Supplementary Table 2. Cis-acting elements analysis of 5'-upstream regulatory elements and
their positions in bi-directional promoter (672 bp) identified by PLACE and PLANTCARE.
Name of
element
ABRE
the Signal Sequence
ACE
AAACGTTA
Box-4
ATTAAT
Box-1
Box-III
Box-W1
TTTCAAA
CATTTACACT
TTGACC
Position relative Functional description
to ATG
+137
Cis-acting element involved in the
abscisic acid responsiveness.
+164
Cis-acting element involved in light
responsiveness.
+329
Part of a conserved DNA module
involved in light responsiveness.
-345
Light responsive element.
-552
Protein binding site.
+605, -617
Fungal elicitor responsive element.
CATT motif
CGTCA-motif
GCATTC
CGTCA
+216
+569, -224
ERE
ATTTCAAA
-345
G-Box
CACGTA
-137
G-Box
GTACGTG
TACGTG
CACGTC
+136, +137, -225
GA-motif
AAAGATGA
-12
Part of a light responsive element.
Skn-1-motif
GTCAT
+477
Sp1
TC-rich repeats
CC(G/A)CCC
GTTTTCTTAC
-357
+661
TGACG-motif
TGACG
+224, -569
W box
TTGACC
+605, -617
Cis-acting regulatory element
required for endosperm expression.
Light responsive element.
Cis-acting element involved in
defense and stress responsiveness.
Cis-acting regulatory element
involved in the MeJAresponsiveness.
-
WUN-motif
TCATTACGAA
-627
Wound-responsive element.
as-2-box
GATAatGATG
-1, -7, -4
Involved in shoot-specific expression
and light responsiveness.
2SSEEDPROTB
ANAPA
CAAACAC
+500, -130
Conserved in many storage-protein
gene promoters; May be important
for high activity of the napA
promoter.
TACGTG
Part of a light responsive element.
Cis-acting regulatory element
involved in the MeJAresponsiveness.
Ethylene-responsive element.
Cis-acting regulatory element
involved in light responsiveness.
Cis-acting regulatory element
involved in light responsiveness.
Organism
Arabidopsis
thaliana
Petroselinum
crispum
Petroselinum
crispum
Pisum sativum
Pisum sativum
Petroselinum
crispum
Zea mays
Hordeum
vulgare
Dianthus
caryophyllus
Antirrhinum
majus
Oryza sativa,
Daucus
carota,
Zea mays
Helianthus
annuus
Oryza sativa
Zea mays
Nicotiana
tabacum
Hordeum
vulgare
Arabidopsis
thaliana
Brassica
oleracea
Nicotiana
tabacum
Brassica
napus
ABRELATERD1
ACGTG
+138
ACGTABREMO
TIFA2OSEM
ACGTGKC
+226
ACGTATERD1
ACGT
+138, +167, +226
+574, -138, -167,
-226, -574
ACGTOSGLUB1 GTACGTG
+136
ACGTTBOX
AACGTT
+ 166, -166
AMYBOX1
TAACARA
-305
ARR1AT
NGATT
+315, -25, -275
ASF1MOTIFCA
MV
TGACG
+224, -569
CACTFTPPCA1
YACT
+68, 66, +90, 453, +108, -539,
+310, -542,
+483, -552, +654
-648
CANBNNAPA
CNAACAC
+500, +130
ABRE-like sequence (from -199 to 195) required for etiolation-induced
expression of erd1 (early responsive
to dehydration) in Arabidopsis
Experimentally determined sequence
requirement of ACGT-core of motif
A in ABRE of the rice gene, DRE
and ABRE are interdependent in the
ABA-responsive expression of the
rd29A.
Arabidopsis
thaliana
ACGT sequence (from -155 to -152)
required for etiolation-induced
expression of erd1 (early responsive
to dehydration) in Arabidopsis
ACGT motif" found in GluB-1 gene
in rice, Required for endospermspecific expression; Conserved in the
5'-flanking region of glutelin genes.
Arabidopsis
thaliana
Plant bZIP Proteins gather at ACGT
elements.
Conserved sequence found in 5'upstream region of alpha-amylase
gene.
Plant
"ARR1-binding element" found in
Arabidopsis; ARR1 is a response
regulator; N=G/A/C/T, AGATT is
found in the promoter of rice nonsymbiotic haemoglobin-2 gene.
