Table 1.
Novel ncRNAs validated in this study
| Name | Beginning | End | length(nt) | 5'-start | Promoter | Adjacent genes | Strand | Conservation | Prediction |
|---|---|---|---|---|---|---|---|---|---|
| CRISPR locus | |||||||||
| Cr 1-1 | 149430 | 147916 | 60 | 149408 | Cons (53 nt) | PAB0095/PABt02 | →←← | All§ | H/R |
| Cr 4-4 | 1760062 | 1761854 | 60 | 1760285 | Cons (53 nt) | PAB1170/PaBt46 | ←→→ | H/R | |
| Cr 4-12 | 60 | 1760832 | |||||||
| Conserved unique locus | |||||||||
| sRk11 | 197248 | 197534 | 50 | 197484 | TATA | PAB2227/PAB2402 | ←←← | All | H/R |
| sRk28 | 527697 | 527833 | 70/100 | 527798 | - | PAB1992/PAB1991 | ←←← | All except Tsi | H/R |
| sRk33* | 636804 | 636904 | 100 | 636804 | Cons | PAB1916/PAB0465 | ←→→ | All | H/R |
| sRk61 | 1348633 | 1348700 | 60/95 | 1348615 | - | PAB1455/PAB0921 | ←→→ | Pho | R |
| Conserved repetitive locus | |||||||||
| sRk48 | 985849 | 986002 | 130 | 985805 | Cons | PAB0686/PAB0686.1n | →→→ | Pho, Pfu, Tko, Tsi | H/R |
| sRk49 | 1067535 | 1067886 | 150/220 | 1067923 | TATA (60 nt) | PAB0740/PAB0741 | →←→ | Pho | R |
| sRk52 | 1104008 | 1104286 | 130/190 | 1104056 | Cons | PABt30/PAB0766 | ←→→ | Pho, Pfu, Tko, Tsi | H/R |
| Specific repetitive locus | |||||||||
| sRkB | 809887 | 810256 | 216/343 | 810048 | Cons | PAB1794/PAB0571 | ←→→ | H | |
| sRkC | 1612986 | 1613347 | 145/220 | 1613195 | Cons | PAB1080.4n/PAB1080.5n | ←←← | H | |
The positions indicate the beginning and the end of each predicted region. The RNA lengths are based on Northern blot analysis. The 5' ends of ncRNAs were determined by primer extension experiments (Additional file 3, Figure S2). Promotors were predicted based on search of entire (Cons: BRE/TATA) or partial (TATA) motif consensus located 15 to 30 nt (otherwise pointed out in parenthesis) upstream of the 5' transcription start. Conservation among the 7 annotated thermococcal genomes: P. abyssi, P. horikoshii (Pho), P. furiosus (Pfu), T. kodokarensis (Tko), T. sibiricus(Tsi), T. gammatolerans and T. onnurineus. Prediction tools are denoted for each region: bias composition (H) and comparative analysis (R). § CRISPR 1 and 4 direct repeats are conserved. * sRk33 is annotated as SscA in P. furiosus [22].