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Table 1 Putative bidirectional gene pairs identified with 100–600 bp between transcription start sites (TSS) and containing at least two G-Box elements

From: Bidirectional promoters in seed development and related hormone/stress responses

FWgene

RVgene

len

DRE

CE3

FWgene annotation

RVgene annotation

FWlocation

RVlocation

AT1G04635

AT1G04630

202

y

 

AtPOP5

maternal effect embryo arrest 4 (MEE4)

nucleolus

mitochondrion

AT1G07510

AT1G07500

347

  

FtsH10 protease

unknown protein

mitochondrion

cytosol

AT1G07660

AT1G07645

452

  

Histone superfamily

vicinal oxygen chelate (VOC) metalloenzyme

nucleus

cytosol

AT1G07985

AT1G07980

478

  

Expressed protein

nuclear factor Y, subunit C10

nucleus

plastid

AT1G15330

AT1G15320

333

  

Cystathionine beta-synthase (CBS)

unknown protein

cytosol

extracellular

AT1G16740

AT1G16730

378

  

Ribosomal protein L20

unknown protein 6 (UP6)

mitochondrion

nucleus

AT1G19980

AT1G19970

327

  

cytomatrix protein-related

ER lumen protein retaining receptor family

nucleus

ER

AT1G28540

AT1G28530

164

  

unknown protein

unknown protein

cytosol

plastid

AT1G31420

AT1G31410

259

y

 

LRR kinase (FEI1)

putrescine-binding transporter protein

membrane

plastid

AT1G32560

AT1G32550

367

y

 

LEA4-1

Ferredoxin C2

nucleus

plastid

AT1G48840

AT1G48830

264

y

 

unknown function (DUF639)

Ribosomal protein S7e family

membrane

cytosol

AT1G50440

AT1G50430

161

  

RING/FYVE/PHD zinc finger

DWARF 5 (DWF5) -STEROL DELTA7 REDUCTASE

nucleus

membrane

AT1G52230

AT1G52220

139

  

PHOTOSYSTEM I SUBUNIT H2

unknown protein

plastid

plastid

AT1G54870

AT1G54860

375

  

ChlADR aldehyde reductase

Glycoprotein membrane GPI-anchored

cytosol

extracellular

AT1G56170

AT1G56165

391

  

CCAAT motif binding complex

non-coding RNA

nucleus

cytosol

AT1G61790

AT1G61780

237

  

Oligosaccharyltransferase

postsynaptic protein-related

ER

nucleus

AT1G65140

AT1G65130

595

  

Ubiquitin c-terminal hydrolase

Ubiquitin c-terminal hydrolase

cytosol

nucleus

AT1G71090

AT1G71080

370

  

Auxin efflux carrier

RNA pol II transcription elongation factor

membrane

nucleus

AT1G72030

AT1G72020

434

  

Acyl-CoA N-acyltransferase

unknown protein

plastid

mitochondrion

AT1G77370

AT1G77360

307

  

Glutaredoxin

Tetratricopeptide repeat (TPR)-like

extracellular

mitochondrion

AT2G20490

AT2G20480

189

  

NOP10; EDA27 (RNA binding)

unknown protein

nucleolus

nucleus

AT2G25890

AT2G25880

470

  

Oleosin

Ser/Thr kinases - Ataurora2 (AUR2)

lipid body

nucleus

AT2G29560

AT2G29550

523

  

phosphoenolpyruvate enolase

beta-tubulin (TUB7)

cytosol

nucleus

AT2G38040

AT2G38025

385

y

 

acetyl-CoA carboxylase subunit

Cysteine proteinase superfamily

plastid

plastid

AT2G38660

AT2G38650

183

  

Amino acid dehydrogenase

galacturonosyltransferase 7 (GAUT7)

mitochondrion

golgi

AT2G39460

AT2G39450

331

y

 

60S ribosomal protein L23aA

manganese transporter

cytosol

golgi

AT2G43190

AT2G43180

187

  

AtPOP4 (RNA processing)

Phosphoenolpyruvate carboxylase family

nucleolus

plastid

AT2G45740

AT2G45730

556

y

 

peroxin11 (PEX11) family

eukaryotic initiation factor 3 ⊠ subunit

peroxisome

cytosol

AT3G03160

AT3G03150

264

y

y

unknown protein

unknown protein

endomembrane

mitochondrion

AT3G03320

AT3G03310

135

  

RNA-binding protein

lecithin:cholesterol acyltransferase 3

cytosol

plasma membrane

AT3G12320

AT3G12300

580

y

 

unknown protein

unknown protein

nucleus

cytosol

AT3G13190

AT3G13180

559

  

unknown function (DUF827)

rRNA small subunit methyltransferase B

nucleus

plastid

AT3G14340

AT3G14330

305

  

unknown protein

Tetratricopeptide repeat (TPR)-like

membrane

mitochondrion

AT3G15290

AT3G15280

304

  

3-hydroxyacyl-CoA DH

unknown protein

peroxisome

mitochondrion

AT3G16010

AT3G16000

197

  

