Methanococcus jannaschii sRNAs

Name		C Box		D' Box		C' Box		D Box
sR1	`TATTTGGCAG`	`ATGATGA`	`CGTTTATCCCCGT`	`CTGA`	`GTTA`	`TGATGA`	`GTAGCAAGCCGG`	`CTGA`	`TGCCACTTTT`
sR2	`TTTATGGCGG`	`ATGATGA`	`ACGGAGTAGCTG`	`CTGA`	`GCTA`	`TGATGA`	`TTGATGGGCGAA`	`CTGA`	`CGCCACTTTT`
sR3	`AAATATGGCA`	`ATGATGA`	`AAAGAGGGTTAG`	`CTGA`	`ACTG`	`TGATGA`	`TACTTACCCGAA`	`CTGA`	`GCCATTATTT`
sR4	`TATTAACGCG`	`ATGATGA`	`GTGCCGACTTCA`	`CTGA`	`ACTG`	`TGATGA`	`AACCTGGGACAG`	`CTGA`	`GCGTTACTAT`
sR5	`TAATTCCTCG`	`ATGATGA`	`GCAATAAAAAG`	`CTGA`	`CTTAATA`	`TGATGA`	`ACCTTTCGGGGTAT`	`CTGA`	`GAGGAATTAT`
sR6	`ATATTTGGCG`	`ATGATGA`	`CAATTTCGCTAT`	`CTGA`	`TTCTG`	`TGATGA`	`CTACTCCCGCAG`	`CTGA`	`GCCAAACCAT`
sR7	`TTTTATGGGG`	`ATGATGA`	`TACATCGATGTG`	`CTGA`	`ATAT`	`TGATGA`	`TGAACGCGCCCTTCT`	`CTGA`	`CCTTTAAAAA`
sR8	`AAAATCGCCA`	`ATGATGA`	`CGATTGGCTTTG`	`CTGA`	`GTCTG`	`TGATGA`	`ACCGTATGAGCA`	`CTGA`	`GGCGATTTAT`

Predictions Mja sR1-sR8 have been verified as RNA transcripts by primer extension. Exceptions to consensus box features shown in red. Predicted methylation guide regions with Watson-Crick/G-U base pairings to target RNAs shown in green. Predicted terminal stem pairings shown in blue. 5' and 3' ends of sRNAs were not determined experimentally (an invariant 10 nucleotides of sequence flanking the C box and D boxes is displayed).