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Table 2 Novel non-coding RNA (ncRNA) candidates (150 in total) based on transcriptome sequencing and ribosomal profiling. ncRNAs are identified by their start position on the genome given in the name (abbreviated as ncR#)

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

Length

Max. ORF (nt)

Strand

Number of transcriptome reads

Number of footprint reads

RPKM transcriptome

RPKM footprints

RCV

Northern Blot

CopraRNA

CopraRNA term

ncR1085800

72

-

+

11274

532

8857

898

0.1

positive

  

ncR1481381

99

9

+

11208

516

6404

634

0.1

positive

  

ncR3690952

145

54

-

4898

26

1911

22

0.01

negative

1.18

ecc00620:Pyruvate metabolism

ncR1636218

78

27

-

1034

22

750

34

0.05

negative

1.31a

GO:0042364~water-soluble vitamin biosynthetic process

ncR3545929

41

-

+

542

2

748

6

0.01

   

ncR3665651

109

45

-

1442

2

748

2

0

negative

1.24

GO:0045426~quinone cofactor biosynthetic process

ncR3860554

73

24

-

637

3

494

5

0.01

 

0.98

2Fe-2S

ncR1088953

37

-

+

295

4

451

13

0.03

   

ncR3066135

48

-

+

354

0

417

0

0

   

ncR1484560

42

-

+

294

0

396

0

0

   

ncR5355946

47

21

-

246

4

296

10

0.04

   

ncR16920

36

-

-

164

4

258

14

0.05

   

ncR165975

49

9

+

216

4

249

10

0.04

negative

  

ncR5223290

66

-

+

265

3

227

6

0.02

   

ncR1641710

114

105

-

430

28

213

30

0.14

   

ncR1765944

114

54

+

406

33

201

35

0.18

 

5.48a

membrane

ncR2358348

45

-

-

151

1

190

3

0.01

   

ncR1888606

46

18

-

147

4

181

11

0.06

   

ncR2530362

64

6

-

196

0

173

0

0

   

ncR5133665

29

-

-

86

0

168

0

0

   

ncR2638864

38

-

-

100

2

149

6

0.04

   

ncR326492

42

-

+

110

9

148

26

0.18

   

ncR622277

95

63

+

248

1

148

1

0.01

negative

  

ncR2549762

59

45

-

150

2

144

4

0.03

   

ncR2287

90

45

-

218

8

137

11

0.08

   

ncR1019437

57

-

-

130

2

129

4

0.03

   

ncR1694864

51

18

+

116

1

129

2

0.02

   

ncR1864748

174

105

-

370

32

120

22

0.19

 

4.00a

cell membrane

ncR3526958

96

45

-

193

9

114

11

0.1

 

2.92a

ecd00190:Oxidative phosphorylation

ncR867065

45

21

-

76

1

96

3

0.03

   

ncR1079732

27

-

-

41

2

86

9

0.11

   

ncR3020266

116

57

+

168

9

82

9

0.12

   

ncR1328373

40

21

-

55

1

78

3

0.04

   

ncR3094200

36

9

+

47

3

74

10

0.14

   

ncR774709

58

39

+

74

1

72

2

0.03

   

ncR3725111

44

-

-

52

1

67

3

0.04

   

ncR451977

43

21

-

50

3

66

8

0.13

   

ncR4881271

105

75

+

123

7

66

8

0.12

 

1.70a

GO:0022900~electron transport chain

ncR4922734

44

27

+

49

2

63

6

0.09

   

ncR1748457

38

9

-

40

0

60

0

0

   

ncR4393950

74

-

-

78

5

60

8

0.14

   

ncR5324582

92

24

+

94

4

58

5

0.09

   

ncR1847082

38

-

+

38

1

57

3

0.06

   

ncR2820623

107

66

-

105

9

56

10

0.18

 

