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Table 4 sRNA candidates identified in previous studies

From: A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti

ID

Type

Position

St.

Size

Rfam

St.

Ov.

ID[36]

St.

Ov.

ID[37]

St.

ID[38]

St.

Ov.

North.

SmelC011

3

46011-46166

-

156

      

sra02

n

    

SmelC023

1

201679-201825

+

147

   

C7

+

100

sra03

+

SmrC7

+

98

[3739]

SmelC035

2

259927-260032

+

106

RF00169

+

97

   

sra05

+

    

SmelC037

3

267059-267152

+

94

        

Sm76

+

59

[39]

SmelC051

3

318407-318497

+

91

      

sra09

n

    

SmelC057

4

364136-364231

-

96

        

Sm134

+

32

 

SmelC073

1

424110-424268

+

159

        

Sm131

+

72

 

SmelC089

3

523807-524015

+

209

        

Sm39

+

33

 

SmelC100

3

580087-580184

-

98

RF00521

-

76

   

sra13

n

    

SmelC116

2

658552-658723

-

172

        

Sm105

-

49

 

SmelC119

1

701950-702109

+

160

      

sra16

-

    

SmelC132

3

757653-757739

+

87

        

Sm139

+

100

 

SmelC213

2

1048676-1048864

+

189

      

sra25

+

   

[38, 39]

SmelC222

3

1071388-1071540

-

153

        

Sm145

-

67

[39]

SmelC226

1

1091100-1091291

+

192

        

Sm10

+

100

 

SmelC246

3

1238618-1238804

-

187

      

sra29

-

   

[38]

SmelC289

1

1398278-1398426

-

149

   

C9

-

81

sra32

-

SmrC9

-

99

[3739]

SmelC291

1

1411678-1411848

+

171

   

C10

+

77

sra33

+

   

[38]

SmelC302

3

1458322-1458424

+

103

      

sra34

-

   

[38]

SmelC306

4

1461414-1461561

+

148

      

sra35

+

    

SmelC311

3

1464122-1464318

+

197

      

sra36

+

    

SmelC337

1

1518791-1518985

+

195

        

Sm30

+

100

 

SmelC365

4

1599106-1599255

+

150

        

Sm55

-

24

 

SmelC378

4

1635062-1635243

+

182

        

Sm9

-

15

 

SmelC381

1

1637121-1637244

+

124

      

sra37

-

Sm50

-

48

 

SmelC397

1

1667491-1667614

-

124

   

C14

-

100

  

SmrC14

-

100

[37]

SmelC398

1

1667766-1667982

-

217

      

sra38

n

Sm7

-

99

 

SmelC411

1

1698618-1698731

-

114

RF00519

-

62

C15

-

100

  

SmrC15

-

100

[37]

SmelC412

1

1698818-1698948

-

131

RF00519

-

57

C16

-

100

sra41

n

SmrC16

-

98

[37, 38]

SmelC414

3

1706675-1706765

-

91

        

Sm23

-

56

 

SmelC416

1

1718814-1718919

-

106

        

Sm138

-

85

 

SmelC419

5

1728029-1728277

-

249

        

Sm6

-

97

 

SmelC434

1

1821211-1821366

+

156

        

Sm118

+

100

 

SmelC435

1

1823103-1823231

+

129

        

Sm48

+

100

 

SmelC445

3

1879868-1879947

-

80

      

sra44

n

    

SmelC475

1

2059726-2059795

-

70

        

Sm29

-

100

 

SmelC483

1

2098461-2098583

-

123

   

C17

+

100

      

SmelC488

1

2129185-2129292

-

108

        

Sm135

-

99

 

SmelC525

1

2291226-2291466

+

241

      

sra49

+

    

SmelC531

2

2321050-2321287

-

238

        

Sm26

-

98

[39]

SmelC549

1

2371597-2371855

+

259

        

Sm4

+

99

 

SmelC559

4

2398177-2398336

+

160

RF00050

+

100

C20

+

91

      

SmelC561

4

2436481-2436577

+

97

        

