Table S2. Predicted cis elements identified for GmActin, GmRpS11 and GmHsp90 promoters using the PLACE database (Higo et al. 1999). Elements related to development and tissue-specificity are in bold. Shaded rows indicate that putative cis-regulatory elements were detected in all 3 promoters.

cis Element / Sequence / Number of Elements / Predicted Function
GmActin / GmRpS11 / GmHsp90
-10PEHVPSBD / TATTCT / 1 / 2 / 0 / -10 promoter element, light regulation and circadian rhythms, chloroplast gene
2SSEEDPROTBANAPA / CAAACAC / 0 / 1 / 0 / Conserved in many storage-protein gene promoters, seed
AACACOREOSGLUB1 / AACAAAC / 3 / 0 / 0 / Involved in controlling endosperm-specific expression
ABRELATERD1 / ACGTG / 3 / 2 / 1 / ABA responsive element, ABA response, early response to dehydration
ABREOSRAB21 / ACGTSSSC / 1 / 0 / 0 / ABA signaling and response
ABRERATCAL / MACGYGB / 1 / 1 / 0 / Calcium ion (Ca2+) response and regulation
ACGTABREMOTIFA2OSEM / ACGTGKC / 1 / 0 / 0 / ABA signaling and response
ACGTATERD1 / ACGT / 5 / 2 / 3 / Required for etiolation-induced expression of erd1 (early response to dehydration)
ACIIIPVPAL2 / GTTAGGTTC / 0 / 0 / 1 / Required for vascular-specific gene expression
AMMORESIVDCRNIA1 / CGAACTT / 1 / 0 / 0 / Involved in ChlamydomonasNia1 transcription repression, N metabolism
ANAERO1CONSENSUS / AAACAAA / 1 / 0 / 0 / Involved in the fermentative pathway in silico
ANAERO3CONSENSUS / TCATCAC / 0 / 1 / 0 / Involved in the fermentative pathway in silico
ARR1AT / NGATT / 2 / 0 / 11 / ARR1 binding element, cytokinin signaling and response
ASF1MOTIFCAMV / TGACG / 0 / 1 / 1 / Auxin and/or salicylic acid signaling, and light regulation
ATHB1ATCONSENSUS / CAATWATTG / 1 / 0 / 0 / Recognition sequence of Arabidopsis Athb-1 protein
ATHB5ATCORE / CAATNATTG / 1 / 0 / 0 / Consensus binding sequence Arabidopsis class I Hdzip (Homeodomein-leucine zipper) protein
BIHD1OS / TGTCA / 1 / 1 / 0 / Binding site of OsBIHD1, a rice BELL homeodomain transcription factor, disease response
BOXIINTPATPB / ATAGAA / 0 / 0 / 1 / Conserved in several NCII (nonconsensus type II) promoters of plastid genes
BOXIIPCCHS / ACGTGGC / 1 / 0 / 0 / Essential for light regulation
BOXLCOREDCPAL / ACCWWCC / 1 / 0 / 0 / Consensus of the putative core sequences of box-L-like sequences, UV-B induction
BP5OSWX / CAACGTG / 0 / 1 / 0 / OsBP-5 (a MYC protein) binding site in Wx promoter;
CAATBOX1 / CAAT / 7 / 0 / 4 / CAAT box
CACTFTPPCA1 / YACT / 7 / 6 / 6 / Found in the distal region of the phosphoenolpyruvate carboxylase, photosynthesis
CANBNNAPA / CNAACAC / 0 / 1 / 0 / In storage protein genes; seed specificity;
CAREOSREP1 / CAACTC / 0 / 0 / 1 / Found in the promoter region of a cysteine proteinase, GA signaling
CARGATCONSENSUS / CCWWWWWWGG / 0 / 1 / 0 / Involved in flowering timing
CARGCW8GAT / CWWWWWWWWG / 1 / 0 / 0 / Binding site for AGL15 (AGAMOUS-like 15), embryo development
CBFHV / RYCGAC / 0 / 0 / 1 / Binding site of CBF1, abiotic stress
CCAATBOX1 / CCAAT / 1 / 0 / 0 / Act cooperatively with HSEs
CURECORECR / GTAC / 2 / 1 / 0 / Copper-response and some oxygen-response
