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Table 3 Selection of highly potential novel ncRNA candidates of A. aeolicus

From: Genomewide comparison and novel ncRNAs of Aquificales

ID

Location

GC

cDNA

Annotation

Structure and Sequence

 

Remarks

 

5’ boundary

3’ boundary

Strand

 

(+/-)

(NCBI/BacProt)

RNALfold

Cons_p

Cons_t

RNAz_p

RNAz_t

 

Known ncRNAs

45

567675

567915

-

0.53

2237/899

murF/UDP

-3.89

11

7

No

0.9990

Downstream of 5S RNA

74

1153499

1153856

-

0.65

83/31

tmRNA/no

-5.04

6

11

No

0.9996

tmRNA

78

1219679

1219903

+

0.55

382/1384

pheT/pheT

-6.59

11

11

No

No

6S RNA

85

1303758

1303875

+

0.57

5239/456

No/no

-4.15

11

11

No

0.7085

SRP RNA

Putative Novel ncRNAs

2

15301

15474

+

–

0/0

No/no

-3.66

No

5

No

No

Plasmid region

6

69101

69198

-

0.37

809/545

No/no

-4.71

11

11

No

No

 

25

328934

328995

+

0.37

582/250

No/no

No

9

9

No

No

 

48

620054

620211

-

0.44

41/71

No/no

-3.13

11

9

No

No

 

58

739705

739811

+

0.44

41/144

No/no

-3.92

11

11

No

No

 

68

989704

989840

+

0.50

476/756

aq_1392/permease

-4.53

4

2

No

No

Aae-65 [85]

74

1153547

1153769

+

0.65

326/51

No/no

-5.04

6

11

No

0.9996

 

75

1168974

1169071

-

0.55

158/79

aq_1666/no

-3.84

3

3

No

No

 

80

1231909

1232006

+

0.38

860/2339

No/no

-3.74

11

2

No

No

 

97

1491199

1491559

-

0.40

10/297

rfaG/glycosyltransferase

-4.60

11

11

No

No

 

Tail to tail Transcripts (T2T)

t2t10

608075

608182

+

0.52

60/20

aq_880/no

-3.70

11

11

No

No

 
 

608075

608308

-

0.48

22/12

aq_881/DOXP synthase

-3.70

11

11

No

No

 

t2t17

1336433

1336708

+

0.46

380/87

aq_1896/predicted

No

11

11

No

No

 
 

1336544

1336642

-

0.51

100/55

folD/folD

No

11

11

No

No

 

t2t20

1479248

1479345

+

0.44

180/117

prmA/prmA

No

11

8

No

No

 
 

1479168

1479508

-

0.43

12/62

acs’/predicted

-3.19

11

8

No

No

 

tRNAs with sense transcripts only

t06;43

383154

383390

-

0.52

9/2

recN; tRNA/predicted

-3.53

11

10

No

0.9943

 

tRNAs with sense and various antisense transcripts

t34;15

1356464

1356743

+

0.64

23/5

tRNA/no

-5.43

11

10

0.9996

0.9992

 
 

1356461

1356575

-

0.60

61/15

No/no

-5.43

11

9

0.9996

0.9992

 

t44;20

1531016

1531131

+

0.58

1141/437

ihfB/no

-4.33

7

9

No

0.9951

 
 

1531004

1531130

-

0.56

335/136

tRNA/no

-4.33

7

9

No

0.9951

 
  1. The genomic locations and GC-content are listed in columns 2-4. cDNA – the maximal number of observed read counts in the (+)- and (-)-library; Annotation – overlap to predicted proteins by NCBI and BacProt; RNALfold – energy in kcal/mol of locally stable RNA secondary structure predicted by RNALfold; Cons_p and Cons_t – number of species with homologous regions aligned by Pomago and TBA; RNAz – probabilities >0.5 (based on multiple sequence alignments calculated by Pomago (p) or TBA (t)). Further observations, for example that Aae-65 was described earlier in [85], are noted in the last column. A complete list of novel ncRNA candidates, and tRNAs can be found in the Supplemental Material.
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BMC Genomics

ISSN: 1471-2164

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