| Matrix_110 | ATABI4;AT3G57600 | Not available | Upstream | -1605 |
| | | Upstream | -1606 |
| Matrix_144 | AT5G08330;AT5G23280 | Not available | Upstream | -1885 |
| | | Upstream | -1886 |
| | | Upstream | -1887 |
| Matrix_154 | AT1G22190;AT1G36060;AT1G64380;RAP2.4;AT2G20880;AT2G22200;AT4G13620;AT4G28140;AT4G39780;AT5G65130 | Not available | Upstream | -1605 |
| | | Upstream | -1606 |
| Matrix_171 | LBD3;LBD4 | Not available | Upstream | -1533 |
| | | Upstream | -1747 |
| | | Upstream | -1856 |
| Matrix_179 | AtMYB84;MYB36;MYB68;O49746_ARATH | Not available | Upstream | -1604 |
| | | Upstream | -1830 |
| Matrix_19 | PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling | Upstream | -30 |
| Matrix_196 | TCP20;AT5G41030 | Not available | Upstream | -1826 |
| | | Upstream | -1827 |
| | | Upstream | -1883 |
| | | Upstream | -1884 |
| Matrix_224 | ERF1 | Not available | Upstream | -1607 |
| Matrix_232 | TCP23 | Not available | Upstream | -1884 |
| | | Upstream | -1885 |
| Matrix_243 | RAP2.12;RAP2.2 | Not available | Upstream | -1749 |
| Matrix_272 | DEAR4 | Not available | Upstream | -1603 |
| | | Upstream | -1604 |
| Matrix_281 | TCP13 | Not available | Upstream | -1887 |
| Matrix_287 | ERF2 | Not available | Upstream | -1743 |
| Matrix_294 | MEE35 | Not available | Upstream | -1887 |
| | | Upstream | -1888 |
| Matrix_297 | TCP15 | Not available | Upstream | -1825 |
| | | Upstream | -1826 |
| | | Upstream | -1884 |
| | | Upstream | -1885 |
| Matrix_343 | AT2G33710 | Not available | Upstream | -1603 |
| | | Upstream | -1604 |
| Matrix_348 | AT5G51910 | Not available | Upstream | -1824 |
| | | Upstream | -1825 |
| | | Upstream | -1885 |
| | | Upstream | -1886 |
| | | Upstream | -1887 |
| Matrix_35 | YAB5;YAB3 | Not available | Upstream | -1747 |
| | | Upstream | -1748 |
| Matrix_371 | MYB7;AtMYB6;AtMYB32;ATMYB4 | Not available | Upstream | -1831 |
| Matrix_374 | AT5G07580;AT5G61590 | Not available | Upstream | -1747 |
| Matrix_377 | AT1G75490;DREB2C;AT2G40350;AT5G18450 | Not available | Upstream | -1604 |
| | | Upstream | -1605 |
| Matrix_385 | DEAR4 | Not available | Upstream | -1604 |
| Matrix_395 | AT1G19210;ORA47;AT4G31060;AT5G21960 | Not available | Upstream | -1605 |
| | | Upstream | -1606 |
| Matrix_40 | TCP2 | Not available | Upstream | -1885 |
| | | Upstream | -1886 |
| Matrix_401 | MYB55 | Not available | Upstream | -1830 |
| Matrix_409 | DEAR3 | Not available | Upstream | -1604 |
| | | Upstream | -1605 |
| Matrix_416 | ASL5 | Not available | Upstream | -1858 |
| Matrix_42 | AT2G45680 | Not available | Upstream | -1824 |
| | | Upstream | -1825 |
| | | Upstream | -1885 |
| | | Upstream | -1886 |
| | | Upstream | -1887 |
| Matrix_452 | MYB46 | Not available | Upstream | -1830 |
| Matrix_455 | MYB111 | Not available | Upstream | -1830 |
| Matrix_47 | AtMYB77 | Not available | Upstream | -1603 |
| Matrix_48 | PI | Not available | Upstream | -1753 |
| Matrix_507 | TCP3 | Not available | Upstream | -1886 |
| Matrix_510 | AtMYB84 | More than 80 R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana | Upstream | -1604 |
| | | Upstream | -1830 |
| Matrix_57 | WIN1;SHN3;SHN2 | Not available | Upstream | -1604 |
| | | Upstream | -1605 |
| Matrix_59 | AT4G00238;AT4G00250 | Not available | Upstream | -1746 |
| | | Upstream | -1747 |
| | | Upstream | -1748 |
| Matrix_64 | PIF5 | Not available | Upstream | -528 |
| Matrix_66 | AtLEC2 | Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis | Upstream | -1819 |
| Matrix_82 | TCP17 | Not available | Upstream | -1887 |
| Matrix_91 | CRF3 | Not available | Upstream | -1607 |
| | | Upstream | -1608 |
| Matrix_92 | AT1G33760 | Not available | Upstream | -1604 |
| Matrix_94 | TCP5 | Not available | Upstream | -1887 |
| Motif_119 | ABI3 | Gene regulation during late embryogenesis: the RY motif of maturation-specific gene promoters is a direct target of the FUS3 gene product | Upstream | -1819 |
| 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) | Downstream | 3319 |
