Table 4.
Compilation of npcRNA candidates overlapping with ORFs in sense orientation
| npcRNAs | cDNA (nt) | Orient. | Overlap (nt) | Gene ID | Presence in E. coli | N. blot S. typhi / E. coli | Growth reg., S. typhi / E. coli | Specificity | Comments | Acc. No. | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Partially overlapping with 5′-end of ORF | ||||||||||||
| StyR-9 | 145 | > | 11 | 1071490 | No | +/− | +/− | S. typhi,S. para C | FJ746436 | |||
| StyR-15 | 306 | > | 129 | 1070087 | Yes | nd | nd | Sal. sp. | FJ746437 | |||
| StyR-29 | 245 | < | 116 | 1067535 | Yes | +/+ | +/− | FJ746440 | ||||
| StyR-64 | 108 | < | 30 | 1071363 | Yes | nd | nd | FJ746443 | ||||
| StyR-77 | 114 | > | 49 | 1069758 | Yes | nd | nd | FJ746446 | ||||
| StyR-84 | 77 | < | 8 | 1067059 | Yes | nd | nd | FJ746447 | ||||
| StyR-145 | 327 | > | 108 | 1069487 | No | nd | nd | S. typhi,S. para C | FJ746448 | |||
| StyR-228 | 111 | > | 2 | 1070302 | No | −/− | −/− | Sal. sp. | FJ746452 | |||
| StyR-255 | 243 | > | 100 | 1067871 | Yes | −/− | −/− | FJ746453 | ||||
| StyR-282 | 86 | > | 72 | 1068122 | Yes | nd | nd | FJ746457 | ||||
| StyR-296 | 293 | > | 71 | 1069730 | Yes | +/+ | +/+ | FJ746454 | ||||
| StyR-335 | 263 | < | 97 | 1069119 | Yes | −/− | −/− | FJ746455 | ||||
| StyR-364 | 176 | > | 77 | 1067975 | Yes | nd | nd | FJ746456 | ||||
| Partially overlapping with 3′-end of ORF | ||||||||||||
| StyR-6 | 159 | > | 112 | 1068275 | Yes | nd | nd | FJ746435 | ||||
| StyR-26 | 223 | < | 150 | 1067805 | Yes | nd | nd | FJ746438 | ||||
| StyR-27 | 146 | > | 29 | 1071267 | No | +/− | +/− | FJ746439 | ||||
| StyR-51 | 87 | > | 4 | 1067741 | Yes | +/+ | +/+ | FJ746441 | ||||
| StyR-68 | 95 | > | 43 | 1068476 | Yes | nd | nd | FJ746444 | ||||
| StyR-74 | 87 | < | 12 | 1069270 | Yes | nd | nd | ρ-ind. term. | FJ746442 | |||
| StyR-76 | 241 | > | 112 | 1069147 | Yes | nd | nd | FJ746445 | ||||
| StyR-149 | 83 | > | 19 | 1070930 | No | nd | nd | Sal. sp. | FJ746449 | |||
| StyR-165 | 105 | > | 40 | 1069332 | Yes | nd | nd | FJ746450 | ||||
| StyR-192 | 71 | > | 33 | 1071394 | Yes | nd | nd | ρ-ind. term. | FJ746451 | |||
npcRNAs, reference identifications of S. typhi npcRNA candidates; cDNA (nt), length of cDNA clones in nt; Orient., orientation of npcRNA; Overlap, number of nucleotides overlapping the ORF; Gene ID, ID of protein-coding genes; Presence in E. coli, npcRNA is present in the E. coli K12 genome; N. blot S. typhi/E. coli, northern blot was positive (+) or negative (−) for the given transcript; nd, not done; Growth reg. S. typhi /E. coli, npcRNA was (+) or was not (−) growth phase-regulated; Specificity, species specificity; Sal sp, Salmonella species specific; S. typhi, S. typhi specific; Comments, ρ-ind. term., probable ρ-independent terminator detected; Acc. No., accession number of npcRNA sequence in DDBJ/EMBL/GenBank databases.