TGACG motifs are found in many
promoters and are involved in
transcriptional activation of several
genes by auxin and/or salicylic acid.
(CACT) is a key component of
Mem1 (mesophyll expression
module 1) found in the Cisregulatory element in the distal
region of the phosphoenolpyruvate
carboxylase (ppcA1) of the C4 dicot
F. trinervia.
Core of "(CA)n element" in storage
protein genes in Brassica napus,
Embryo and endosperm-specific
transcription of napA gene, seed
Oryza sativa,
Arabidopsis
thaliana
Oryza sativa
Hordeum
vulgare,
Oryza sativa,
Triticum
aestivum
Arabidopsis
thaliana
Cauliflower
mosaic virus,
Nicotiana
Tabacum,
Arabidopsis
thaliana
Flaveria
trinervia
Brassica
napus
specificity; activator and repressor.
A variant of CArG motif, with a
longer A/T-rich core; Binding site for
AGL15.
Common sequence found in the 5'non-coding regions of eukaryotic
genes.
The sequence critical for cytokininenhanced Protein Binding in vitro,
found in -490 to -340 of the promoter
of the cucumber POR (NADPHprotochlorophyllide reductase) gene.
GTAC is the core of a CuRE
(copper-response element) found in
Cyc6 and Cpx1 genes in
Chlamydomonas, also involved in
oxygen-response of these genes.
Core site required for binding of Dof
proteins in maize.
CARGCW8GAT
CWWWWWWW
WG
+ 205, + 328, 205, -328
Arabidopsis
thaliana
CCAATBOX1
CCAAT
+ 341, -73
CPBCSPOR
TATTAG
+62
CURECORECR
GTAC
+67, +89, +136, 67,
-89, -136
DOFCOREZM
AAAG
+300, -16, +379, 174, +523, -221,
+533, -405,
485, -603
DPBFCOREDC
DC3
ACACNNG
-550
A novel class of bZIP transcription
factors, DPBF-1 and 2 (Dc3
promoter-binding factor-1 and 2)
binding core sequence.
Daucus
carota,
Arabidopsis
thaliana
EBOXBNNAPA
CANNTG
+550, -550
Brassica
napus
EECCRCAH1
GANTTNC
+104
ELRECOREPCR
P1
TTGACC
+605, -617
ERELEE4
AWTTCAAA
-345
E-box of napA storage-protein gene
of Brassica napus, (also known as Rresponse element).
"EEC"; Consensus motif of the two
enhancer elements, EE-1 and EE-2,
both found in the promoter region of
the Chlamydomonas Cah1 (encoding
a periplasmic carbonic anhydrase);
Binding site of Myb transcription
factor LCR1.
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 (ethylene responsive element)"
of tomato E4 and carnation GST1
genes. ERE motifs mediate ethyleneinduced activation of the U3
promoter region.
Eukaryotes,,Gl
ycine max
Cucumis
sativus
Chlamydomon
as reinhardtii
Zea mays
Chlamydomon
as reinhardtii
Petroselinum
crispum);
Nicotiana
tabacum
Lycopersicon
esculentum,
Dianthus
caryophyllus,
Lycopersicon
chilense
GADOWNAT
ACGTGTC
+226
GARE1OSREP1
TAACAGA
-305
GT1CONSENSU
S
GRWAAW
+76, +390, +469,
-17, -242, -264
GTGANTG10
GTGA
+142
HEXMOTIFTAH ACGTCA
3H4
(-) 224
IBOX
GATAAG
+449
IBOXCORE
GATAA
+390, +449,
+469, -243
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.
"Gibberellin-responsive element
(GARE)" found in the promoter
region of a cystein proteinase (REP1) gene in rice.
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; R=A/G;
W=A/T .GT-1 can stabilize the
TFIIA-TBP-DNA (TATA box)
complex; Binding of GT-1-like
factors to the PR-1a promoter
influences the level of SA-inducible
gene expression.
"GTGA motif" found in the promoter
of the tobacco late pollen gene g10
which shows homology to pectate
lyase and is the putative homologue
of the tomato gene lat56; Located
between -96 and -93.
