| Matrix_101 | ERF5 | Not available | Intron | 1859 |
| Matrix_174 | ZAT2 | Not available | Upstream | -720 |
| Matrix_23 | ANAC46 | Not available | Upstream | -738 |
| Matrix_25 | AP3 | Not available | Upstream | -382 |
| Matrix_269 | FHY3/FAR1 | Not available | Upstream | -163 |
| | | Upstream | -160 |
| Matrix_296 | GBF2 | Not available | Upstream | -284 |
| Matrix_300 | bZIP68;bZIP16 | Not available | Upstream | -284 |
| Matrix_326 | AT5G07310;Rap2.6L;AT5G61890 | Not available | Intron | 1858 |
| Matrix_362 | DEAR3 | Not available | Intron | 2127 |
| Matrix_372 | ANAC81 | DNA binding specificity of ATAF2, a NAC domain transcription factor targeted for degradation by Tobacco mosaic virus | Intron | 2407 |
| | | Intron | 2413 |
| Matrix_377 | AT1G75490;DREB2C;AT2G40350;AT5G18450 | Not available | Intron | 1859 |
| Matrix_387 | ORA47 | Not available | Intron | 1857 |
| | | Intron | 2125 |
| Matrix_39 | AP1 | Not available | Upstream | -173 |
| Matrix_396 | AP3 | Not available | Upstream | -216 |
| Matrix_409 | DEAR3 | Not available | Intron | 1858 |
| Matrix_438 | AtbZIP63 | Not available | Upstream | -287 |
| Matrix_454 | AT1G77200;ATERF38;AT4G16750;AT5G52020 | Not available | Intron | 1858 |
| Matrix_458 | MGP;AT1G14580;AtIDD7;AtIDD5;AtIDD4;AtIDD12;JKD;AT5G66730 | Not available | Upstream | -291 |
| Matrix_47 | AtMYB77 | Not available | Intron | 1859 |
| Matrix_472 | ZN_C2_H2 | Not available | Upstream | -720 |
| Matrix_68 | AtMYB77 | More than 80 R2R3-MYB regulatory genes in the genome of Arabidopsis thaliana. Plant J 14: 273-84 | Intron | 1859 |
| Matrix_91 | CRF3 | Not available | Intron | 1859 |
| 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 | -302 |
| | | Upstream | -300 |
| Motif_129 | GAGAGMGSA1 | GAGA element found in the promoter of the heme and chlorophyll synthesis gene Gsa1 in soybean; GAGA binding protein (GBP) binds to (GA)n/(CT)n DNA | Upstream | -512 |
| | | Upstream | -510 |
| | | Upstream | -508 |
| | | Upstream | -506 |
| | | Upstream | -504 |
| | | Upstream | -502 |
| 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 | -435 |
| Motif_143 | VND6 | Arabidopsis VASCULAR-RELATED NAC-DOMAIN6 directly regulates the genes that govern programmed cell death and secondary wall formation during xylem differentiation | Upstream | -279 |
| Motif_168 | IBOX | I box; I-box; Conserved sequence upstream of light-regulated genes; Sequence found in the promoter region of rbcS of tomato and Arabidopsis; I box; Binding site of LeMYB1, that is a member of a novel class of myb-like proteins; LeMYBI act as a transcriptional activator; An evolutionarily conserved protein binding sequence upstream of a plant light-regulated gene | Upstream | -344 |
| Motif_174 | SREATMSD | sugar-repressive element (SRE) found in 272 of the 1592 down-regulated genes after main stem decapitation in Arabidopsis | Upstream | -362 |
| Motif_184 | PROXBBNNAPA | prox B (proximal portion of B-box) found in napA gene of Brassica napus; CA-rich sequence; Found between -130 and -124; Required for seed specific expression and ABA responsiveness; 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 | -194 |
| 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 | -718 |
| | | Intron | 1849 |
| 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 | -688 |
| Motif_22 | RYREPEATLEGUMINBOX | RY repeat (CATGCAY) or legumin box found in seed-storage protein genes in legume such as soybean | Upstream | -1334 |
| 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 | Intron | 2130 |
