| Matrix_123 | FUSCA3 | Not available | Upstream | -170 |
| Matrix_127 | AtMYB15 | More than 80R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana | Upstream | -152 |
| Matrix_179 | AtMYB84;MYB36;MYB68;O49746_ARATH | Not available | Upstream | -152 |
| Matrix_211 | MYB3 | Not available | Upstream | -153 |
| Matrix_27 | ATAIB;ATNIG1 | Not available | Upstream | -163 |
| Matrix_299 | PFG3 | Not available | Upstream | -152 |
| Matrix_315 | MYB111 | Not available | Upstream | -152 |
| Matrix_320 | MYC4 | Not available | Upstream | -163 |
| Matrix_352 | LEC2 | Not available | Upstream | -171 |
| | | Upstream | -168 |
| Matrix_365 | AT1G10120;AT1G25330;CIB5;AT1G68920;AT3G23690;CIB1 | Not available | Upstream | -163 |
| Matrix_369 | AT2G18300 | Not available | Upstream | -166 |
| Matrix_371 | MYB7;AtMYB6;AtMYB32;ATMYB4 | Not available | Upstream | -151 |
| Matrix_455 | MYB111 | Not available | Upstream | -152 |
| Matrix_496 | ATMYB15 | Not available | Upstream | -152 |
| Matrix_510 | AtMYB84 | More than 80 R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana | Upstream | -152 |
| Matrix_64 | PIF5 | Not available | Upstream | -163 |
| 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 | -163 |
| | | Upstream | -161 |
| Motif_179 | CACGTGMOTIF;BES1;PIF4;PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling;A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana; CACGTG motif; G-box; Binding site of Arabidopsis GBF4; C. roseus G-box binding factor 1 (CrGBF1) and 1 (CrGBF2) can act as transcriptional repressors of the Str promoter via direct interaction with the G-box; Essential for expression of beta-phaseolin gene during embryogenesis in bean, tobacco, Arabidopsis; Tomato Pti4 (ERF) regulates defense-related gene expression via GCC box and non-GCC box cis-element (Myb1 (GTTAGTT) and G-box (CACGTG)); Isolation and characterization of a fourth Arabidopsis thaliana G-box-binding factor, which has similarities to Fos oncoprotein; Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -162 |
| Motif_192 | BOXLCOREDCPAL | Consensus of the putative core sequences of box-L-like sequences in carrot; PAL1 promoter region; DCMYB1 bound to these sequences in vitro | Upstream | -150 |
| 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 | -162 |
| 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 | -1348 |
| 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 | -163 |
| Motif_22 | RYREPEATLEGUMINBOX | RY repeat (CATGCAY) or legumin box found in seed-storage protein genes in legume such as soybean | Upstream | -169 |
| | | Upstream | -166 |
| 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 | -237 |
| | | Upstream | -150 |
| 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 | -149 |
| 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 | -215 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -162 |
| Motif_395 | RHE_element | Functional Conservation of a Root Hair Cell-Specific cis-Element in Angiosperms with Different Root Hair Distribution Patterns | Upstream | -168 |
| Motif_419 | MYB4 binding site motif | Not available | Upstream | -237 |
| | | Upstream | -150 |
| Motif_469 | QELEMENTZMZM13 | Q(quantitative)-element in maize ZM13 gene promoter; Found at -107 to -102; Involved in expression enhancing activity; ZM13 is a maize homolog of tomato LAT52 gene; ZM13 is a pollen-specific maize gene | Upstream | -226 |
| 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 | -1349 |
| Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | Upstream | -238 |
| | | Upstream | -151 |
| Motif_585 | ATB2/AtbZIP53/AtbZIP44/GBF5 BS in ProDH | PRE (Pro- or hypoosmolarity-responsive element) found in the promoter region of proline dehydrogenase (ProDH) gene in Arabidopsis; Core of 9-bp sequence ACTCATCCT which is necessary for the efficient expression of ProDH in response to L-Pro and hypoosmolarity; ATB2-binding site; Similar to GCN4 motif (ATGA(C/G)TCAT); ATB2 subgroup of bZIP transcription factors function as transcriptional activator for hypoosmolarity-inducible ProDH; A Novel Subgroup of bZIP Proteins Functions as Transctiptional Activators in Hypsosmolarity-Responsive Expression of the ProDH gene in Arabidopsis | Upstream | -232 |
| Motif_640 | RYREPEATBNNAPA | RY repeat found in RY/G box (the complex containing the two RY repeats and the G-box) of napA gene in Brassica napus; Found between -78 and -50; Required for seed specific expression;dist B ABRE mediated transactivation by ABI3 adn ABI3-dependent response to ABA; a tetramer of the composite RY/G complex mediated only ABA-independent transactivation by ABI3; B2 domain of ABI3 is necessary for ABA-independent and ABA-dependent activation through the dist B ABRE | Upstream | -168 |
| | | Upstream | -166 |
| Motif_666 | MYB binding site promoter | A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes | Upstream | -238 |
| | | Upstream | -151 |
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