| Matrix_143 | GATA14;GATA6;GATA5 | Not available | Upstream | -337 |
| Matrix_203 | GATA9;GATA12 | Not available | Upstream | -337 |
| Matrix_25 | AP3 | Not available | Upstream | -611 |
| | | Upstream | -473 |
| Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Upstream | -694 |
| Matrix_39 | AP1 | Not available | Upstream | -656 |
| | | Upstream | -476 |
| Matrix_414 | AGL15 | Not available | Upstream | -609 |
| Matrix_48 | PI | Not available | Upstream | -656 |
| | | Upstream | -603 |
| | | Upstream | -476 |
| Matrix_74 | LFY | Not available | Upstream | -932 |
| Motif_1 | GT1CORE | Critical for GT-1 binding to box II of rbcS; Transcriptional activation by Arabidopsis GT-1 may be through interaction with TFIIA-TBP-TATA complex | Upstream | -548 |
| 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 | -456 |
| Motif_15 | AMYBOX2 | amylase box; amylase element; Conserved sequence found in 5'upstream region of alpha-amylase gene of rice, wheat, barley | Upstream | -259 |
| Motif_181 | IBOXCORENT | I-box core motif in the CAMs (conserved DNA modular arrays) associated with light-responsive promoter regions | Upstream | -685 |
| Motif_193 | GLK1 | GLK transcription factors coordinate expression of the photosynthetic apparatus in Arabidopsis | Upstream | -625 |
| Motif_222 | AGMOTIFNTMYB2 | AG-motif found at -114 of the promoter of NtMyb2 gene; NtMyb2 is a regulator of the tobacco retrotransposon Tto1 and the defence-related gene phenylalanine ammonia lyase (PAL), which are induced by various stress such as wounding or elicitor treatment; AGP1 (GATA-type zinc finger protein) binding site | Upstream | -74 |
| Motif_286 | SEBFCONSSTPR10A | Binding site of the potato silencing element binding factor (SEBF) gene found in promoter of pathogenesis-related gene (PR-10a); Located between -45 and -39; Similar to the auxin response element | Upstream | -770 |
| 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 | Upstream | -769 |
| 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 | -438 |
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