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 |
||||||||||||
