| Matrix_124 | AtHB23;ATHB13;ATHB20;ATHB5 | Not available | Upstream | -286 |
| Matrix_140 | ATHB5 | DNA-binding and dimerization preferences of Arabidopsis homeodomain-leucine zipper transcription factors in vitro | Upstream | -286 |
| Matrix_208 | AP1 | Not available | Upstream | -1086 |
| Matrix_431 | ATHB21;HB-3 | Not available | Upstream | -286 |
| Matrix_439 | AP3 | Not available | Upstream | -346 |
| 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 | Upstream | -531 |
| Motif_125 | BOXIINTPATPB | Box II found in the tobacco plastid atpB gene promoter; Conserved in several NCII (nonconsensus type II) promoters of plastid genes; Important for the activity of this NCII promoter | Upstream | -460 |
| 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 | -233 |
| | | Upstream | -235 |
| | | Upstream | -237 |
| | | Upstream | -239 |
| | | Upstream | -241 |
| | | Upstream | -243 |
| | | Upstream | -245 |
| | | Upstream | -247 |
| | | Upstream | -249 |
| | | Upstream | -251 |
| | | Upstream | -253 |
| | | Upstream | -255 |
| | | Upstream | -257 |
| | | Upstream | -259 |
| Motif_165 | AP3SV40 | AP-3 binding site consensus sequence in enhancer regions of SV40, MMTV, MLV, IL2 | Upstream | -222 |
| Motif_183 | TRANSINITDICOTS | Context sequence of translational initiation codon in dicots | Upstream | -356 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -233 |
| | | Upstream | -235 |
| | | Upstream | -237 |
| | | Upstream | -239 |
| | | Upstream | -241 |
| | | Upstream | -243 |
| | | Upstream | -245 |
| | | Upstream | -247 |
| | | Upstream | -249 |
| | | Upstream | -251 |
| | | Upstream | -253 |
| | | Upstream | -255 |
| | | Upstream | -257 |
| | | Upstream | -259 |
| | | Upstream | -261 |
| Motif_495 | TRANSINITMONOCOTS | Context sequence of translational initiation codon in monocots | Upstream | -356 |
| 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 | -379 |
| 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 | -302 |
| Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Upstream | -224 |
| 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 | -354 |
| | | Upstream | -463 |
| Motif_682 | GT1GMSCAM4 | GT-1 motif found in the promoter of soybean CaM isoform, SCaM-4; Plays a role in pathogen- and salt-induced SCaM-4 gene expression | Upstream | -354 |
| | | Upstream | -463 |
| 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 | -234 |
| | | Upstream | -236 |
| | | Upstream | -238 |
| | | Upstream | -240 |
| | | Upstream | -242 |
| | | Upstream | -244 |
| | | Upstream | -246 |
| | | Upstream | -248 |
| | | Upstream | -250 |
| | | Upstream | -252 |
| | | Upstream | -254 |
| | | Upstream | -256 |
| | | Upstream | -258 |
| | | Upstream | -260 |
| | | Upstream | -262 |
| | | Upstream | -264 |
| | | Upstream | -266 |
| | | Upstream | -268 |
| Motif_83 | CIACADIANLELHC | Region necessary for circadian expression of tomato Lhc gene | Upstream | -386 |
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