Table 6

Top 12 predicted RNAs, ranked by their RPKM score

Conserved region in Mtb H37Rv1

Region in M. Smegmatis3


id

start

Orient-ation5

length

# reads

RPKM

Evo-fold?2

Genes flanking the intergenic region

Start

Stop

# reads

RPKM


RNA14

1612987

--+

58

1013

69526

Y

Rv1435c (secreted protein)

Rv1436 (GAPDH)

756567

756626

100

626


RNA24

1374224

---

46

567

30071

Y

Rv1230c (membrane prot.)

Rv1231c (membrane prot.)

-

-

-


RNA34

1393055

---

85

111

9251

Y

Rv1248c (sucA)

Rv1249c (membrane prot.)

5147110

5147242

173

489


RNA4

483829

-++

49

55

2139

Y

Rv0403c (membrane prot. mmpS1)

Rv0404 (fadD30)

-

-

-


RNA5

1200514

-++

93

81

2055

Y

Rv1075c (exported protein)

Rv1076 (lipase lipU)

5363400

5363474

10

50


RNA6

987053

-++

92

174

6767

Y

Rv0887c (cons. Hypo. prot)

Rv0888 (hyp. Exported prot.)

-

-

-


RNA7

1810184

+++

44

517

9280

Y

Rv1610 (cons. membrane protein)

Rv1611 (trpC)

3296996

3297034

291

2804


RNA8

3587635

-++

56

83

6917

N

Rv3210c (cons. hypo. prot.)

Rv3211 (rhlE)

2009575

2009665

6

25


RNA94

4224925

--+

41

502

24405

N

Rv3778c (aminotransf.)

Rv3779 (membrane prot.)

6420618

6420674

36

237


RNA10

659351

+++

39

58

1829

Y

Rv0567 (methyltransferase)

Rv0568 (cyp135B1)

-

-

-


RNA11

1794708

-++

48

375

18231

Y

Rv1593c (cons. hypo. prot)

Rv1594 (nadA)

3277552

3277599

70

548


RNA12

2447526

---

74

332

9684

Y

Rv2185c (cons. hypo. prot)

Rv2186c (cons. hypo. prot)

4335086

4335137

111

802


1Conserved intergenic regions determined by Gumby.

2Indicates whether this region is predicted to fold by Evofold.

3Region in M. smegmatis that aligns with the conserved region in Mtb, and its corresponding RPKM value.

4Tested experimentally

5Orientation relative to neighboring genes. The first and last characters give the strands of the flanking genes; the middle character gives the strand for the predicted RNA.

McGuire et al. BMC Genomics 2012 13:120   doi:10.1186/1471-2164-13-120

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