Arabidopsis
thaliana
"Hexamer motif" found in promoter
of wheat histone genes H3 and H4;
CaMV35S; NOS; Binding with HBP1A and HBP-1B; Binding site of
wheat nuclear protein HBP-1
(histone DNA binding protein-1);
HBP-1 has a leucine zipper motif;
"hexamer motif" in type 1 element
may play important roles in
regulation of replication- dependent
but not of replication-independent
expression of the wheat histone H3
gene; Rice OBF1-homodimerbinding site.
Conserved sequence upstream of
light-regulated genes; Sequence
found in the promoter region of rbcS
of tomato and Arabidopsis; Binding
site of LeMYB1, (transcriptional
activator) that is a member of a novel
class of myb-like proteins.
Conserved sequence upstream of
light-regulated genes.
Triticum
aestivum,
CaMV, Oryza
sativa
Oryza sativa
Pisum
sativum,
Avena sativa,
Oryza sativa,
Nicotiana
tabacum,
Arabidopsis
thaliana,
Spinacia
oleracea, bean
Triticum
aestivum,
CaMV, Oryza
sativa
Lycopersicon
esculentum,
Arabidopsis
thaliana
Monocots and
dicots.
INRNTPSADB
YTCANTYY
+177
LECPLEACS2
TAAAATAT
+392
MYB1AT
WAACCA
+324
MYBCORE
CNGTTR
+306
MYBST1
GGATA
-643, -650
MYCCONSENS
USAT
CANNTG
+550, -550
NAPINMOTIFB
N
TACACAT
-420
NODCON1GM
and
OSE1ROOTNO
DULE
AAAGAT
+300, -14, -601
NODCON2GM
and
OSE2ROOTNO
CTCTT
+564
Initiator elements found in the
tobacco psaDb gene promoter
without TATA boxes; Lightresponsive transcription of psaDb
depends on Inr, but not TATA box.
Core element in LeCp (tomato Cys
protease) binding cis-element (from 715 to -675) in LeAcs2 gene.
Nicotiana
tabacum
MYB recognition site found in the
promoters of the dehydrationresponsive gene rd22 and many other
genes in Arabidopsis.
Binding site for all animal MYB and
at least two plant MYB proteins
ATMYB1 and ATMYB2, both;
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.
Core motif of MybSt1 (a potato
MYB homolog) binding site.
MYC recognition site found in the
promoters of the dehydrationresponsive gene rd22 and many other
genes in Arabidopsis; Binding site of
ATMYC2 (previously known as
rd22BP1); (E-box; CANNTG),
(MYCATRD22); N=A/T/G/C; 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.
Sequence found in 5' upstream region
(-6, -95, -188) of napin gene in
Brassica napus; Interact with a
protein present in crude nuclear
extracts from developing seeds.
One of two putative nodulin
consensus sequences.
Arabidopsis
thaliana
One of two putative nodulin
consensus sequences.
Glycine max
Lycopersicon
esculentum
Arabidopsis
thaliana,
animal,
Petunia
hybrida
Solanum
tuberosum
Arabidopsis
thaliana
Brassica
napus
Glycine max
DULE
NRRBNEXTA
TAGTGGAT
- 651
POLASIG1
AATAAA
+ 296, + 429,
+529, -60
POLASIG2
AATTAAA
+149
POLASIG3
AATAAT
+579
POLLEN1LELA
T52
AGAAA
PRECONSCRHS
P70A
"NRR (negative regulatory region)"
in promoter region of Brassica napus
extA gene; Removal of this region
leads to expression in all tissues
within the stem internode, petiole and
root.
PolyA signal found in legA gene of
pea, rice alpha-amylase; -10 to -30 in
the case of animal genes. Near
upstream elements (NUE) in
Arabidopsis.
Poly A signal found in rice alphaamylase; -10 to -30 in the case of
animal genes.
Consensus sequence for plant
polyadenylation signal.
Brassica
napus
+521, -171, -663
One of two co-dependent regulatory
elements responsible for pollen
specific activation of tomato lat52
gene; Found at -72 to -68 region;
Also found in the promoter of tomato
endo-beta-mannanase gene.
Lycopersicon
esculentum
SCGAYNRNNN
NNNNNNNNNN
NNHD
+ 99
Chlamydomon
as reinhardtii
QELEMENTZM
ZM13
AGGTCA
+ 616
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.
"Q (quantitative)-element" in maize
ZM13 gene (pollen-specific maize
gene.) promoter; Found at -107 to 102; Involved in expression
enhancing activity.
