Table 1 3′ UTR encoded sRNAs

sRNA name

Parent mRNA

Start

end

length

sRNA

mRNA

(based on RPKMs)

promoters

−35

−10

TSS

binding site

fwd_4

rbsB

14355

14537

183

596.8

102.8

Independent

1

14317

14342

14357

rpoD17, cynR, rpoD15, rpoD16, phoB

fwd_6

polA

28634

28755

122

549.8

110.5

Independent

1

28656

28676

28691

cytR, arcA, crp, rpoD15, rpoD17

fwd_15

ECA0044

55039

55291

253

66.8

27.4

Independent

1

55009

55029

55044

rpoD17, fis, rpoD15, rpoD16, phoB

fwd_19

expI

126355

126501

147

338.5

588.1

Co-expression

1

126418

126435

126450

metR, rpoD16

reg_seq13

aldA

139913

140154

242

136.8

30.4

Independent

1

140046

140063

140078

reg_seq27

ECA0332

380584

380826

243

1660.5

389.3

Independent

1

380610

380631

380646

metJ

reg_seq31

ECA0449

515673

515910

238

363.3

528.7

Co-expression

1

515790

515813

515828

glpR, ihf, argR2, nagC, argR2, fnr, fis

reg_seq43

mdH

758603

758857

255

1759.1

1895.7

Co-expression

2

758751

758770

758789

glpR, fis, arcA, purR

758444

758464

758479

reg_seq142

ECA2516

2832294

2832530

237

514.2

77.5

Independent

1

2832185

2832205

2832220

purr, rpoD16

fwd_rfam4

rpiL

255260

255321

62

775.5

1856.1

Independent

lrp, hns

comp_seq5

glnA

34992

35234

243

858.8

1209.3

Co-expression

1

35262

35241

35226

rpoD15, rpoD16, phoB

comp_seq11

slmA

164026

164334

309

196.4

454.0

Independent

1

164395

164375

164360

arcA, rpoD17, rpoD15, rpoD16, phoB

comp_seq130

ECA2950

3295111

3295347

237

197.9

222.9

Co-expression

2

3295196

3295176

3295161

rpoD16, argR, arcA, ihf

3295506

3295485

3295470

rev_rfam22

glpC

4651380

4651485

109

348.2

40.8

Independent

1

4651583

4651562

4651547

Ada, rpoE, tyrR, fur, fur

dapZ

ECA3872 (dapB)

4332178

4332288

111

20.9

110.8

Independent

1

4332302

4332284

4332269

Ihf, argR2, rpoD16, argR,, fis, crp