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 tissuespecificity are in bold. Shaded rows indicate that putative cis-regulatory elements were detected
in all 3 promoters.
cis Element
Sequence
Number of Elements
GmActin
GmRpS11
GmHsp90
1
2
0
Predicted Function
-10 promoter element, light
-10PEHVPSBD
TATTCT
regulation and circadian rhythms,
chloroplast gene
2SSEEDPROTBANAPA
CAAACAC
0
1
0
AACACOREOSGLUB1
AACAAAC
3
0
0
ACGTG
3
2
1
Conserved in many storage-protein
gene promoters, seed
Involved in controlling endospermspecific expression
ABA responsive element, ABA
ABRELATERD1
response, early response to
dehydration
ABREOSRAB21
ACGTSSSC
1
0
0
ABRERATCAL
MACGYGB
1
1
0
ACGTABREMOTIFA2OSEM
ACGTGKC
1
0
0
ABA signaling and response
Calcium ion (Ca2+) response and
regulation
ABA signaling and response
Required for etiolation-induced
ACGTATERD1
ACGT
5
2
3
expression of erd1 (early response to
dehydration)
ACIIIPVPAL2
GTTAGGTTC
0
0
1
CGAACTT
1
0
0
Required for vascular-specific gene
expression
Involved in Chlamydomonas Nia1
AMMORESIVDCRNIA1
transcription repression, N
metabolism
ANAERO1CONSENSUS
AAACAAA
1
0
0
ANAERO3CONSENSUS
TCATCAC
0
1
0
ARR1AT
NGATT
2
0
11
ASF1MOTIFCAMV
TGACG
0
1
1
Involved in the fermentative pathway
in silico
Involved in the fermentative pathway
in silico
ARR1 binding element, cytokinin
signaling and response
Auxin and/or salicylic acid signaling,
and light regulation
cis Element
ATHB1ATCONSENSUS
Sequence
CAATWATTG
Number of Elements
GmActin
GmRpS11
GmHsp90
1
0
0
Predicted Function
Recognition sequence of Arabidopsis
Athb-1 protein
Consensus binding sequence
ATHB5ATCORE
CAATNATTG
1
0
0
Arabidopsis class I Hdzip
(Homeodomein-leucine zipper)
protein
Binding site of OsBIHD1, a rice BELL
BIHD1OS
TGTCA
1
1
0
homeodomain transcription factor,
disease response
Conserved in several NCII
BOXIINTPATPB
ATAGAA
0
0
1
(nonconsensus type II) promoters of
plastid genes
BOXIIPCCHS
ACGTGGC
1
0
0
Essential for light regulation
Consensus of the putative core
BOXLCOREDCPAL
ACCWWCC
1
0
0
sequences of box-L-like sequences,
UV-B induction
BP5OSWX
CAACGTG
0
1
0
CAATBOX1
CAAT
7
0
4
OsBP-5 (a MYC protein) binding site
in Wx promoter;
CAAT box
Found in the distal region of the
CACTFTPPCA1
YACT
7
6
6
phosphoenolpyruvate carboxylase,
photosynthesis
In storage protein genes; seed
CANBNNAPA
CNAACAC
0
1
0
CAREOSREP1
CAACTC
0
0
1
CARGATCONSENSUS
CCWWWWWWGG
0
1
0
CARGCW8GAT
CWWWWWWWWG
1
0
0
RYCGAC
0
0
1
Binding site of CBF1, abiotic stress
CCAATBOX1
CCAAT
1
0
0
Act cooperatively with HSEs
CURECORECR
GTAC
2
1
0
CBFHV
specificity;
Found in the promoter region of a
cysteine proteinase, GA signaling
Involved in flowering timing
Binding site for AGL15 (AGAMOUSlike 15), embryo development
Copper-response and some oxygenresponse
cis Element
DOFCOREZM
Sequence
AAAG
Number of Elements
GmActin
GmRpS11
GmHsp90
11
5
8
Predicted Function
Core site required for binding of Dof
