| Matrix_109 | GBF3 | Not available | Upstream | -203 |
| Matrix_192 | FHY3/FAR1 | Not available | Upstream | -205 |
| Matrix_296 | GBF2 | Not available | Upstream | -202 |
| Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -202 |
| Matrix_331 | GBF1 | Not available | Upstream | -203 |
| Matrix_438 | AtbZIP63 | Not available | Upstream | -202 |
| Matrix_456 | bZIP60 | Not available | Upstream | -202 |
| Matrix_56 | BZIP17;BZIP28;BZIP49 | Not available | Upstream | -201 |
| Matrix_74 | LFY | Not available | Upstream | -85 |
| 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 | -20 |
| Motif_136 | SEF4MOTIFGM7S | SEF4 binding site; Soybean consensus sequence found in 5'upstream region (-199) of beta-conglycinin (7S globulin) gene (Gmg17.1); Binding with SEF4 (soybean embryo factor 4) | Upstream | -82 |
| Motif_150 | RBCSCONSENSUS | rbcS general consensus sequence; AATCCAA or AATCCAAC | Upstream | -180 |
| Motif_165 | AP3SV40 | AP-3 binding site consensus sequence in enhancer regions of SV40, MMTV, MLV, IL2 | Upstream | -74 |
| Motif_174 | SREATMSD | sugar-repressive element (SRE) found in 272 of the 1592 down-regulated genes after main stem decapitation in Arabidopsis | Upstream | -191 |
| Motif_193 | GLK1 | GLK transcription factors coordinate expression of the photosynthetic apparatus in Arabidopsis | Upstream | -182 |
| | | Upstream | -76 |
| Motif_244 | ABRE-like binding site motif | Not available | Upstream | -202 |
| Motif_274 | MYB1 binding site motif | Isolation and characterization of a fourth Arabidopsis thaliana G-box-binding factor, which has similarities to Fos oncoprotein | Upstream | -179 |
| Motif_275 | AtbZIP1 | The arabidopsis bZIP1 transcription factor is involved in sugar signaling, protein networking, and DNA binding | Upstream | -202 |
| 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 | -177 |
| Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Upstream | -147 |
| | | Upstream | -122 |
| Motif_332 | SV40COREENHAN | SV40 core enhancer; Similar sequences found in rbcS genes | Upstream | -75 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Upstream | -200 |
| Motif_391 | REALPHALGLHCB21 | REalpha found in Lemna gibba Lhcb21 gene promoter; Located at -134 to -129; Binding site of proteins of whole-cell extracts; The DNA binding activity is high in etiolated plants but much lower in green plants; Required for phytochrome regulation | Upstream | -175 |
| | | Upstream | -78 |
| Motif_399 | UPRMOTIFIAT | Motif I in the conserved UPR (unfolded protein response) cis-acting element in Arabidopsis genes coding for SAR1B, HSP-90, SBR-like, Ca-ATPase 4, CNX1, PDI, etc. | Upstream | -201 |
| Motif_440 | TGA1 binding site motif | Hex motif; Binding site of Arabidopsis bZIP protein TGA1 and G box binding factor GBF1; TGA1 and members of the GBF family differ in their DNA binding properties; G-Box-like element;TGA1 and G-box binding factors: two distinct classes of Arabidopsis leucine zipper proteins compete for the G-box-like element TGACGTGG | Upstream | -201 |
| Motif_453 | HEXMOTIFTAH3H4 | hexamer motif found in promoter of wheat histone genes H3 and H4; CaMV35S; NOS; Binding with HBP-1A and HBP-1B; Binding site of wheat nuclear protein HBP-1 (histone DNA binding protein-1); HBP-1 has a leucine zipper motif; hexamer motif in type 1 element may play important roles in regulation of replication- dependent but not of replication-independent expression of the wheat histone H3 gene;Rice OBF1-homodimer-binding site | Upstream | -199 |
| 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 | -203 |
| | | Upstream | -89 |
| Motif_558 | BOXIIPCCHS | Core of Box II/G box found in the parsley chs genes; Essential for light regulation | Upstream | -202 |
| Motif_576 | TGACGTVMAMY | TGACGT motif found in the Vigna mungo alpha-Amylase (Amy) gene promoter; Located between -128 and -123; Required for high level expression of alpha-Amylase in the cotyledons of the germinated seeds | Upstream | -199 |
| Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Upstream | -79 |
| Motif_627 | ACGTABREMOTIFA2OSEM | Experimentally determined sequence requirement of ACGT-core of motif A in ABRE of the rice gene, OSEM; DRE and ABRE are interdependent in the ABA-responsive expression of the rd29A in Arabidopsis | Upstream | -202 |
| Motif_652 | AUXRETGA2GMGH3 | TGA-box #2 in putative auxin-resonsive element (AUXRE) E1 of soybean GH3 promoter; Strong binding site for proteins in plant nuclear extracts; Hex-like element; E1 element=-249 to -203; E2 element=-241 to -224 | Upstream | -202 |
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