1.89a

lipoprotein

ncR1114186

94

60

-

91

3

55

4

0.07

   

ncR3583650

35

-

-

34

1

55

3

0.06

   

ncR1509794

96

60

-

91

5

54

6

0.12

   

ncR4391372

28

-

-

26

2

53

9

0.17

   

ncR4546182

36

12

-

34

2

53

7

0.13

   

ncR612919

36

-

+

32

0

50

0

0

   

ncR426804

47

-

+

41

3

49

8

0.16

   

ncR3164662

66

9

+

56

3

48

6

0.12

   

ncR2585184

44

-

+

36

1

46

3

0.06

   

ncR2930972

38

6

-

30

2

45

6

0.14

   

ncR3527530

119

51

-

95

4

45

4

0.09

 

1.97a

GO:0046395~carboxylic acid catabolic process

ncR4520884

50

24

+

40

3

45

7

0.16

   

ncR2498369

53

33

-

41

1

44

2

0.05

   

ncR4161484

42

39

+

33

1

44

3

0.07

   

ncR2699447

35

18

+

26

1

42

3

0.08

   

ncR5210782

28

18

+

21

0

42

0

0

   

ncR205409

74

45

-

53

0

41

0

0

 

1.02

IPR014021:Helicase, superfamily 1 and 2, ATP-binding

ncR1868696

103

30

-

72

6

40

7

0.18

   

ncR3915561

37

-

-

26

2

40

7

0.17

   

ncR1462015

40

21

-

27

0

38

0

0

   

ncR1475353

73

-

-

48

4

37

7

0.18

   

ncR397399

68

-

-

44

0

37

0

0

   

ncR4645569

57

15

-

36

0

36

0

0

   

ncR1239030

54

-

+

33

1

35

2

0.07

   

ncR1645154

42

-

-

26

1

35

3

0.08

   

ncR3553461

57

33

+

35

1

35

2

0.06

   

ncR4853400

65

15

+

40

3

35

6

0.16

   

ncR1143400

43

18

+

25

2

33

6

0.17

   

ncR2693045

49

6

-

29

2

33

5

0.15

   

ncR3735643

69

45

+

40

2

33

4

0.11

   

ncR3991822

44

9

-

26

0

33

0

0

   

ncR4714439

67

6

-

39

2

33

4

0.11

   

ncR1960332

35

-

+

20

1

32

3

0.11

 

1.96a

GO:0034660~ncRNA metabolic process

ncR2885483

44

-

-

25

1

32

3

0.09

   

ncR4463425

63

12

-

36

1

32

2

0.06

   

ncR501481

70

21

+

39

0

32

0

0

   

ncR963596

50

9

-

28

1

32

2

0.08

   

ncR1152534

90

51

+

50

4

31

5

0.17

 

0.84

ecq00052:Galactose metabolism

ncR2602372

62

12

-

34

2

31

4

0.13

   

ncR2062548

38

-

+

20

0

30

0

0

   

ncR4770438

40

12

+

21

1

30

3

0.1

   

ncR865067

103

51

-

54

1

30

1

0.04

   

ncR11537

73

48

+

37

2

29

3

0.12

   

ncR3040352

77

18

-

40

3

29

5

0.16

   

ncR4249267

64

9

+

33

2

29

4

0.13

   

ncR1592436

48

9

-

24

1

28

3

0.09

   

ncR3583545

40

-

-

20

1

28

3

0.11

   

ncR725615

61

-

+

30

2

28

4

0.14

   

ncR1066434

66

21

-

32

1

27

2

0.07

   

ncR4163613

125

45

+

59

5

27

5

0.18

 