DOFCOREZM / AAAG / 11 / 5 / 8 / Core site required for binding of Dof proteins in maize, C4 photosynthesis
DPBFCOREDCDC3 / ACACNNG / 2 / 0 / 0 / DPBF-1 and 2 binding core sequence; ABA response, late embryogenesis- abundant genes, seed-related
EBOXBNNAPA / CANNTG / 4 / 0 / 1 / E-box of napA storage-protein gene of Brassica napus, seed
EECCRCAH1 / GANTTNC / 1 / 1 / 0 / EEC binding site of Myb transcription factor LCR1
GARE2OSREP1 / TAACGTA / 0 / 0 / 1 / Gibberellin-responsive element (GARE), GA signaling
GATABOX / GATA / 7 / 0 / 2 / GATA box in chlorophyll a/b binding protein Cab22 gene, light regulation
GT1CONSENSUS / GRWAAW / 3 / 4 / 7 / Involved in light-regulation; SA-signaling pathway
GT1GMSCAM4 / GAAAAA / 2 / 1 / 1 / Involved in response to salt and pathogen stress
GTGANTG10 / GTGA / 3 / 5 / 3 / GTGA motif found in late pollen gene g10 which shows homology to pectatelyase
HDZIP2ATATHB2 / TAATMATTA / 1 / 0 / 0 / Binding site of the homeobox gene (ATHB-2) regulated by light signals
IBOX / GATAAG / 1 / 0 / 0 / I box; light-regulated genes
IBOXCORE / GATAA / 2 / 0 / 1 / I box, light regulation
IBOXCORENT / GATAAGR / 1 / 0 / 0 / I-box core motif, light-responsive promoter regions
INRNTPSADB / YTCANTYY / 1 / 0 / 0 / Inr (initiator) elements found in gene promoter without TATA boxes
INTRONLOWER / TGCAGG / 0 / 1 / 0 / 3' intron-exon splice junctions
LECPLEACS2 / TAAAATAT / 0 / 0 / 1 / Core element in LeCp binding cis-element, elicitor signaling
MYB1AT / WAACCA / 2 / 0 / 0 / MYB recognition site, ABA signaling, stress response, seed/leaf related
MYB26PS / GTTAGGTT / 0 / 0 / 1 / Myb26 binding site, involved in phenylpropanoid biosynthesis
MYB2AT / TAACTG / 2 / 0 / 0 / Binding site for ATMYB2, response to water stress and ABA, seed/leaf related
MYB2CONSENSUSAT / YAACKG / 2 / 0 / 0 / MYB recognition site, involved in response to water stress
MYBCORE / CNGTTR / 0 / 1 / 0 / Binding site for ATMYB1 and ATMYB2, response to ABA and water stress
MYBCOREATCYCB1 / AACGG / 2 / 0 / 0 / Myb core
MYBPLANT / MACCWAMC / 0 / 1 / 0 / Plant MYB binding site; involved in phenylpropanoid biosynthesis
MYCCONSENSUSAT / CANNTG / 4 / 0 / 1 / MYC recognition site
NODCON1GM / AAAGAT / 2 / 0 / 1 / One of two putative nodulin consensus sequences; nodule specific
NODCON2GM / CTCTT / 3 / 0 / 3 / One of two putative nodulin consensus sequences, nodule specific
NTBBF1ARROLB / ACTTTA / 1 / 0 / 0 / NtBBF1 binding site in rolB gene, required for tissue-specific expression and auxin induction
OSE1ROOTNODULE / AAAGAT / 2 / 0 / 1 / One of the consensus sequence motifs of organ-specific elements (OSE), nodule formation
OSE2ROOTNODULE / CTCTT / 3 / 0 / 3 / One of the consensus sequence motifs of organ-specific elements (OSE), nodule formation
POLASIG1 / AATAAA / 3 / 1 / 4 / PolyA signal; poly A signal found in legA gene of pea, rice alpha-amylase, Arabidopsis near upstream elements
POLASIG2 / AATTAAA / 0 / 0 / 2 / PolyA signal in rice alpha-amylase, germination
POLASIG3 / AATAAT / 7 / 0 / 2 / Plant polyA signal
POLLEN1LELAT52 / AGAAA / 4 / 3 / 4 / One of two co-dependent regulatory elements responsible for pollen specific activation of tomato
