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Table 6 Top 12 predicted RNAs, ranked by their RPKM score

From: Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis

  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
  1. 1Conserved intergenic regions determined by Gumby.
  2. 2Indicates whether this region is predicted to fold by Evofold.
  3. 3Region in M. smegmatis that aligns with the conserved region in Mtb, and its corresponding RPKM value.
  4. 4Tested experimentally
  5. 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.