RAV1AAT
REALPHALGL
HCB21
CAACA
AACCAA
-184, -336
-407
Lemna gibba
ROOTMOTIFTA
POX1
S1FBOXSORPS
1L21
ATATT
-395, -582
ATGGTA
-19
"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.
Motif found both in promoters of
rolD
"S1F box" conserved both in spinach,
RPS1 and RPL21 genes encoding the
plastid ribosomal protein S1 and L21,
respectively; Negative element;
Pisum
sativum,
Oryza sativa,
Arabidopsis
thaliana.
Oryza sativa,
animal
Zea mays
Zea mays
Agrobacteriu
m rhizogenes
Spinacia
oleracea
SEF4MOTIFGM
7S
RTTTTTR
-47
TAAAGSTKST1
TAAAG
-16
TATABOXOSP
AL
TATTTAA
+206
TATAPVTRNA
LEU
TTTATATA
+457
TATCCACHVA
L21
TATCCAC
+ 650
TATCCAOSAM
Y
TATCCA
+643, + 650
TATCCAYMOT
IFOSRAMY3D
TGACGTVMA
MY
TATCCAY
+650
TGACGT
+ 224
WBBOXPCWR
TTTGACY
+ 604, -497
Might play a role in downregulating
RPS1 and RPL21 promoter activity.
Consensus sequence found in
5'upstream region (-199) of betaconglycinin (7S globulin) gene;
"Binding with SEF4 (soybean
embryo factor 4.
Target site for trans-acting StDof1
protein controlling guard cellspecific gene expression; KST1 gene
encodes a K+ influx channel of guard
cells.
Binding site for OsTBP2, found in
the promoter of rice pal gene
encoding phenylalanine ammonialyase; OsTFIIB stimulated the DNA
binding and bending activities of
OsTBP2 and synergistically
enhanced OsTBP2-mediated
transcription from the pal promoter.
Frequently observed upstream of
plant tRNA genes; Found in maize
glycolytic glyceraldehyde-3-phospate
dehydrogenase 4 (GapC4) gene
promoter; Binding site of TATA
binding protein (TBP).
"TATCCAC box" is a part of the
conserved Cis-acting response
complex (GARC) that most often
contain three sequence motifs, the
TAACAAA box , GA-responsive
element (GARE); the pyrimidine
box, CCTTTT ; and the TATCCAC
box, which are necessary for a full
GA response
"TATCCA" element found in alphaamylase promoters of rice at
positions 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.
TATCCAY motif and G motif are
responsible for sugar repression.
Required for high level expression
of alpha-Amylase in the cotyledons
of the germinated seeds
"WB box"; WRKY proteins bind
Glycine max
Solanum
tuberosum
Oryza sativa
Phaseolus
vulgaris, Zea
mays
Hordeum
vulgare
Oryza sativa
Oryza sativa
Vigna mungo
Ipomoea
KY1
specifically to the DNA sequence
motif (T)(T)TGAC(C/T), which is
known as the W box
WBOXATNPR1
TTGAC
WBOXHVISO1
TGACT
+223, +605, -498,
-570, -618
+143, -476, -497
WBOXNTERF3
TGACY
+143, +606, -476,
-497, -617
WRKY71OS
TGAC
+143, +224,
+606, -477, -498,
-570, -618
WUSATAg
+556, -327
"W-box" found in promoter of
Arabidopsis thaliana NPR1 gene;
SUSIBA2 bind to W-box element in
barley iso1 (encoding isoamylase1)
promoter
"W box" found in the promoter
region of a transcriptional repressor
ERF3 gene in tobacco;
"A core of TGAC-containing Wbox" of, e.g., Amy32b promoter;
Binding site of rice WRKY71, a
transcriptional repressor of the
gibberellin signaling pathway.
Target sequence of WUS in the
intron of AGAMOUS gene in
Arabidopsis
(+) stands for 5'-3' orientation and (-) stands for 3'-5' orientation
batatas,
Triticum
aestivum,
Hordeum
vulgare,
Avena fatua,
Petroselium
crispum,
Arabidopsis
thaliana
Arabidopsis
thaliana
Hordeum
vulgare
Nicotiana
tabacum
Oryza sativa,
Petroselinum
crispum
Oryza sativa