Table 1.
Compilation of npcRNA candidates from intergenic regions in S. typhi
| npcRNAs | cDNA (nt) | Orient. | Adj. genes (ID) | Presence in E. coli | N. Blot S. typhi /E. coli | Growth reg. S. typhi /E. coli | Specificity | Comments | Acc. No. |
|---|---|---|---|---|---|---|---|---|---|
| Promoter-associated npcRNAs | |||||||||
| StyR-3 | 144 | < < > | 1067322/1069368 | No | +/− | −/− | Sal. sp | FJ746361 | |
| StyR-8 | 94 | > > > | 1069235/1069233 | Yes | −/− | −/− | FJ746362 | ||
| StyR-10 | 147 | < < > | 1067006/1067023 | Yes | +/+ | +/− | FJ746363 | ||
| StyR-88 | 109 | > > > | 1067919/1067920 | Yes | +/− | +/− | FJ746366 | ||
| StyR-99 | 32 | < > > | 1067609/1068774 | No | −/− | −/− | Sal. sp | FJ746367 | |
| StyR-134 | 72 | > > > | 1069120/1069122 | No | −/− | −/− | Sal. sp | FJ746369 | |
| StyR-241 | 152 | < < > | 1068271/1068273 | Yes | +/+ | +/+ | ρ-ind. term. | FJ746373 | |
| StyR-262 | 156 | < > > | 1069506/1069507 | Yes | −/− | −/− | FJ746374 | ||
| StyR-287 | 50 | > > > | 1067282/1069315 | No | −/− | −/− | Sal. sp | FJ746376 | |
| StyR-293 | 59 | < > > | 1070460/1070461 | Yes | −/− | −/− | FJ746378 | ||
| StyR-362 | 141 | < > > | 1070630/1070631 | No | −/− | −/− | Sal. sp | ρ-ind. term. | FJ746382 |
| StyR-383 | 22 | < < > | 1068808/1068821 | No | −/− | −/− | Sal. sp | FJ746384 | |
| Terminator-associated npcRNAs | |||||||||
| StyR-169 | 32 | < < < | 1069647/1067454 | Yes | +/+ | +/+ | FJ746371 | ||
| StyR-288 | 44 | > > < | 1070605/1070606 | Yes | +/+ | −/− | FJ746377 | ||
| Operon-derived npcRNAs | |||||||||
| StyR-55 | 77 | < < < | 1068343/1071526 | Yes | +/+ | +/+ | FJ746364 | ||
| StyR-126 | 34 | < < < | 1069335/1067249 | Yes | +/+ | +/+ | FJ746368 | ||
| StyR-175 | 77 | > > > | 1069764/1069765 | Yes | +/+ | +/+ | FJ746372 | ||
| StyR-280 | 102 | < > > | 1068036/1068041 | Yes | +/+ | +/+ | FJ746375 | ||
| StyR-306 | 28 | > > > | 1071397/1071398 | No | +/− | +/− | FJ746379 | ||
| StyR-333 | 40 | < < < | 1067027/1067676 | No | +/− | +/− | S. typhi | FJ746380 | |
| StyR-354 | 46 | < < < | 1067015/1068236 | No | −/− | −/− | Sal. sp | FJ746381 | |
| Possible individual intergenic npcRNA genes | |||||||||
| StyR-59 | 162 | > < < | 1068621/1068614 | No | +/− | −/− | S. typhi | ρ-ind. term. | FJ746365 |
| StyR-161 | 132 | > < > | 1068552/1069548 | No | +/− | +/− | S. typhi, S. para C | ρ-ind. term. | FJ746370 |
| StyR-381 | 73 | > > > | 1067420/1067421 | No | +/− | −/− | S. typhi, S. para C and S. dublin | ρ-ind. term. | FJ746383 |
npcRNAs, reference identifications of npcRNA candidates; cDNA (nt), length of cDNAs in nt; Orient., orientation of npcRNA (middle arrow) and adjacent genes (right and left arrows); Adj. Genes (ID), gene ID numbers of genes flanking the npcRNA candidates; Presence in E. coli, npcRNA homolog is present (Yes) or not present (No) in the E. coli K12 genome; N. blot S. typhi/E. coli, northern blots were positive (+) or negative (−) for the given npcRNAs; Growth reg. S. typhi/E. coli, npcRNA is (+) or is not (−) growth phase-regulated in S. typhi/E. coli; Specificity, species specific; Sal sp, Salmonella species specific; S. typhi, S. typhi specific; S. para C, npcRNA is present in S. paratyphi C; Comments: ρ-ind. term., probable ρ-independent/intrinsic terminator detected; Acc. No., accession number of npcRNA sequence in DDBJ/EMBL/GenBank databases.