1.29

antibiotic resistance

ncR15950

44

18

+

20

0

26

0

0

   

ncR2452385

45

18

-

21

0

26

0

0

   

ncR2841773

79

18

+

37

0

26

0

0

   

ncR3320428

75

51

+

34

1

26

2

0.06

   

ncR2903620

140

33

-

61

3

25

3

0.11

   

ncR3042903

164

57

-

69

3

24

2

0.09

   

ncR543583

67

51

+

29

0

24

0

0

   

ncR1585703

88

48

+

36

2

23

3

0.12

   

ncR1999946

51

15

+

21

0

23

0

0

   

ncR5077759

50

6

-

20

1

23

2

0.11

   

ncR1640190

56

-

-

22

2

22

4

0.2

   

ncR1752346

64

-

+

25

0

22

0

0

   

ncR3074598

54

36

-

21

0

22

0

0

   

ncR3320341

85

18

+

33

0

22

0

0

   

ncR3330508

57

-

-

22

0

22

0

0

   

ncR4096595

60

-

-

23

2

22

4

0.19

   

ncR4137844

268

195

-

102

7

22

3

0.15

   

ncR4414172

53

-

-

21

0

22

0

0

   

ncR492696

51

-

-

20

0

22

0

0

   

ncR1215540

74

21

+

28

2

21

3

0.15

   

ncR2254917

76

-

+

28

2

21

3

0.15

   

ncR2902855

104

-

-

39

3

21

4

0.17

   

ncR752395

172

66

+

64

2

21

1

0.07

   

ncR283226

71

27

+

25

0

20

0

0

   

ncR1049002

77

48

-

26

1

19

2

0.08

 

1.84a

GO:0050890~cognition

ncR1216838

100

12

-

33

1

19

1

0.07

   

ncR4829752

78

-

-

26

1

19

2

0.08

   

ncR1483108

77

63

+

23

1

17

2

0.09

   

ncR155024

78

18

+

23

0

17

0

0

   

ncR4156147

78

-

-

23

1

17

2

0.09

 

1.75a

GO:0032196~transposition

ncR4788281

97

78

-

30

0

17

0

0

 

0.99

topological domain:Periplasmic

ncR1854285

91

48

-

25

1

16

1

0.09

   

ncR1942672

85

-

+

24

1

16

1

0.09

 

2.09a

GO:0015031~protein transport

ncR2614043

86

57

-

25

0

16

0

0

   

ncR4741832

75

30

-

21

0

16

0

0

   

ncR484751

94

51

-

27

2

16

3

0.16

   

ncR5283975

98

84

-

28

0

16

0

0

 

2.14a

GO:0009386~translational attenuation

ncR1314229

101

48

+

26

2

15

2

0.17

   

ncR1893573

187

87

-

48

4

15

3

0.18

   

ncR3609575

74

-

+

20

0

15

0

0

 

1.72a

eum00660:C5-Branched dibasic acid metabolism

ncR3724967

105

42

-

28

0

15

0

0

   

ncR4245110

118

48

+

30

1

14

1

0.07

   

ncR866957

79

42

-

20

0

14

0

0

   

ncR336953

96

27

+

22

2

13

3

0.2

   

ncR3997954

104

81

+

23

2

13

2

0.19

   

ncR411208

99

6

-

22

2

13

2

0.2

 

2.64a

GO:0015980~energy derivation by oxidation of organic compounds

ncR1736783

100

57

-

22

1

12

1

0.1

   

ncR745748

107

54

+

23

1

12

1

0.09

   

ncR3609372

201

-

+

38

1

11

1

0.06

  

Rfam match: tRNA RF00005b

ncR3890479

104

51

-

20

1

11

1

0.11

   

ncR1087411

224

135

+

41

2

10

1

0.11

   

ncR3874837

127

48

-

22

2

10

2

0.2

   

ncR4187491

122

9

-

22

0

10

0

0

   

ncR769665

198

102

+

34

2

10

1

0.13

   

ncR5157894

218

114

+

33

3

9

2

0.2

   

ncR196880

135

81

-

20

1

8

1

0.11

 

1.23

ecc00330:Arginine and proline metabolism

  1. aDAVID enrich. score; signif. ≥ 1.3. btRNA
  2. The longest potential ORF is indicated for each ncRNA. RPKM values of transcriptome and translatome are shown, as well as the ribosome coverage value (RCV). A transcript is considered non-coding if it has at least 20 reads in the transcriptome data and the RCV is below 0.197 (α = 0.01). Transcripts examined via Northern blots are indicated and CopraRNA functional enrichments are shown