Sm52

-

100

 

SmelC576

4

2524155-2524249

+

95

        

Sm136

-

27

 

SmelC587

3

2575832-2575947

-

116

        

Sm104

-

67

 

SmelC617

1

2695496-2695642

-

147

        

Sm49

-

100

 

SmelC642

3

2921789-2922084

+

296

      

sra54

n

    

SmelC646

3

2924467-2924555

-

89

      

sra55

n

    

SmelC653

3

2937985-2938127

-

143

RF00517

-

34

         

SmelC667

2

2972090-2972252

-

163

RF00013

-

98

C22

-

83

sra56

-

   

[3739]

SmelC671

1

2986421-2986520

+

100

        

Sm84

+

100

[39]

SmelC689

1

3046710-3046789

+

80

RF00519

+

81

     

Sm8

+

96

[39]

SmelC691

1

3048822-3048904

+

83

      

sra57

n

    

SmelC706

1

3105298-3105445

-

148

RF00518

-

100

C45

-

52

     

[37]

SmelC752

3

3439569-3439771

+

203

      

sra67

+

    

SmelC762

3

3461772-3461886

+

115

RF00521

+

63

         

SmelC764

4

3472924-3473053

+

130

RF00519

+

44

         

SmelC778

1

3522269-3522383

+

115

        

Sm5

+

97

 

SmelC779

3

3532867-3532968

+

102

RF00059

+

100

         

SmelC804*

1

1599291-1599363

 

73

        

Sm55

-

73

 

SmelC805*

1

1677330-1677472

 

143

      

sra40

n

    

SmelC809*

1

2356793-2357134

 

342

RF00010

-

100

C19

-

100

sra50

+

    

SmelA033

1

512140-512221

-

82

   

A2

+

100

  

smA3a

-

83

 

SmelA035

1

552854-552983

+

130

RF00519

+

55

     

smA4b

+

98

 

SmelA075

1

1220693-1220808

+

116

        

smA8

+

99

 

SmelA099

1

1328175-1328334

-

160

   

A6

+

100

      

SmelA102

3

1351156-1351309

-

154

RF00490

-

43

         

SmelA103

2

1351298-1351357

+

60

RF00489

+

73

         

SmelB001

1

24911-24992

-

82

   

B29

+

100

      

SmelB006

2

56486-56620

+

135

RF00489

+

35

B30

+

52

      

SmelB011

1

66261-66326

+

66

RF00174

+

100

B31

+

21

      

SmelB019

1

213497-213616

+

120

        

smB1

+

93

 

SmelB027

2

334403-334483

-

81

   

B34

+

100

      

SmelB032

1

379136-379275

+

140

        

smB2

+

91

 

SmelB044

1

541771-541909

-

139

        

smB3b

-

100

 

SmelB050

1

574628-574763

+

136

        

smB5a

+

100

 

SmelB053

1

577730-577873

+

144

   

B35

+

99

  

smrB35

+

97

[37]

SmelB085

3

871959-872147

-

189

RF00435

-

50

         

SmelB110

2

1192051-1192144

-

94

RF00059

-

100

         

SmelB126

1

1325476-1325586

+

111

        

smB9

+

100

 

SmelB169

1

1633737-1633873

+

137

RF00059

+

80

         
  1. Overlap, percent overlap of the candidates from the cited studies or database compared to the region covered by a sRNA candidate in this study. n, strand was not or not undoubtedly determined.
  2. ID; RNA ID (this study); Type, RNA type; St., strand; Ov., overlap (%); ID [], RNA ID corresponding to the given reference; North., experimentally validated by Northern blot, given are the references for the Northern hybridizations. RNA ID: *, Solexa candidate. RNA type: 1, trans-encoded sRNA; 2, cis-encoded antisense sRNA; 3, mRNA leader; 4, sense sRNA; 5, Open reading frame. The presumed location of the sRNAs predicted by Ulvé et al. [37], derived from the location of the Dot Blot probes. Thus an overlap analysis to our candidates could not be performed.