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Table 2 List of experimentally and computationally defined upstream regulatory sequences, and their cognate transcriptional regulators that determine spatio-temporal control of rice genes

From: Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining

Cis-element

Consensus core motif

Transcriptional regulator

Biological function

Auxin responseelement (AuxRE1)

TGTCTC

Auxin responsefactor (ARF1, ARF2)

Primary regulator of auxin-regulated expression

Auxin responseelement (AuxRE2)

GACACA

Auxin responsefactor (ARF1, ARF2)

Primary regulator of auxin-regulated expression

Auxin responseelement (AuxRE3)

GACActGACA

Auxin responsefactor (ARF1)

Primary regulator of auxin-regulated expression

Gibberellin responseelement (GARE)

TAACCACC

GAMyb factors

Primary regulator of GA-regulated expression; primary regulator of sugar sensitivity of GA-responsive genes

Glut element

AACA/ACGT

Unknown

Regulator of endosperm-specific expression of rice seed storage protein glutelin (OsGlut)

Gt1/Gt2 box-I

ATATCATGAGTCACTTCA

GT1, GT2

Positive regulator of endosperm-specific expression of rice glutelin (OsGlut) genes

Gt1/Gt2 box-II

CTTTCGTGTACCACA

GT1, GT2

Positive regulator of endosperm-specific expression of rice glutelin (OsGlut) genes

Gt1/Gt2 box-III

ACAATGCTGCTCAATTA

GT1, GT2

Positive regulator of endosperm-specific expression of rice glutelin (OsGlut) genes

Gt1/Gt2 box-IV

ATTATCCAATGTCATATTG

GT1/GT2

Positive regulator of endosperm-specific expression of rice glutelin (OsGlut) genes

Gt1/Gt2 box-V

TAAGTCACGTTTGATGA

GT1, GT2

Positive regulator of endosperm-specific expression of rice glutelin (OsGlut) genes

Gt3 box

ATATCATGAGTCACTTCA

GT1, GT2, GT3

Positive regulator of endosperm-specific expression of rice glutelin (OsGlut) genes

PB-1 element

AAGCAACACACAAC

Dof-type P-boxBinding factor (PBF)

Positive regulator of endosperm-specific expression

Prolamin box

TGTAGAA, TGTTTTAATATGACGTGG

Dof-type P-boxbinding factor (PBF)

Positive regulator of endosperm-specific expression

SP8/SURE

TACTATT, TCACTATT,

Opaque-2 transcriptionfactor

Positive regulator of endosperm-specific expression

LPSE1

ATTTGAGCTGCC

Unknown

Positive spatial regulator of expression in green leaves, stem and young panicle

LPSE2

TTGATATATTTGT

Unknown

Positive regulator of expression on green leaves and negative regulator of expression in young panicle and roots

LPSRE1

CGGCGCGCCAC

Unknown

Positive regulator of expression in green leaves and negative regulator of expression in panicle and stem

LPSRE2

TTAGATAATGGA

Unknown

Positive spatial regulator of expression in green leaves, stem root, and young panicles

PSE1

TTTATCTATTTCC

Unknown

Negative regulator of expression in young panicle and stem

PSE2

TCTTTGGCAGAG

Unknown

Positive regulator of expression in green leaves and negative regulator of expression in stem and young panicles

Ethylene and jasmonic acid responsive element

GCC-CORE

Ethylene response factor

Regulator of senescence-induced gene expression (OsERF)

GS2

TTCGAAATTGAACGTGCT-TAACCAAGAGAACAC

WRKY transcription factors

Senescence box

ABRE (ACGT-type)

CGMCACGTB

OsABI5, OREB1

ABA-response element for ABA regulated gene expression during stress response and seed maturation

CE1

TGCCACCGG

OsABI5, OREB1

ABRE coupling factor

CE3

ACGCGTGTCCTC

OsABI5, OREB1

ABRE coupling factor

DRT/CRE

(a/g)CCGAC

OsDREB1, OsDREB2

Dehydration response element for abiotic stress regulated gene expression independent of ABA

Abiotic/oxidative stress Element

CACG

OsNAC6, OsNAC5, OsSNAC2

Regulator of abiotic stress-responsive gene expression independent of the DREB regulon

as1/ocs/TGA-like element

AATTTGAT, TAATTTGA

OsTGA10

Regulator of chilling mediated oxidative stress signaling

Pyrimidine-box/Myb2-box element

AAAGAAAAA, TAGTTTTT

OsMyb4

Regulator of chilling mediated oxidative stress signaling

JARE

CGTCA, TGACG, VCGCGB

Ethylene response factors (ERF)

Jasmonic acid response element; regulator of responses to pathogens and herbivores

GCC-box

TAAGAGCCGCC

Ethylene response factors (ERF)

Negative regulator of responses to Magnaporthe oryzae

P-box

CCGCCCTCCA

Ethylene response factors (ERF)

Disease responsive element

W-box

TTGAC element

OsWRKY45, OsWRKY71, OsWRKY03, OsWRKY53, OsWRKY31, OsWRKY30, OsWRKY76

Disease responsive

E-box

CAGTCG, CACCTG

OsbHLH65

Pathogen and herbivore response element; regulator of responses to Magnaporthe Oryzae and Nilaparvata lugens

  1. List was based on seminal studies published in the literature and annotated in public databases.