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Table 1 Transcriptome and translatome profiles of 115 ncRNAs known from E. coli O157:H7 EDL933

From: Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq – ryhB encodes the regulatory RNA RyhB and a peptide, RyhP

Name

Start position in the genome

Length

Strand

Number of transcriptome reads

Number of footprint reads

RPKM transcriptome

RPKM footprints

RCV

P value*

Northern Blot/Shine Dalgarno

DicF_1/Z1327

1255006

52

-

2

7

2

16

8.00

1.55E-11

 

STnc70

719959

94

+

47

141

28

182

6.50

4.83E-11

 

RyhB

4367464

65

-

92

192

80

359

4.49

1.77E-09

 

OmrA-B_2

3766084

82

-

504

844

348

1251

3.59

1.47E-08

 

OrzO-P_2

2954314

76

+

5057

8198

3764

13114

3.48

1.97E-08

taaagtggt

STnc100_10

2995675

210

-

496

742

134

430

3.21

4.12E-08

tatgggata

STnc550

2412748

391

-

533

779

77

242

3.14

4.96E-08

caaatagtg

RtT_3

1824178

132

-

22

28

9

26

2.89

1.03E-07

 

RprA

2445280

108

+

568

745

297

839

2.82

1.25E-07

 

STnc180

2250970

203

-

1225

1534

341

919

2.70

1.86E-07

caagcgggg

GadY

4474223

114

+

213

248

106

264

2.49

3.55E-07

 

STnc630

5216481

166

+

502

572

171

419

2.45

4.05E-07

aacggagga

STnc100_1

902843

159

+

1046

1049

372

802

2.16

1.11E-06

 

CyaR_RyeE

2912765

86

+

16620

16668

10932

23563

2.16

1.11E-06

 

sroE

3426663

92

-

64

63

39

83

2.13

1.22E-06

 

Z6077/DicF_4

2325956

52

+

118

112

128

262

2.05

1.64E-06

 

C0299

1763522

79

+

1

1

1

2

2.00

1.96E-06

 

RtT_2

1824000

132

-

3

2

1

2

2.00

1.96E-06

gaccaaggt

QUAD_7

4002118

150

-

859

791

324

641

1.98

2.12E-06

 

tpke11

14107

78

+

59

51

43

79

1.84

3.64E-06

 

STnc100_5

1866224

209

+

5038

4068

1364

2366

1.73

5.48E-06

 

MicA

3606250

72

+

1500

1180

1178

1992

1.69

6.54E-06

 

STnc100_3

1353605

206

+

2403

1688

660

996

1.51

1.41E-05

 

sroD

2565135

86

-

94

65

62

92

1.48

1.58E-05

 

MicC

2113860

122

-

43

29

20

29

1.45

1.83E-05

 

frnS

2168565

118

-

175

106

84

109

1.30

3.70E-05

tcagggcaa

OmrA-B_1

3765887

88

-

696

380

447

525

1.17

6.73E-05

 

ArcZ

4160147

108

+

3234

1708

1694

1923

1.14

8.20E-05

 

STnc130

1161203

135

-

2

1

1

1

1.00

1.66E-04

 

STnc560

1939628

214

+

132

58

35

33

0.94

2.27E-04

 

sraL

5161197

141

-

627

265

252

228

0.90

2.81E-04

 

RydB

2439675

61

-

280

102

260

203

0.78

5.76E-04

 

RtT_4

1824474

131

-

30

10

13

9

0.69

9.91E-04

 

sroC

767984

163

-

3945

1269

1369

946

0.69

9.99E-04

 

CRISPR-DR4_2

1058550

28

+

3

1

6

4

0.67

1.16E-03

 

STnc100_2

1267542

167

+

3718

1129

1259

822

0.65

1.27E-03

 

sok_15/sokX

3674872

152

-

93

28

35

22

0.63

1.49E-03

tcaggtata

STnc100_4

1641323

191

+

4486

1215

1329

773

0.58

2.02E-03

positive

GcvB

3732394

206

+

13532

3307

3716

1952

0.53

2.96E-03

negative/tgagccgga

Spot_42/spf

4914606

119

+

323

77

154

79

0.51

3.22E-03

gtagggtac

STnc450

5326800

58

-

20

5

20

10

0.50

3.52E-03

 

CRISPR-DR4_1

1058490

28

+

4

1

8

4

0.50

3.52E-03

 

STAXI_4

1482887

131

+

4

1

2

1

0.50

3.52E-03

 

RybB

1014999

79

-

1953

439

1398

676

0.48

3.95E-03

gcagggcat

sroB

572997

84

+

704

151

474

219

0.46

4.59E-03

 

P26

5058572

62

+

261

52

238

102

0.43

5.83E-03

 

sok_14

2777459

175

-

1539

298

497

207

0.42

6.35E-03

tgaggccca

sroH

5068058

161

-

606

114

213

86

0.40

6.97E-03

 

DicF_2

1881271

52

-

5

1

5

2

0.40

7.16E-03

 

rdlD_3

1807675

60

+

58

10

55

20

0.36

9.36E-03

 

OrzO-P_1

2953705

74

+

7227

1195

5524

1963

0.36

9.96E-03

 

sok_10

1888482

175

+

3663

598

1184

415

0.35

1.03E-02

tgaggctca

ryfA

3444344

305

+

16

3

3

1

0.33

1.18E-02

 

IS061

2172064

180

-

10

1

3

1

0.33

1.18E-02

 

rdlD_4

4509509

66

+

78

11

67

20

0.30

1.49E-02

 

rdlD_2

1807146

60

+

59

8

56

16

0.30

0.02

 

sok_7

1480784

158

+

2602

366

932

282

0.29

0.02

 