proteins in maize, C4 photosynthesis
DPBF-1 and 2 binding core
DPBFCOREDCDC3
ACACNNG
2
0
0
sequence; ABA response, late
embryogenesis- abundant genes,
seed-related
EBOXBNNAPA
CANNTG
4
0
1
EECCRCAH1
GANTTNC
1
1
0
GARE2OSREP1
TAACGTA
0
0
1
GATA
7
0
2
GRWAAW
3
4
7
GT1GMSCAM4
GAAAAA
2
1
1
GTGANTG10
GTGA
3
5
3
GATABOX
GT1CONSENSUS
E-box of napA storage-protein gene
of Brassica napus, seed
EEC binding site of Myb transcription
factor LCR1
Gibberellin-responsive element
(GARE), GA signaling
GATA box in chlorophyll a/b binding
protein Cab22 gene, light regulation
Involved in light-regulation; SAsignaling pathway
Involved in response to salt and
pathogen stress
GTGA motif found in late pollen gene
g10 which shows homology to
pectate lyase
HDZIP2ATATHB2
Binding site of the homeobox gene
TAATMATTA
1
0
0
GATAAG
1
0
0
I box; light-regulated genes
GATAA
2
0
1
I box, light regulation
IBOXCORENT
GATAAGR
1
0
0
INRNTPSADB
YTCANTYY
1
0
0
TGCAGG
0
1
0
TAAAATAT
0
0
1
IBOX
IBOXCORE
INTRONLOWER
LECPLEACS2
(ATHB-2) regulated by light signals
I-box core motif, light-responsive
promoter regions
Inr (initiator) elements found in gene
promoter without TATA boxes
3' intron-exon splice junctions
Core element in LeCp binding ciselement, elicitor signaling
cis Element
MYB1AT
MYB26PS
Sequence
Number of Elements
GmActin
GmRpS11
GmHsp90
WAACCA
2
0
0
GTTAGGTT
0
0
1
Predicted Function
MYB recognition site, ABA signaling,
stress response, seed/leaf related
Myb26 binding site, involved in
phenylpropanoid biosynthesis
Binding site for ATMYB2, response
MYB2AT
TAACTG
2
0
0
to water stress and ABA, seed/leaf
related
MYB2CONSENSUSAT
YAACKG
2
0
0
MYBCORE
CNGTTR
0
1
0
MYB recognition site, involved in
response to water stress
Binding site for ATMYB1 and
ATMYB2, response to ABA and
water stress
AACGG
2
0
0
Myb core
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
MYBCOREATCYCB1
MYBPLANT
One of two putative nodulin
consensus sequences; nodule
specific
One of two putative nodulin
NODCON2GM
CTCTT
3
0
3
consensus sequences, nodule
specific
NtBBF1 binding site in rolB gene,
NTBBF1ARROLB
ACTTTA
1
0
0
required for tissue-specific
expression and auxin induction
One of the consensus sequence
OSE1ROOTNODULE
AAAGAT
2
0
1
motifs of organ-specific elements
(OSE), nodule formation
One of the consensus sequence
OSE2ROOTNODULE
CTCTT
3
0
3
motifs of organ-specific elements
(OSE), nodule formation
PolyA signal; poly A signal found in
POLASIG1
AATAAA
3
1
4
legA gene of pea, rice alphaamylase, Arabidopsis near upstream
elements
cis Element
Sequence
Number of Elements
GmActin
GmRpS11
GmHsp90
POLASIG2
AATTAAA
0
0
2
POLASIG3
AATAAT
7
0
2
POLLEN1LELAT52
AGAAA
4
3
4
Predicted Function
PolyA signal in rice alpha-amylase,
germination
Plant polyA signal
One of two co-dependent regulatory
elements responsible for pollen
specific activation of tomato
PRE (Pro- or hypo-osmolarity-
PREATPRODH
ACTCAT
0
1
0
responsive element) found in proline