| Motif_139 | RHERPATEXPA7 | Right part of RHEs (Root Hair-specific cis-Elements) conserved among the Arabidopsis thaliana A7 (AtEXPA7) orthologous (and paralogous) genes from diverse angiosperm species with different hair distribution patterns | Upstream | -527 |
| | | Upstream | -529 |
| | | Upstream | -1532 |
| | | Upstream | -1557 |
| | | Upstream | -1635 |
| Motif_171 | TCP binding consensus | found enriched in peaks in chip-seq data for SEP3 | Upstream | -1857 |
| | | Upstream | -1858 |
| Motif_179 | CACGTGMOTIF;BES1;PIF4;PIF5 | Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling;A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana; CACGTG motif; G-box; Binding site of Arabidopsis GBF4; C. roseus G-box binding factor 1 (CrGBF1) and 1 (CrGBF2) can act as transcriptional repressors of the Str promoter via direct interaction with the G-box; Essential for expression of beta-phaseolin gene during embryogenesis in bean, tobacco, Arabidopsis; Tomato Pti4 (ERF) regulates defense-related gene expression via GCC box and non-GCC box cis-element (Myb1 (GTTAGTT) and G-box (CACGTG)); Isolation and characterization of a fourth Arabidopsis thaliana G-box-binding factor, which has similarities to Fos oncoprotein; Interaction between BZR1 and PIF4 integrates brassinosteroid and environmental responses | Upstream | -528 |
| | | Upstream | -1634 |
| Motif_193 | GLK1 | GLK transcription factors coordinate expression of the photosynthetic apparatus in Arabidopsis | Downstream | 3297 |
| | | Upstream | -1615 |
| 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 | -1634 |
| 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 | -754 |
| Motif_218 | ABRERATCAL | ABRE-related sequence or Repeated sequence motifs identified in the upstream regions of 162 Ca(2+)-responsive upregulated genes; see also ABRE | Upstream | -528 |
| | | Upstream | -1633 |
| Motif_244 | ABRE-like binding site motif | Not available | Downstream | 3067 |
| | | Upstream | -1632 |
| Motif_249 | DPBF1&2 binding site motif | A novel class of bZIP transcription factors, DPBF-1 and 2 (Dc3 promoter-binding factor-1 and 2) binding core sequence; Found in the carrot Dc3 gene promoter; Dc3 expression is normally embryo-specific, and also can be induced by ABA; The Arabidopsis abscisic acid response gene ABI5 encodes a bZIP transcription factor; abi5 mutant have a pleiotropic defects in ABA response; ABI5 regulates a subset of late embryogenesis-abundant genes; GIA1 (growth-insensitivity to ABA) is identical to ABI5; Isolation of a novel class of bZIP transcription factors that interact with ABA-responsive and embryo-specification elements in the Dc3 promoter using a modified yeast one-hybrid system | Upstream | -1633 |
| Motif_258 | -10PEHVPSBD | -10 promoter element found in the barley (H.v.) chloroplast psbD gene promoter; Involved in the expression of the plastid gene psbD which encodes a photosystem II reaction center chlorophyll-binding protein that is activated by blue, white or UV-A light | Downstream | 2678 |
| Motif_262 | WRKY70 | Identification of a novel type of WRKY transcription factor binding site in elicitor-responsive cis-sequences from Arabidopsis thaliana | Upstream | -702 |
| Motif_270 | ELRECOREPCRP1 | ElRE (Elicitor Responsive Element) core of parsley PR1 genes; consensus sequence of elements W1 and W2 of parsley PR1-1 and PR1-2 promoters; Box W1 and W2 are the binding site of WRKY1 and WRKY2, respectively; ERE; WA box; One of the W boxes found in the Parsley WRKY1 gene promoter; Required for elicitor responsiveness; WC box WB box and WC box constitute a palindrome; WRKY1 protein binding site; W-box found in thioredoxin h5 gene in Arabidopsis | Downstream | 3032 |
| Motif_305 | SP1SV40 | SP-1 binding site (GC box) in enhancer regions of SV40 and human metallothionein IIA (hMT IIA) | Upstream | -59 |
| | | Upstream | -1607 |
| Motif_310 | ANAERO3CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1); Arbitrary named ANAERO3CONSENSUS by the PLACEdb curator | Upstream | -1637 |
| Motif_339 | ABRE-like binding site motif | Molecular responses to dehydration and low temperature | Downstream | 3067 |
| | | Upstream | -528 |
