Hex-like element; E1 element=-249 to -203; E2 element=-241 to -224 | Upstream | -687 |
| 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 | -1489 |
| 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 | -242 |
| | | Upstream | -240 |
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