Table 1

Streptomyces sRNAs predicted using Rho-independent terminators

ID#

Exp.†

Length

Strand*

Genomic coordinates

E-value

5' flanking gene distance

5' flanking gene termination&

RNAz probability @


4

++

78

← ⇒ ←

3082276..3082354

7 × 10-25

267

1

17

-0

161

← ⇒ ←

6702716..6702877

4 × 10-53

131

1

36

-0

72

← ⇒ →

7719646..7719718

2 × 10-30

274

0.98

73

++

53

→ ⇒ ←

6800040..6800093

2 × 10-22

122

0.91

84

-0

32

← ⇒ →

4153086..4153118

2 × 10-27

111

0.59

95

+-

312

← ⇒ →

6412268..6412579

3 × 10-127

10

0.7

96

-0

92

→ ⇐ →

6393104..6393196

3 × 10-77

0

-

114, 5S RNA

+0

132

← ⇐ ←

1916439..1916571

9 × 10-47

0

1

115

+-

246

→ ⇒ →

4530291..4530536

3 × 10-118

275

C-rich, 4530261..4530290

0.99

116

-0

122

→ ⇐ →

6266683..6266805

5 × 10-77

0

1

126

-0

118

→ ⇒ →

6144157..6144275

7 × 10-60

32

C-rich, 6143954..6144005

1

146

+-

80

→ ⇐ →

6005563..6005643

6 × 10-31

0

-

155

++

149

← ⇒ →

5922111..5922259

4 × 10-57

11

0.96

156

+-

93

→ ⇐ →

5912196..5912289

2 × 10-32

0

0.94

200

+-

150

→ ⇐ →

5647597..5647746

4 × 10-127

1

1

222

++

84

← ⇐ ←

5400596..5400680

4 × 10-47

25

?

0.9

234

-0

94

← ⇐ →

6033508..6033602

4 × 10-67

164

-

261, tRNA ala

+0

85

← ⇐ ←

3481828..3481913

6 × 10-26

0

C-rich, 3482039..3482068

0.99

270

++

118

← ⇒ ←

3506180..3506297

1 × 10-16

1

0.58

274

+-

189

← ⇒ ←

5040566..5040754

1 × 10-50

60

1

329, 4.5S

++

155

← ⇒ →

4456953..4457107

2 × 10-42

0

0.84

341

++

96

→ ⇐ ←

4375750..4375846

4 × 10-40

0

C-rich, 4375909..4375880

1

390

++

203

← ⇐ →

3933499..3933702

8 × 10-74

0

1

389

++

184

→ ⇐ →

3934660..3934844

3 × 10-65

0

1

413.1

++

338

← ⇒ →

3690627..3690965

3 × 10-120

412

1

413.2

-0

302

← ⇒ →

3690627..3691287

3 × 10-120

90

1

445

-0

192

→ ⇒ →

5076164..5076355

7 × 10-67

29

Rho-ind., 5076138..5076163

0.97

458

-0

210

← ⇐ →

5179518..5179728

6 × 10-107

0

0.67

462

-0

367

← ⇐ →

3321271..3321638

7 × 10-156

63

0.99

470, tmRNA

++

512

→ ⇐ ←

3226537..3227049

2 × 10-130

1

C-rich, 3227036..3227062

1

472

++

219

→ ⇐ ←

3208599..3208817

6 × 10-51

69

Rho-ind., 3208818..3208856

1

482, tRNA lys

+0

72

→ ⇐ ←

3079118..3079190

3 × 10-50

0

Rho-ind., 3079251..3079289

1

493

-0

48

← ⇒ ←

2984116..2984164

4 × 10-65

46

0.97

528

+-

170

← ⇒ ←

2646934..2647104

3 × 10-27

1

0.62

624

+-

159

← ⇒ ←

1765024..1765183

3 × 10-21

2

0.95

640, tRNA gly

+0

83

← ⇐ →

4469872..4469955

2 × 10-27

0

1

676

+-

308

← ⇒ →

1457688..1457996

1 × 10-98

23

1


† The first symbol stands for detection of expression by microarrays (expressed: '+', not expressed: '-'), the second one for RT-PCR confirmation of the expression (expressed: '+', not expressed: '-'). '0' stands for not applied.

* The double arrows represent sRNA gene, the arrows flanking genes. Right sided arrows show the complementary strand.

& Applicable only if the predicted sRNA and the gene flanking its 5' end are on the same strand. 'C-rich' and 'Rho-ind.' terms indicate the type of the transcription termination of the genes flanking 5' end of the predicted sRNAs. Genomic coordinates of the termination factors follow. The question mark for ID# 222 indicates a questionable C-rich stretch.

@ RNAz RNA-class probability. The higher this value, the more confident is the prediction of the functional RNA.

Pánek et al. BMC Genomics 2008 9:217   doi:10.1186/1471-2164-9-217

Open Data