PPR-like superfamily

plastid DNA-binding protein; MFP1

mitochondrion

plastid

AT3G18215

AT3G18210

245

  

unknown function, DUF599

2OG and Fe(II)-dependent oxygenase

membrane

nucleus

AT3G26618

AT3G26616

464

  

eukaryotic release factor 1-3

unknown protein

cytosol

cytosol

AT3G52230

AT3G52220

139

  

unknown protein

Kinase phosphorylation domain

plastid

nucleus

AT3G53180

AT3G53170

477

  

glutamate-ammonia ligases

Tetratricopeptide repeat (TPR)-like

cytosol

cytosol

AT3G59500

AT3G59490

190

  

HRF1 family protein

unknown protein

ER membrane

nucleus

AT4G00030

AT4G00026

168

  

Plastid-lipid associated (PAP)

SD3 (Segregation Distortion 3); TIM21

plastid

mitochondrion

AT4G01270

AT4G01265

577

y

 

RING/U-box superfamily

raffinose synthase family pseudogene

nucleus

NA

AT4G02430

AT4G02425

189

y

 

S/R-Rich Protein Splicing Factors

unknown protein

nucleus

nucleus

AT4G11985

AT4G11980

129

  

pre-tRNA/non-coding RNA

nudix hydrolase homolog 14

nucleus/cytosol

plastid

AT4G16160

AT4G16155

205

y

 

OEP16-S

dihydrolipoyl dehydrogenase

plastid

plastid

AT4G17560

AT4G17550

541

y

 

Ribosomal protein L19 family

glycerol-3-phosphate permease gene family

plastid

mitochondrion

AT4G17730

AT4G17720

440

  

syntaxin23

RNA-binding (RRM/RBD/RNP motifs) family

cytosol

cytosol

AT4G18240

AT4G18230

169

  

starch synthase 4 (SS4)

unknown protein

plastid

plasma membrane

AT4G18370

AT4G18360

447

  

DEG5 - photosystem II repair

Aldolase-type TIM barrel family

plastid

peroxisome

AT4G19020

AT4G19010

277

  

chromomethylase 2 (CMT2)

AMP-dependent synthetase and ligase family

nucleus

peroxisome

AT4G21280

AT4G21270

267

  

PsbQ subunit photosystem II

kinesin-like motor protein

plastid

nucleus

AT4G23840

AT4G23820

254

  

Leucine-rich repeat (LRR) family

Pectin lyase-like superfamily

cytosol

extracellular

AT4G25140

AT4G25130

366

  

Oleosin1

chloroplast methionine sulfoxide reductase

lipid body

plastid

AT4G25580

AT4G25570

561

  

cold acclimation protein (CAP160)

cytochrome b561

nucleus

plasma membrane

AT4G31080

AT4G31070

351

  

unknown function (DUF2296)

Tetratricopeptide repeat (TPR)-like

ER

cytosol

AT4G33540

AT4G33530

365

  

metallo-beta-lactamase family

K + UPTAKE PERMEASE 5 (KUP5)

plastid

plasma membrane

AT5G05490

AT5G05480

293

  

SYN1 (RAD21-like) gene

Peptide-N4-asparagine amidase A protein

nucleus

plasma membrane

AT5G05987

AT5G05980

509

y

 

prenylated RAB acceptor 1.A2

folylpolyglutamate synthetase isoform

membrane

mitochondrion

AT5G07320

AT5G07315

363

  

Mito ATP-Mg/Pi transporter

pre-tRNA/non-coding RNA

mitochondrion

nucleus/cytosol

AT5G10080

AT5G10070

409

  

Eukaryotic aspartyl protease

RNase L inhibitor protein-related

membrane

cytosol

AT5G10745

AT5G10740

275

  

unknown protein

Protein phosphatase 2C family protein

membrane

nucleus

AT5G16760

AT5G16750

331

  

inositol-trisphosphate 5/6-kinase

TORMOZEMBRYO DEFECTIVE (TOZ)

cytosol

nucleolus

AT5G37350

AT5G37340

232

  

RIO1 kinase

ZPR1 zinc-finger domain protein

nucleus

cytosol

AT5G51540

AT5G51530

529

  

Zincin-like metalloproteases

Ubiquitin c-terminal hydrolase

plastid

cytosol

AT5G54062

AT5G54060

424

  

unknown protein

anthocyanin 3-O-glucoside

extracellular

membrane

AT5G54970

AT5G54960

449

  

unknown protein

pyruvate decarboxylase-2

cytosol

cytosol

AT5G61940

AT5G61930

481

y

 

Ubiquitin c-terminal hydrolase

ACCUMULATION OF PHOTOSYSTEM ONE 3

nucleus

mitochondrion

AT5G62490

AT5G62480

537

  

AtHVA22 family

glutathione transferase

extracellular

cytosol

AT5G64220

AT5G64210

582

  

Calmodulin-binding activator

isoform of alternative oxidase

nucleus

mitochondrion

AT5G67230

AT5G67220

514

  

GT43 glycosyltransferase family

FMN-linked oxidoreductase superfamily

mitochondrion

mitochondrion

  1. Presence of a DRE and/or CE3 motif (not derived from an ACGT-core sequence) also indicated by ‘y’.
  2. The only gene pair with a DRE and a CE3 element is highlighted.