| Motif_243 | TELOBOXATEEF1AA1 | telo-box (telomere motif) found in the Arabidopsis (A.t.) eEF1AA1 gene promoter; Conserved in all known plant eEF1A gene promoters; Found in the 5' region of numerous genes encoding components of the translational apparatus; Required for the activation of expression in root primordia; Acts co-operatively with tef-box; Binding site of AtPur alpha-1; Plant interstitial telomere mitifs participate in the control of gene expression in root meristems | Upstream | -215 |
| Motif_254 | MYB46;MYB83 | MYB46 and MYB83 bind to the SMRE sites and directly activate a suite of transcription factors and secondary wall biosynthetic genes | Upstream | -218 |
| Motif_309 | GATA promoter motif | Arabidopsis thaliana GATA factors: organisation, expression and DNA-binding characteristics | Upstream | -762 |
| Motif_317 | GAREAT | GARE (GA-responsive element); Occurrence of GARE in GA-inducible, GA-responsible, and GA-nonresponsive genes found in Arabidopsis seed germination was 20, 18, and 12%, respectively | Intron | 1846 |
| Motif_323 | MYB1LEPR | Tomato Pti4(ERF) regulates defence-related gene expression via GCC box and non-GCC box cis elements (Myb1(GTTAGTT), G box (CACGTG)) | Intron | 2132 |
| Motif_346 | SND1;VND6;VND7;NST1;NST2 | Global analysis of direct targets of secondary wall NAC master switches in Arabidopsis | Upstream | -332 |
| | | Upstream | -284 |
| Motif_349 | QARBNEXTA | QAR (quantitative activator region) in promoter region of Brassica napus extA extensin gene | Upstream | -688 |
| Motif_358 | UP2ATMSD | Up2 motif found in 193 of the 1184 up-regulated genes after main stem decapitation in Arabidopsis | Upstream | -215 |
| Motif_371 | DRE-like promoter motif | The Expression Profile Matrix of Arabidopsis Transcription Factor Genes Suggests Their Putative Functions in Response to Environmental Stresses | Intron | 1859 |
| | | Intron | 2127 |
| Motif_410 | ANAERO1CONSENSUS | One of 16 motifs found in silico in promoters of 13 anaerobic genes involved in the fermentative pathway (anaerobic set 1); Arbitrary named ANAERO1CONSENSUS by the PLACEdb curator | Upstream | -402 |
| Motif_411 | PRECONSCRHSP70A | Consensus sequence of PRE (plastid response element) in the promoters of HSP70A in Chlamydomonas; Involved in induction of HSP70A gene by both MgProto and light | Upstream | -360 |
| | | Intron | 1841 |
| Motif_419 | MYB4 binding site motif | Not available | Upstream | -218 |
| | | Intron | 2132 |
| 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 | Upstream | -358 |
| Motif_441 | GAGA8HVBKN3 | GA octodinucleotide repeat found in intron IV of the barley gene Bkn3; Binding site for GAGA-binding factor BBR | Upstream | -512 |
| | | Upstream | -510 |
| | | Upstream | -508 |
| | | Upstream | -506 |
| | | Upstream | -504 |
| | | Upstream | -502 |
| | | Upstream | -500 |
| Motif_454 | DRECRTCOREAT | Core motif of DRE/CRT (dehydration-responsive element/C-repeat) cis-acting element found in many genes in Arabidopsis and in rice; Os DREB1A bound to GCCGAC more preferentially than to ACCGAC whereas At DREB1A bound to both GCCGAC and ACCGAC efficiently; Maize ZmDREB1A bound to DRE; HaDREB2 in Helianthus annuus (sunflower) | Intron | 1860 |
| | | Intron | 2128 |
| 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 | -280 |
| Motif_51 | MYB46 | Identification of a cis-acting regulatory motif recognized by MYB46, a master transcriptional regulator of secondary wall biosynthesis | Upstream | -219 |
| Motif_511 | RYREPEATGMGY2 | RY repeat motif (CATGCAT); Present in the 5' region of the soybean glycinin gene (Gy2) | Upstream | -1334 |
| Motif_520 | AMYBOX1 | amylase box; Conserved sequence found in 5'-upstream region of alpha-amylase gene of rice, wheat, barley | Intron | 1846 |
