| Matrix_184 | AGL15 | Not available | Intron | 486 |
| | | Intron | 480 |
| Matrix_269 | FHY3/FAR1 | Not available | Upstream | -381 |
| | | Upstream | -384 |
| | | Upstream | -386 |
| | | Upstream | -387 |
| Matrix_290 | AP2 | Not available | Intron | 675 |
| Matrix_366 | ARR14 | Not available | Intron | 400 |
| Matrix_371 | MYB7;AtMYB6;AtMYB32;ATMYB4 | Not available | Upstream | -525 |
| Matrix_39 | AP1 | Not available | Upstream | -384 |
| Matrix_401 | MYB55 | Not available | Upstream | -524 |
| Motif_116 | INRNTPSADB | Inr (initiator) elements found in the tobacco psaDb gene promoter without TATA boxes; Light-responsive transcription of psaDb depends on Inr, but not TATA box | Downstream | 3651 |
| 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 | -414 |
| | | Upstream | -416 |
| | | Upstream | -418 |
| | | Upstream | -420 |
| | | Upstream | -422 |
| | | Upstream | -424 |
| | | Upstream | -426 |
| | | Upstream | -428 |
| Motif_150 | RBCSCONSENSUS | rbcS general consensus sequence; AATCCAA or AATCCAAC | Upstream | -509 |
| Motif_216 | PYRIMIDINEBOXHVEPB1 | Pyrimidine box found in the barley EPB-1 (cysteine proteinase) gene promoter; Located between -120 to -113; Required for GA induction | Upstream | -260 |
| 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 | -1774 |
| 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 | -518 |
| 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 | -1770 |
| Motif_365 | ARF1 binding site motif | ARF (auxin response factor) binding site found in the promoters of primary/early auxin response genes of Arabidopsis thaliana; AuxRE;Binding site of Arabidopsis ARF1 (Auxin response factor1); Sequence found in NDE element in Soybean SAUR (Small Auxin-Up RNA) 15A gene promoter;Found in D1 or D4 element in Soybean GH3 promoter; This element was enriched in the 5'-flanking region of genes up-regulated by both IAA and BL;Dimerization and DNA binding of auxin response factors | Downstream | 3589 |
| Motif_419 | MYB4 binding site motif | Not available | Upstream | -1774 |
| Motif_437 | ANAERO2CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1) | Intron | 389 |
| | | Upstream | -446 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -414 |
| | | Upstream | -416 |
| | | Upstream | -418 |
| | | Upstream | -420 |
| | | Upstream | -422 |
| | | Upstream | -424 |
| | | Upstream | -426 |
| | | Upstream | -428 |
| | | Upstream | -430 |
| 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 | -506 |
| Motif_549 | TBF1 | The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition | Upstream | -385 |
| 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 | -25 |
| Motif_662 | MYB26PS | Myb26 binding site; Myb26 recognizes the c-Myb and P-box-like binding sites representing cis-elements in the promoter regions of several phenylpropanoid biosynthetic genes; Identical to P-box in maize, and to Myb305 binding site in snapdragon | Upstream | -1774 |
| Motif_666 | MYB binding site promoter | A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes | Upstream | -1774 |
| 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 | -413 |
| | | Upstream | -415 |
| | | Upstream | -417 |
| | | Upstream | -419 |
| | | Upstream | -421 |
| | | Upstream | -423 |
| | | Upstream | -425 |
| | | Upstream | -427 |
| | | Upstream | -429 |
| | | Upstream | -431 |
| | | Upstream | -433 |
| | | Upstream | -435 |
| | | Upstream | -437 |
| 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 | -653 |
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