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Table 1 Novel ncRNAs validated in this study

From: Identification of CRISPR and riboswitch related RNAs among novel noncoding RNAs of the euryarchaeon Pyrococcus abyssi

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
  1. 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].