| | | Upstream | -1531 |
| | | Upstream | -1634 |
| Motif_348 | WBBOXPCWRKY1 | WB box; WRKY proteins bind specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box; Found in amylase gene in sweet potato, alpha-Amy2 genes in wheat, barley, and wild oat, PR1 gene in parsley, and a transcription factor gene in Arabidopsis | Downstream | 3322 |
| | | Upstream | -1571 |
| 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 | -1551 |
| | | Upstream | -1735 |
| Motif_392 | PALBOXAPC | Box A; Consensus; One of three putative cis-acting elements (boxes P, A, and L) of phenylalanine ammonia-lyase (PAL; EC 4.3.1.5) genes in parsley (P.c.); None of these elements (boxes P, A, and L) alone, or the promoter region containing all of them together, conferred elicitor or light responsiveness. These elements appear to be necessary but not sufficient for elicitor- or light-mediated PAL gene activation; See also Box P, Box L | Upstream | -1481 |
| Motif_422 | SP8BFIBSP8BIB | One of SPBF binding site (SP8b); Found at -330, -220, and -200 of gSPO-B1 (sporamin) gene, and also at -80 of gB-Amy (beta-amylase) gene; SP8BF recognizes both SP8a and SP8b sequences; See also SP8BFIBSP8AIB; SP8BF activity is also found in tobacco; SP8b found in the 5' upstream region of three differnt genes coding for sporamin and beta-amylase; Binding site of SPF1; SPF1 also binds to the SP8b | Downstream | 3052 |
| 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 | -1602 |
| Motif_48 | BES1 | A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana | Downstream | 3158 |
| | | Upstream | -1533 |
| Motif_483 | ABREMOTIFAOSOSEM | motif A ABRE-like sequence found in rice Osem gene promoter; Essential for activation by VP1; Important for regulation by ABA;TRAB1, bZIP transcription factor, interacts with VP1 and mediates abscisic acid-induced transcritption;ABRE motif A found in the promoter of the rice Osem gene; ACGT-containing ABRE; Required for ABA-responsiveness and VP1 activation; Binding site of TRAB1; Motif A and CE3 are functionally equivalent; TRAB1, bZIP transcription factor, interacts with VP1 and mediates abscisic acid-induced transcritption | Downstream | 3067 |
| Motif_490 | PROLAMINBOXOSGLUB1 | Prolamine box found in the rice GluB-1 gene promoter; Involved in quantitative regulation of the GluB-1 gene | Upstream | -1818 |
| Motif_502 | MYB98 | The MYB98 subcircuit of the synergid gene regulatory network includes genes directly and indirectly regulated by MYB98 | Upstream | -1808 |
| Motif_618 | MYB1AT | MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis | Upstream | -1552 |
| 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 | Downstream | 3066 |
| 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 | Downstream | 3310 |
| Motif_630 | WBOXNTCHN48 | W box identified in the region between -125 and -69 of a tobacco class I basic chitinase gene CHN48; NtWRKY1, NtWRKY2 and NtWRKY4 bound to W box; NtWRKYs possibly involved in elicitor-respsonsive transcription of defense genes in tobacco | Upstream | -1576 |
| Motif_640 | RYREPEATBNNAPA | RY repeat found in RY/G box (the complex containing the two RY repeats and the G-box) of napA gene in Brassica napus; Found between -78 and -50; Required for seed specific expression;dist B ABRE mediated transactivation by ABI3 adn ABI3-dependent response to ABA; a tetramer of the composite RY/G complex mediated only ABA-independent transactivation by ABI3; B2 domain of ABI3 is necessary for ABA-independent and ABA-dependent activation through the dist B ABRE | Upstream | -1821 |
| 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 | -1595 |
| 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 | -1595 |
| 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 | -1757 |
| | | Upstream | -1759 |
| | | Upstream | -1761 |
| | | Upstream | -1763 |
| Motif_72 | GADOWNAT | Sequence present in 24 genes in the GA-down regulated d1 cluster (106 genes) found in Arabidopsis seed germination; This motif is similar to ABRE | Downstream | 3066 |
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