dehydrogenase (ProDH) promoter
prox B (proximal portion of B-box)
PROXBBNNAPA
CAAACACC
0
1
0
required for seed specific expression
and ABA responsiveness
PYRIMIDINEBOXOSRAMY1A
CCTTTT
1
0
0
RAV1AAT
CAACA
6
0
0
Pyrimidine box partially involved in
sugar repression and GA response
Binding consensus sequence
transcription factor RAV1 in rosette
leaves and roots
RHERPATEXPA7
KCACGW
0
0
1
ROOTMOTIFTAPOX1
ATATT
3
0
4
S1FBOXSORPS1L21
ATGGTA
0
1
1
Right part of RHEs (Root Hairspecific cis-Elements)
Motif found both in promoters of rolD;
S1F box, negative element
downregulating RPS1 and RPL21
promoter activity in plastid
SEF4MOTIFGM7S
RTTTTTR
6
0
2
SEF4 binding site binding with SEF4
(soybean embryo factor 4)
Site II element found in cytochrome
gene promoter, blue light signaling;
SITEIIATCYTC
TGGGCY
0
1
0
Overrepresented in the promoters of
nuclear genes related to oxidative
phosphorylation, meristem-specific
One of Sequences Over-
SORLIP1AT
GCCAC
3
0
0
Represented in Light-Induced
Promoters (SORLIPs) in Arabidopsis
cis Element
Sequence
Number of Elements
GmActin
GmRpS11
Predicted Function
GmHsp90
One of Sequences Over-
SORLIP5AT
GAGTGAG
1
0
0
Represented in Light-Induced
Promoters (SORLIPs) in Arabidopsis
SP8BFIBSP8BIB
TACTATT
0
0
1
SREATMSD
TTATCC
0
1
0
One of SPBF binding site (SP8b),
tuberous root
Sugar-repressive element (SRE)
found in down-regulated genes after
main stem decapitation
Core of sulfur-responsive element
SURECOREATSULTR11
GAGAC
1
0
0
T/GBOXATPIN2
AACGTG
1
1
1
TAAAGSTKST1
TAAAG
0
1
4
TATABOX4
TATATAA
2
0
1
TATA box
TATABOX5
TTATTT
3
1
4
TATA box
TATABOXOSPAL
TATTTAA
1
0
0
TATAPVTRNALEU
TTTATATA
1
0
0
ACTTTG
0
0
1
(SURE) involved auxin response
Involved in jasmonate (JA) induction
Involved in guard cell-specific gene
expression
Binding site for OsTBP2, involved in
phenylpropenoid pathway
TATA-like motif
Tbox found in GAPB gene promoter;
TBOXATGAPB
involved in light-activated gene
transcription
telo-box (telomere motif) found in
eEF1AA1 gene promoter; Required
TELOBOXATEEF1AA1
AAACCCTAA
0
0
1
for the activation of expression in
root primordia; Binding site of AtPur
alpha-1
Required for high level expression of
TGACGTVMAMY
TGACGT
0
1
0
alpha-Amylase in the cotyledons of
the germinated seeds
UP2ATMSD
AAACCCTA
0
0
2
Up2 motif found genes after main
stem decapitation in Arabidopsis
W-box recognized specifically by
WBOXATNPR1
TTGAC
0
0
1
salicylic acid (SA)-induced WRKY
DNA binding proteins, disease
response
cis Element
Sequence
Number of Elements
GmActin
GmRpS11
Predicted Function
GmHsp90
W-box element in barley iso1
WBOXHVISO1
TGACT
0
2
1
(encoding isoamylase1) promoter,
sugar response
WBOXNTERF3
TGACY
0
2
1
WRKY71OS
TGAC
1
4
3
WUSATAg
TTAATGG
1
0
0
W box involved in activation of ERF3
gene, wounding response
A core of TGAC-containing W-box,
disease response
Target sequence of WUS in the
intron of AGAMOUS gene, flower
development