PREATPRODH / ACTCAT / 0 / 1 / 0 / PRE (Pro- or hypo-osmolarity-responsive element) found in proline dehydrogenase (ProDH) promoter
PROXBBNNAPA / CAAACACC / 0 / 1 / 0 / prox B (proximal portion of B-box) required for seed specific expression and ABA responsiveness
PYRIMIDINEBOXOSRAMY1A / CCTTTT / 1 / 0 / 0 / Pyrimidine box partially involved in sugar repression and GA response
RAV1AAT / CAACA / 6 / 0 / 0 / Binding consensus sequence transcription factor RAV1 in rosette leaves and roots
RHERPATEXPA7 / KCACGW / 0 / 0 / 1 / Right part of RHEs (Root Hair-specific cis-Elements)
ROOTMOTIFTAPOX1 / ATATT / 3 / 0 / 4 / Motif found both in promoters of rolD;
S1FBOXSORPS1L21 / ATGGTA / 0 / 1 / 1 / S1F box, negative element downregulatingRPS1 and RPL21 promoter activity in plastid
SEF4MOTIFGM7S / RTTTTTR / 6 / 0 / 2 / SEF4 binding site binding with SEF4 (soybean embryo factor 4)
SITEIIATCYTC / TGGGCY / 0 / 1 / 0 / Site II element found in cytochrome gene promoter, blue light signaling; Overrepresented in the promoters of nuclear genes related to oxidative phosphorylation, meristem-specific
SORLIP1AT / GCCAC / 3 / 0 / 0 / One of Sequences Over-Represented in Light-Induced Promoters (SORLIPs) in Arabidopsis
SORLIP5AT / GAGTGAG / 1 / 0 / 0 / One of Sequences Over-Represented in Light-Induced Promoters (SORLIPs) in Arabidopsis
SP8BFIBSP8BIB / TACTATT / 0 / 0 / 1 / One of SPBF binding site (SP8b), tuberous root
SREATMSD / TTATCC / 0 / 1 / 0 / Sugar-repressive element (SRE) found in down-regulated genes after main stem decapitation
SURECOREATSULTR11 / GAGAC / 1 / 0 / 0 / Core of sulfur-responsive element (SURE) involved auxin response
T/GBOXATPIN2 / AACGTG / 1 / 1 / 1 / Involved in jasmonate (JA) induction
TAAAGSTKST1 / TAAAG / 0 / 1 / 4 / Involved in guard cell-specific gene expression
TATABOX4 / TATATAA / 2 / 0 / 1 / TATA box
TATABOX5 / TTATTT / 3 / 1 / 4 / TATA box
TATABOXOSPAL / TATTTAA / 1 / 0 / 0 / Binding site for OsTBP2, involved in phenylpropenoid pathway
TATAPVTRNALEU / TTTATATA / 1 / 0 / 0 / TATA-like motif
TBOXATGAPB / ACTTTG / 0 / 0 / 1 / Tbox found in GAPB gene promoter; involved in light-activated gene transcription
TELOBOXATEEF1AA1 / AAACCCTAA / 0 / 0 / 1 / telo-box (telomere motif) found in eEF1AA1 gene promoter; Required for the activation of expression in root primordia; Binding site of AtPur alpha-1
TGACGTVMAMY / TGACGT / 0 / 1 / 0 / Required for high level expression of alpha-Amylase in the cotyledons of the germinated seeds
UP2ATMSD / AAACCCTA / 0 / 0 / 2 / Up2 motif found genes after main stem decapitation in Arabidopsis
WBOXATNPR1 / TTGAC / 0 / 0 / 1 / W-box recognized specifically by salicylic acid (SA)-induced WRKY DNA binding proteins, disease response
WBOXHVISO1 / TGACT / 0 / 2 / 1 / W-box element in barley iso1 (encoding isoamylase1) promoter, sugar response
WBOXNTERF3 / TGACY / 0 / 2 / 1 / W box involved in activation of ERF3 gene, wounding response
WRKY71OS / TGAC / 1 / 4 / 3 / A core of TGAC-containing W-box, disease response
WUSATAg / TTAATGG / 1 / 0 / 0 / Target sequence of WUS in the intron of AGAMOUS gene, flower development