| Motif_549 | TBF1 | The HSF-like transcription factor TBF1 is a major molecular switch for plant growth-to-defense transition | Upstream | -163 |
| | | Upstream | -160 |
| Motif_567 | T/GBOXATPIN2 | T/G-box found in tomato proteinase inhibitor II (pin2) and leucine aminopeptidase (LAP) genes; Involved in jasmonate (JA) induction of these genes; bHLH-Leu zipper JAMYC2 and JAMYC10 proteins specifically recognize this motif | Upstream | -687 |
| Motif_585 | ATB2/AtbZIP53/AtbZIP44/GBF5 BS in ProDH | PRE (Pro- or hypoosmolarity-responsive element) found in the promoter region of proline dehydrogenase (ProDH) gene in Arabidopsis; Core of 9-bp sequence ACTCATCCT which is necessary for the efficient expression of ProDH in response to L-Pro and hypoosmolarity; ATB2-binding site; Similar to GCN4 motif (ATGA(C/G)TCAT); ATB2 subgroup of bZIP transcription factors function as transcriptional activator for hypoosmolarity-inducible ProDH; A Novel Subgroup of bZIP Proteins Functions as Transctiptional Activators in Hypsosmolarity-Responsive Expression of the ProDH gene in Arabidopsis | Upstream | -460 |
| Motif_591 | CBFHV | Binding site of barley CBF1, and also of barley CBF2; CBF = C-repeat (CRT) binding factors; CBFs are also known as dehydration-responsive element (DRE) binding proteins (DREBs) | Intron | 1860 |
| | | Intron | 2128 |
| Motif_609 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -401 |
| | | Upstream | -390 |
| | | Intron | 1847 |
| Motif_614 | MYBGAHV | Central element of gibberellin (GA) response complex (GARC) in high-pI alpha-amylase gene in barley; Similar to c-myb and v-myb consensus binding site; GAmyb binds specifically to the TAACAAA box in vitro; GAmyb is the sole GA-regulated transcriptional factor required for transcriptional activation of the high-pI alpha-amylase; GARC consist of the pyrimidine, TAACAAA and TATCCAC boxes; GARE in RAmy1A gene; GARE and pyrimidine box in RAmy1A are partially involved in sugar repression | Intron | 1846 |
| Motif_615 | MARTBOX | T-Box; Motif found in SAR (scaffold attachment region; or matrix attachment region, MAR) | Upstream | -39 |
| 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 | -689 |
| 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 | -1333 |
| Motif_643 | DRE2COREZMRAB17 | DRE2 core found in maize rab17 gene promoter; DBF1 and DBF2 bound to DRE2; rab17 is expressed during late embryogenesis, and is induced by ABA | Intron | 2128 |
| Motif_649 | 2SSEEDPROTBANAPA | Conserved in many storage-protein gene promoters; May be important for high activity of the napA promoter | Upstream | -194 |
| 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 | -795 |
| | | Upstream | -361 |
| Motif_666 | MYB binding site promoter | A flower-specific Myb protein activates transcription of phenylpropanoid biosynthetic genes | Upstream | -219 |
| Motif_672 | AP2 | The floral homeotic protein APETALA2 recognizes and acts through an AT-rich sequence element | Upstream | -401 |
| | | Upstream | -390 |
| | | Intron | 1847 |
| 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 | -513 |
| | | Upstream | -511 |
| | | Upstream | -509 |
| | | Upstream | -507 |
| | | Upstream | -505 |
| | | Upstream | -503 |
| | | Upstream | -501 |
| | | Upstream | -499 |
| | | Upstream | -497 |
| | | Upstream | -495 |
| | | Upstream | -493 |
| Motif_70 | CANBNNAPA | Core of (CA)n element in storage protein genes in Brasica napus; embryo- and endosperm-specific transcription of napin (storage protein) gene, napA; seed specificity; activator and repressor | Upstream | -228 |
| | | Upstream | -194 |
| 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 | Upstream | -689 |
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