| Matrix_126 | RBE | Not available | Upstream | -499 |
| Matrix_130 | TCP16 | Not available | Upstream | -440 |
| Matrix_196 | TCP20;AT5G41030 | Not available | Upstream | -437 |
| Matrix_216 | TCP16 | Not available | Upstream | -440 |
| Matrix_232 | TCP23 | Not available | Upstream | -441 |
| Matrix_266 | TCP16 | Determinants of the DNA binding specificity of class I and class II TCP transcription factors | Upstream | -440 |
| Matrix_269 | FHY3/FAR1 | Not available | Upstream | -1062 |
| Matrix_290 | AP2 | Not available | Upstream | -440 |
| Matrix_294 | MEE35 | Not available | Upstream | -440 |
| Matrix_297 | TCP15 | Not available | Upstream | -441 |
| | | Upstream | -438 |
| Matrix_348 | AT5G51910 | Not available | Upstream | -440 |
| | | Upstream | -439 |
| Matrix_42 | AT2G45680 | Not available | Upstream | -440 |
| Matrix_490 | AtMYB77;ATMYB44 | Not available | Upstream | -491 |
| Matrix_507 | TCP3 | Not available | Upstream | -441 |
| Matrix_82 | TCP17 | Not available | Upstream | -440 |
| Matrix_94 | TCP5 | Not available | Upstream | -440 |
| Motif_150 | RBCSCONSENSUS | rbcS general consensus sequence; AATCCAA or AATCCAAC | Upstream | -18 |
| Motif_155 | NODCON1GM | One of two putative nodulin consensus sequences; See also NODCON2GM; One of the consensus sequence motifs of organ-specific elements (OSE) characteristic of the promoters activated in infected cells of root nodules | Upstream | -524 |
| Motif_165 | AP3SV40 | AP-3 binding site consensus sequence in enhancer regions of SV40, MMTV, MLV, IL2 | Upstream | -24 |
| Motif_181 | IBOXCORENT | I-box core motif in the CAMs (conserved DNA modular arrays) associated with light-responsive promoter regions | Upstream | -1431 |
| 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 | -532 |
| Motif_193 | GLK1 | GLK transcription factors coordinate expression of the photosynthetic apparatus in Arabidopsis | Upstream | -20 |
| 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 | -532 |
| | | Upstream | -491 |
| 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 | -517 |
| Motif_332 | SV40COREENHAN | SV40 core enhancer; Similar sequences found in rbcS genes | Upstream | -23 |
| Motif_336 | MYBMOUSE | Binding site for mouse c-myb protein | Upstream | -532 |
| Motif_435 | E2FBNTRNR | E2Fb found in the tobacco RNR (Ribonucleotide reductase) gene promoter; Binding site of tobacco E2F; Involved in upregulation of the promoter at G1/S transition; dE2F (distal reverse E2F element) important for regulating specific RNR1a gene expression in respsonse to UV-C irradiation | Upstream | -520 |
| Motif_450 | E2FCONSENSUS | E2F consensus sequence of all different E2F-DP-binding motifs that were experimentally verified in plants | Upstream | -520 |
| Motif_459 | SORLIP1 | Identification of key promoter motifs involved in the network of light-regulated gene expression by combined analysis of genomic sequence and microarray data | Upstream | -500 |
| | | Upstream | -322 |
| Motif_628 | TATCCAOSAMY | TATCCA element found in alpha-amylase promoters of rice at positions ca.90 to 150bp upstream of the transcription start sites; Binding sites of OsMYBS1, OsMYBS2 and OsMYBS3 which mediate sugar and hormone regulation of alpha-amylase gene expression; See also AMYBOX2 | Upstream | -935 |
| 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 | -536 |
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