RyeB

2600241

100

-

2380

314

1346

382

0.28

0.02

 

QUAD_1

2898598

149

+

358

47

136

38

0.28

0.02

 

MicF

3117339

94

+

1059

132

637

171

0.27

0.02

 

STnc100_6

1893978

190

+

6373

703

1897

450

0.24

0.03

 

OxyS

5033797

110

-

106

11

55

12

0.22

0.03

 

arrS

4467416

69

-

266

22

201

36

0.18

0.04

 

istR

4712705

130

-

99

8

43

7

0.16

0.05

 

SraB

1590770

169

+

511

38

171

27

0.16

0.05

 

QUAD_6

4001742

150

-

771

54

291

44

0.15

0.06

 

DsrA

2725072

87

-

82

6

53

8

0.15

0.06

 

StyR-44_7

5087479

109

+

1784

125

926

139

0.15

0.06

 

QUAD_5

3861645

151

+

1621

113

607

91

0.15

0.06

 

StyR-44_5

4902290

109

+

1846

127

958

142

0.15

0.06

 

QUAD_4

3861252

151

+

2395

153

897

123

0.14

0.07

 

StyR-44_4

4806012

109

+

1761

112

914

125

0.14

0.07

 

StyR-44_1

228975

109

+

1908

111

990

124

0.13

0.08

 

STnc240

2830003

75

-

112

6

84

10

0.12

0.08

 

Bacteria_small_SRP /ffs

542524

97

+

230378

12741

134343

15969

0.12

0.08

positive

STnc100_9

2773346

167

-

3475

184

1177

134

0.11

0.09

 

GlmZ_SraJ_2

4848834

207

+

7351

364

2009

214

0.11

0.10

positive

SraC_RyeA

2600138

145

+

2011

91

784

76

0.10

0.12

 

GlmY_tke1_2

4848836

149

+

7310

323

2775

264

0.10

0.12

 

StyR-44_6

5046470

109

+

4004

161

2078

180

0.09

0.14

 

STnc100_8

2314989

167

-

706

23

239

17

0.07

0.19

 

RtT_1

867059

143

+

3357

102

1328

87

0.07

0.21

 

C4_2

2673794

88

+

108363

3042

69654

4203

0.06

0.23

 

sok_6

1389612

175

-

934

22

302

15

0.05

0.29

 

STnc100_7

2145571

190

-

327

7

97

4

0.04

0.35

 

CsrB

3714213

360

-

43044

748

6763

253

0.04

0.38

 

CsrC

4915753

254

+

25764

425

5738

203

0.04

0.40

 

RydC

2079463

64

+

1636

27

1446

51

0.04

0.40

 

RNaseP_bact_a /rnpB

4077043

377

-

39359

640

5905

206

0.03

0.40

 

GlmZ_SraJ_1

3481543

185

-

7668

122

2345

80

0.03

0.41

 

GlmY_tke1_1

3481544

148

-

7634

119

2918

98

0.03

0.42

 

6S/ssrS

3860420

184

+

470148

7239

144532

4783

0.03

0.42

 

QUAD_3

2899260

144

+

3436

44

1350

37

0.03

0.47

 

symR

5467620

77

+

726

6

533

9

0.02

0.60

 

sRNA-Xcc1

1392052

89

-

40293

290

25609

396

0.02

0.62

 

rdlD_1

1806611

66

+

2090

8

1791

15

0.01

0.76

 

StyR-44_3

4229125

109

-

2523

2

1309

2

0.00

0.96

 

StyR-44_2

3519339

109

-

2499

1

1297

1

0.00

0.97

 

HPnc0260

2421623

163

-

1

0

0

0

N/A

N/A

 

rseX

2733408

90

+

4

0

3

0

N/A

N/A

 

sok_12

2152486

125

-

13

0

6

0

N/A

N/A

 

SraG

4120940

172

+

1

0

0

0

N/A

N/A

 

STAXI_1

1087216

64

+

6

0

5

0

N/A

N/A

 

STAXI_2

1087280

131

+

2

0

1

0

N/A

N/A

 

STAXI_3

1482823

64

+

3

0

3

0

N/A

N/A

 

STnc100_11

3553828

189

-

387

0

116

0

N/A

N/A

 

STnc410

4777710

158

+

3

0

1

0

N/A

N/A

 

tp2

127504

114

-

1

0

0

0

N/A

N/A

 

sraA

524870

96

-

0

0

0

0

N/A

N/A

 

STnc480

635390

67

+

0

0

0

0

N/A

N/A

 

sar

1661162

67

-

0

0

0

0

N/A

N/A

 

group-II-D1D4-2

2037712

118

-

0

0

0

0

N/A

N/A

 

DicF_3

2159230

56

+

0

0

0

0

N/A

N/A

 

C0465

2649880

76

+

0

0

0

0

N/A

N/A

 

STnc430

5118969

150

-

0

0

0

0

N/A

N/A

 
  1. *; The P values give the probability that the RCV of the given RNA is similar to / results from the RCV distribution of the tRNAs. Thus, RNAs with high P values are probably not translated and vice versa
  2. Annotated ncRNAs which are not independent of translation (e.g. leader peptides or ribosomal RNAs, etc.) are not shown (see text). The genome position (start) of each ncRNA is indicated, the ncRNAs are sorted according to their RCV. Transcripts examined via Northern blots are indicated and putative Shine-Dalgarno sequences are shown. An overview of all data for the 115 known ncRNAs is found in Additional file 8: Table S6