| Matrix_101 | ERF5 | Not available | Upstream | -1598 |
| Matrix_147 | ERF3;AT1G80580 | Not available | Upstream | -1598 |
| Matrix_19 | PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling | Upstream | -1438 |
| Matrix_209 | RAP2.6 | Not available | Upstream | -1596 |
| Matrix_215 | ARF1 | ARF1, a transcription factor that binds to auxin response elements | Upstream | -982 |
| | | Upstream | -983 |
| Matrix_243 | RAP2.12;RAP2.2 | Not available | Upstream | -1599 |
| Matrix_277 | RAP2.6 | Not available | Upstream | -1597 |
| Matrix_285 | DDF1 | Not available | Upstream | -1596 |
| Matrix_287 | ERF2 | Not available | Upstream | -1598 |
| Matrix_295 | ERF1 | Not available | Upstream | -1598 |
| Matrix_334 | AT3G23230 | Not available | Upstream | -1599 |
| Matrix_34 | RAV1_2 | RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants | Upstream | -1438 |
| Matrix_344 | ATERF15;AT4G18450 | Not available | Upstream | -1598 |
| Matrix_360 | ORA59 | Not available | Upstream | -1598 |
| Matrix_374 | AT5G07580;AT5G61590 | Not available | Upstream | -1598 |
| Matrix_39 | AP1 | Not available | Upstream | -193 |
| | | Upstream | -1099 |
| | | Upstream | -1100 |
| Matrix_406 | ATERF-7 | Not available | Upstream | -1596 |
| Matrix_462 | ATERF-8 | Not available | Upstream | -1596 |
| Matrix_467 | RAV1 | Not available | Upstream | -1438 |
| Matrix_477 | RAV1 | Not available | Upstream | -1438 |
| Matrix_48 | PI | Not available | Upstream | -57 |
| | | Upstream | -1099 |
| Matrix_482 | AT2G25650;AT4G00270 | Not available | Upstream | -1600 |
| Matrix_484 | ATERF13 | Not available | Upstream | -1598 |
| Matrix_50 | ATERF14;AT5G43410 | Not available | Upstream | -1597 |
| Motif_104 | CAREOSREP1 | CAREs (CAACTC regulatory elements) found in the promoter region of a cystein proteinase (REP-1) gene in rice | Upstream | -1112 |
| 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 | -1457 |
| 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 | -956 |
| Motif_145 | MYCATERD1 | MYC recognition sequence (from -466 to -461) necessary for expression of erd1 (early responsive to dehydration) in dehydrated Arabidopsis; NAC protein bound specifically to the CATGTG motif; NAC protein bound specifically to the CATGTG motif | Upstream | -1624 |
| 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 | -469 |
| Motif_165 | AP3SV40 | AP-3 binding site consensus sequence in enhancer regions of SV40, MMTV, MLV, IL2 | Upstream | -1626 |
| Motif_171 | TCP binding consensus | found enriched in peaks in chip-seq data for SEP3 | Upstream | -1442 |
| Motif_194 | EBOXBNNAPA | E-box of napA storage-protein gene of Brassica napus;This sequence is also known as RRE (R response element); MYC recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis; Binding site of ATMYC2 (previously known as rd22BP1); see E-box and MYCATRD22; MYC recognition sequence in CBF3 promoter; Binding site of ICE1 (inducer of CBF expression 1) that regulates the transcription of CBF/DREB1 genes in the cold in Arabidopsis; ICE1 | Upstream | -1440 |
| | | Upstream | -1624 |
| 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 | -1545 |
| Motif_235 | C8GCARGAT | Binding site of plant MADS-domain protein AGL15; CArG motif with a longer A/T-rich core;A variant of CArG motif, with a longer A/T-rich core; Binding site for AGL15 (AGAMOUS-like 15) | Upstream | -77 |
| Motif_279 | POLASIG3 | Plant polyA signal; Consensus sequence for plant polyadenylation signal | Upstream | -1753 |
| | | Upstream | -1756 |
| | | Upstream | -1759 |
| | | Upstream | -1762 |
| | | Upstream | -1765 |
| | | Upstream | -1768 |
| | | Upstream | -1771 |
| | | Upstream | -1774 |
| | | Upstream | -1777 |
| | | Upstream | -1780 |
| 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 | -983 |
| Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Upstream | -1587 |
| 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 | -1599 |
| Motif_342 | POLASIG1 | PolyA signal; poly A signal found in legA gene of pea, rice alpha-amylase; -10 to -30 in the case of animal genes. Near upstream elements (NUE) in Arabidopsis | Upstream | -1616 |
| | | Upstream | -1750 |
| 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 | -398 |
| | | Upstream | -659 |
| | | Upstream | -984 |
| Motif_447 | AtMYC2 BS in RD22;PIF4 | Binding site for MYC (rd22BP1) in Arabidopsis dehydration-resposive gene, rd22; MYC binding site in rd22 gene of Arabidopsis thaliana; ABA-induction; Located at ca. -200 of rd22 gene; Also MYB at ca. -141 of rd22 gene; See also MYBATRD22; Role of Arabidopsis MYC and MYB homologs in drought- and abscisic acid-regulated gene expression. Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -1624 |
| Motif_484 | RAV1-B binding site motif | Binding consensus sequence of an Arabidopsis transcription factor, RAV1; RAV1 specifically binds to DNA with bipartite sequence motifs of RAV1-A (CAACA) and RAV1-B (CACCTG); RAV1 protein contain AP2-like and B3-like domains; The AP2-like and B3-like domains recognize the CAACA and CACCTG motifs, respectively; The expression level of RAV1 were relatively high in rosette leaves and roots; RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plants | Upstream | -1440 |
| Motif_495 | TRANSINITMONOCOTS | Context sequence of translational initiation codon in monocots | Upstream | -1594 |
| 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 | -964 |
| | | Upstream | -1111 |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Upstream | -1462 |
| | | Upstream | -1749 |
| Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Upstream | -653 |
| 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 | -476 |
| | | Upstream | -965 |
| | | Upstream | -1091 |
| | | Upstream | -1467 |
| | | Upstream | -1545 |
| | | Upstream | -1546 |
| | | Upstream | -1553 |
| | | Upstream | -1588 |
| | | Upstream | -1631 |
| | | Upstream | -1637 |
| 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 | -1091 |
| | | Upstream | -1467 |
| | | Upstream | -1546 |
| | | Upstream | -1553 |
| 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 | -383 |
| | | Upstream | -385 |
| | | Upstream | -701 |
| 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 | -343 |
| | | Upstream | -407 |
| | | Upstream | -690 |
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