Table 2.
Compilation of antisense npcRNA candidates in S. typhi
| npcRNAs | cDNA (nt) | Orient. | Gene (ID) | Presence in E. coli | N. blot S. typhi /E. coli | Growth reg, S. typhi /E. coli | Specificity | Comments | Acc. No. |
|---|---|---|---|---|---|---|---|---|---|
| npcRNA candidates antisense to the 3′-end of ORF | |||||||||
| StyR-143 | 144 | < | 1068407 | No | −/− | −/− | S. typhi, S. para A | ρ-ind. term. | FJ746389 |
| StyR-219 | 104 | > | 1068601 | Yes | +/+ | +/+ | ρ-ind. term. | FJ746397 | |
| StyR-250 | 222 | > | 1069193 | Yes | −/− | −/− | FJ746402 | ||
| npcRNA candidates antisense to the 5′-end of ORF | |||||||||
| StyR-341 | 49 | > | 1070547 | No | −/− | −/− | Sal. sp | FJ746419 | |
| npcRNA candidates antisense to both 5′- and 3′-end of single ORF | |||||||||
| StyR-281 | 253 | < | 1070369 | Yes | +/− | +/− | FJ746407 | ||
| StyR-47 | 216 | > | Predicted ORF | Yes | −/− | −/− | FJ746385 | ||
| npcRNA candidates antisense to both 5′- and 3′-end of ORFs | |||||||||
| StyR-328 | 78 | < | 1068197 | Yes | −/− | −/− | FJ746417 | ||
| StyR-150 | 46 | > | 1067798/ 1067800 | No | −/− | −/− | Sal. sp | FJ746390 | |
| cis-encoded antisense npcRNA candidates to ORFs of protein-coding genes | |||||||||
| StyR-101 | 45 | < | 1067667 | No | −/− | −/− | S. typhi | FJ746386 | |
| StyR-122 | 25 | > | 1069722 | Yes | +/− | −/− | FJ746387 | ||
| StyR-128 | 83 | < | 1069075 | Yes | −/− | −/− | FJ746388 | ||
| StyR-151 | 109 | > | 1067671 | Yes | +/− | −/− | FJ746391 | ||
| StyR-172 | 57 | < | 1069704 | Yes | −/− | −/− | FJ746392 | ||
| StyR-173 | 76 | < | 1068387 | No | +/− | +/− | Sal. sp | FJ746393 | |
| StyR-178 | 34 | < | 1067312 | Yes | −/− | −/− | FJ746394 | ||
| StyR-196 | 82 | < | 1069862 | Yes | +/− | +/− | FJ746395 | ||
| StyR-199 | 48 | > | 1067680 | Yes | +/− | +/− | FJ746396 | ||
| StyR-222 | 75 | < | 1069061 | Yes | −/− | −/− | FJ746398 | ||
| StyR-234 | 119 | > | 1069670 | Yes | +/+ | +/+ | FJ746399 | ||
| StyR-243 | 135 | > | 1069109 | Yes | +/− | +/− | FJ746400 | ||
| StyR-248 | 211 | > | 1070765 | Yes | +/− | +/− | FJ746401 | ||
| StyR-252 | 162 | < | 1071079 | Yes | −/− | −/− | FJ746403 | ||
| StyR-254 | 98 | < | 1071250 | Yes | +/+ | +/− | FJ746404 | ||
| StyR-264 | 85 | > | 1067864 | Yes | +/+ | −/− | ρ-ind. term. | FJ746405 | |
| StyR-277 | 99 | > | 1069782 | Yes | −/− | −/− | FJ746406 | ||
| StyR-285 | 110 | < | 1070539 | No | −/− | −/− | Sal. sp | FJ746408 | |
| StyR-291 | 61 | > | 1070390 | Yes | −/− | −/− | FJ746409 | ||
| StyR-292 | 38 | > | 1070899 | No | −/− | −/− | Sal. sp | FJ746410 | |
| StyR-295 | 109 | > | 1066997 | Yes | −/− | −/− | FJ746411 | ||
| StyR-302 | 22 | < | 1067039 | No | −/− | −/− | Sal. sp | FJ746412 | |
| StyR-305 | 57 | < | 1067199 | No | −/− | −/− | FJ746413 | ||
| StyR-309 | 32 | > | 1067690 | Yes | −/− | −/− | FJ746414 | ||
| StyR-315 | 69 | < | 1069646 | Yes | −/− | −/− | FJ746415 | ||
| StyR-322 | 90 | < | 1069020 | Yes | −/− | −/− | FJ746416 | ||
| StyR-336 | 199 | > | 1071148 | Yes | −/− | −/− | FJ746418 | ||
| StyR-358 | 113 | < | 1067275 | No | +/− | +/− | Sal. sp | FJ746420 | |
| StyR-369 | 22 | < | 1067888 | No | −/− | −/− | Sal. sp | FJ746421 | |
| StyR-377 | 23 | > | 1069015 | No | −/− | −/− | FJ746422 | ||
| StyR-378 | 23 | < | 1069059 | Yes | −/− | −/− | Sal. sp | FJ746423 | |
npcRNAs, reference identifications of npcRNA candidates; cDNA (nt), length of cDNA clones in nt; Orient, orientation of npcRNA; Gene (ID), ID number of protein-coding genes; 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 transcript; Growth reg. S. typhi /E. coli, npcRNA was (+) or was not (-) growth phase-regulated; Specificity, species specific; Sal sp, Salmonella species-specific, S. typhi, S. typhi-specific, EPEC, enteropathogenic E. coli; EHEC, enterohemorrhagic E. coli;. Comments: ρ-ind. term., probable ρ-independent terminator detected; Acc. No., accession number of npcRNA sequence in DDBJ/EMBL/GenBank databases.