Table 5 PLACE cis-elements found and not found in Arabidopsis REGs

found

ACGTATERD1 ACGT sequence required for etiolation-induced expression of erd1 (early responsive to dehydration) in Arabidopsis;

ABRELATERD1 ABRE-like sequence (from -199 to -195) required for etiolation-induced expression of erd1 (early responsive to dehydration) in Arabidopsis;

LTRECOREATCOR15 Core of low temperature responsive element (LTRE) of cor15a gene in Arabidopsis;

SORLIP1AT one of "Sequences Over-Represented in Light-Induced Promoters (SORLIPs) in Arabidopsis; Computationally identified phyA-induced motifs;

SORLIP2AT one of "Sequences Over-Represented in Light-Induced Promoters (SORLIPs) in Arabidopsis; Computationally identified phyA-induced motifs;

WBOXATNPR1 "W-box" found in promoter of Arabidopsis NPR1 gene; They were recognized specifically by salicylic acid (SA)-induced WRKY DNA binding proteins;

CACGTGMOTIF "CACGTG motif"; "G-box; Binding site of Arabidopsis GBF4;

MYB2CONSENSUSAT MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis; Y = C/T; K = G/T;

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;

SITEIIATCYTC "Site II element" found in the promoter regions of cytochrome genes (Cytc-1, Cytc-2) in Arabidopsis; Y = C/T;

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; K = G/T;

DPBFCOREDCDC3 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;

GADOWNAT Sequence present in 24 genes in the GA-down regulated d1 cluster found in Arabidopsis seed germination;

WUSATAg Target sequence of WUS in the intron of AGAMOUS gene in Arabidopsis;

CDA1ATCAB2 CDA-1 (CAB2 DET1-associated factor 1) binding site in DtRE (dark response element) f of chlorophyll a/b-binding protein2 (CAB2) gene in Arabidopsis;

EMBP1TAEM Binding site of trans-acting factor EMBP-1; wheat Em gene; Binding site of ABFs; ABFs (ABRE binding factors) were isolated from Arabidopsis by a yeast one-hybrid screening system; Involved in ABA-mediated stress-signaling pathway;

HEXAT "Hex motif" ; Binding site of Arabidopsis bZIP protein TGA1 and G box binding factor GBF1; G-Box-like element;

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.;

RAV1AAT Binding consensus sequence of Arabidopsis transcription factor, RAV1; The expression level of RAV1 were relatively high in rosette leaves and roots;

DRECRTCOREAT Core motif of DRE/CRT (dehydration-responsive element/C-repeat) cis-acting element found in many genes in Arabidopsis and in rice; R = G/A;

ELRECOREPCRP1 ElRE (Elicitor Responsive Element) core of parsley (P.c.) 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; W-box found in thioredoxin h5 gene in Arabidopsis (Laloi et al.);

ARR1AT"ARR1-binding element" found in Arabidopsis; ARR1 is a response regulator; N = G/A/C/T;

ARFAT ARF (auxin response factor) binding site found in the promoters of primary/early auxin response genes of Arabidopsis; AuxRE; Binding site of Arabidopsis ARF1 (Auxin response factor1);

HEXAMERATH4 hexamer motif of Arabidopsis histone H4 promoter;

IBOX "I box"; "I-box"; Conserved sequence upstream of light-regulated genes; Sequence found in the promoter region of rbcS of tomato and Arabidopsis;

MYB1AT MYB recognition site found in the promoters of the dehydration-responsive gene rd22 and many other genes in Arabidopsis; W = A/T;

MYB2AT Binding site for ATMYB2, an Arabidopsis MYB homolog; ATMYB2 is involved in regulation of genes that are responsive to water stress in Arabidopsis;

MYCATERD1 MYC recognition sequence necessary for expression of erd1 (early responsive to dehydration) in dehydrated Arabidopsis; NAC protein bound specifically to the CATGTG motif (Tran et al., 2004);

MYCATRD22 Binding site for MYC (rd22BP1) in Arabidopsis dehydration-responsive gene, rd22; MYC binding site in rd22 gene of Arabidopsis; ABA-induction;

PREATPRODH "PRE (Pro- or hypoosmolarity-responsive element) found in the promoter region of proline dehydrogenase (ProDH) gene in Arabidopsis;

RAV1BAT Binding consensus sequence of an Arabidopsis transcription factor, RAV1; The expression level of RAV1 were relatively high in rosette leaves and roots;

SREATMSD "sugar-repressive element (SRE)" found in 272 of the 1592 down-regulated genes after main stem decapitation in Arabidopsis;

TBOXATGAPB "Tbox" found in the Arabidopsis GAPB gene promoter; Mutations in the "Tbox" resulted in reductions of light-activated gene transcription;

AGCBOXNPGLB "AGC box" repeated twice in a 61 bp enhancer element in tobacco (N.p.) class I beta-1,3-glucanase (GLB) gene; "GCC-box"; Binding sequence of Arabidopsis AtERFs;

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;

LEAFYATAG Target sequence of LEAFY in the intron of AGAMOUS gene in Arabidopsis;

LTREATLTI78 Putative low temperature responsive element (LTRE); Found in Arabidopsis low-temperature-induced (lti) genes, lti78/cor78/rd29A and lti65;

MYBATRD22 Binding site for MYB (ATMYB2) in dehydration-responsive gene, rd22; MYB binding site in rd22 gene of Arabidopsis thaliana; ABA-induction;

SORLIP5AT one of "Sequences Over-Represented in Light-Induced Promoters (SORLIPs) in Arabidopsis; Computationally identified phyA-induced motifs;

ABREZMRAB28 ABRE; ABA and water-stress responses; Found in maize (Z.m.) rab28; maize rab28 is ABA-inducible in embryos and vegetative tissues; Found in the Arabidopsis alcohol dehydrogenase (Adh) gene promoter;

CCA1ATLHCB1 CCA1 binding site; CCA1 protein (myb-related transcription factor) interact with two imperfect repeats of AAMAATCT in Lhcb1*3 gene of Arabidopsis ; Related to regulation by phytochrome;

E2FANTRNR "E2Fa element" found in the tobacco RNR (Ribonucleotide reductase) gene promoter and in the Arabidopsis CDC6 gene promoter; Binding site of tobacco and Arabidopsis E2F; Involved in upregulation of the promoter at G1/S transition;

L1BOXATPDF1 "L1 box" found in promoter of Arabidopsis PROTODERMAL FACTOR1 (PDF1) gene; Y = C/T;

OCTAMERMOTIFTAH3H4 "Octamer motif" found in promoter of wheat histone genes H3 and H4, and corn histone genes H3 and H4; Arabidopsis histone H4; "histone-specific octamer";

PIATGAPB "PI" found in the Arabidopsis GAPB gene promoter; Mutations in the "PI" resulted in reductions of light-activated gene transcription;

RYREPEATVFLEB4 "RY repeat motif"; quantitative seed expression; Gene: Vicia faba LeB4; Soybean glycinin (Gy2); other dicot and monocot seed protein genes; Binding site of Arabidopsis B3-domain-containing transcription factor FUS3;

UP2ATMSD "Up2" motif found in 193 of the 1184 up-regulated genes after main stem decapitation in Arabidopsis; W = A/T;

ZDNAFORMINGATCAB1 "Z-DNA-forming sequence" found in the Arabidopsis chlorophyll a/b binding protein gene (cab1) promoter; Involved in light-dependent developmental expression of the gene; "Z-box";