Pyrococcus horikoshii sRNAs

Name		C Box		D' Box		C' Box		D Box
sR1	`AAAGAAGGCG`	`ATGATGA`	`AGCCTTCCGCAC`	`CTGA`	`ATGA`	`TGAGGA`	`GTGGACGGCTTC`	`CTGA`	`GCCTACTCCT`
sR2	`AAAAAGAGGG`	`ATGATGA`	`GTTTTTCCCTCACT`	`CTGA`	`GGAG`	`TGATGA`	`GGAGCCGATGCA`	`CTGA`	`CCTCGATCAT`
sR3	`AATTGTGGCG`	`ATGATGA`	`ATAGCAAGCCAG`	`CTGA`	`AGAG`	`TGATGA`	`AGTGAACACCCC`	`CTGA`	`GCCTACCTAA`
sR4	`CCGAGTTGGG`	`ATGATGA`	`GGGAGATTTCGG`	`CCGA`	`GTGG`	`TGAGGA`	`GACTCGCATGGG`	`CTGA`	`CCTTTCTAAG`
sR5	`ATAAGGTGTG`	`ATGATGA`	`ACGCCATCGATA`	`CTGA`	`GATA`	`TGATGA`	`CCGGATTCCTGG`	`CTGA`	`TTTCTTTTAT`
sR6	`TGGAAATGGG`	`ATGATGA`	`AGTTTGCTACCC`	`CTGA`	`AGAA`	`TGATGA`	`ACCCTGCCGTTA`	`CTGA`	`CCATTTAGCT`
sR7	`GTAATCCGGG`	`ATGATGA`	`ACCTCCATCCCAA`	`CTGA`	`ATAAA`	`TGATGA`	`ATGCACATCAGG`	`CTGA`	`CATTACCTTT`
sR8	`CGAATAGGCG`	`ATGATGA`	`GCTCCATCCCTAC`	`CTGA`	`GTTG`	`TGATGA`	`ATGTAGCGCGCT`	`CTGA`	`GCAACCCTTA`
sR9	`CCGACAGGGG`	`ATGAAGA`	`GCTTTTGCTTTG`	`CTGA`	`GCAGA`	`TGATGA`	`CCACGCCCTTCG`	`CTGA`	`CCTGCTATTT`
sR10	`TTAGCGACTA`	`ATGATGA`	`ACTACTCCCGG`	`CTGA`	`GGGG`	`TGATGA`	`ACCACCTACCGG`	`CTGA`	`GGTGAAAGCA`
sR11	`CTCTAGCGGG`	`ATGATGA`	`CTTTGCCGAGTG`	`CTGA`	`GCTGG`	`TGATGA`	`GTAAACAGTCGT`	`CTGA`	`CTTTCCCTTT`
sR12	`ATCGGCTTGG`	`ATGATGA`	`GCGTTTACCGGT`	`CTGA`	`GCTG`	`TGATGA`	`TATCGGCACTGT`	`CTGA`	`CTAGTAATCT`
sR13	`TCATTGTTGG`	`GTGATGA`	`GATGGCGGATTG`	`CTGA`	`GAGA`	`TGATGA`	`GGACCTTAGGGG`	`CTGA`	`TTAAATTTCG`
sR14	`CTATTAACCA`	`ATGATGA`	`CGGATCAACCGG`	`CTGA`	`TCGAA`	`TGATGA`	`CGTCCGCATCAC`	`CTGA`	`GGGTTTCAAG`
sR15	`AGATGAAGAG`	`ATGATGA`	`GTAAACCCGTTG`	`CTGA`	`GCGG`	`TGATGA`	`GAGGATCGACTAG`	`CTGA`	`ACAACATCTT`
sR16	`ATCAAGTCTG`	`ATGATGA`	`ACCTTCCCCTCAC`	`CTGA`	`AAGG`	`TGATGA`	`GCACACCGGTAGG`	`CTGA`	`GGGTGATAAT`
sR17	`ACGGTCTGCG`	`ATGATGA`	`GAGCGAACTGCA`	`CTGA`	`AAAG`	`TGATGA`	`CAGGGCCTTG`	`CTGA`	`GCGGTGATCG`
sR18	`TTTATTTTTA`	`ATGATGA`	`AACAGCCAGGACC`	`CTGA`	`TGGGA`	`TGATGA`	`GTGGTGGGCTTAG`	`CTGA`	`TGTTGCGGTA`
sR19	`TGGCGGGCTC`	`GTGATGA`	`GCTTTCCCTACGGC`	`CCGA`	`GCTTAGG`	`CGATGA`	`GGAATACAGCCAGGG`	`CTGA`	`TTTTGGTGAT`
sR20	`ATGAATGGCG`	`ATGATGA`	`GGCCTCGATTGG`	`CTGA`	`AT`	`CGATGA`	`TTGAGAGGGACTTGG`	`CTGA`	`GCGGTGATTA`
sR21	`TACCATGCCG`	`ATGATGA`	`GACCGGTACTGG`	`CCGA`	`AGTA`	`TGATGA`	`GCACTCGGTTAG`	`CTGA`	`GGCCTGAAAA`
sR22	`GGAACATCCG`	`ATGATGG`	`GAACAGGGTAGCTG`	`CCGA`	`GT`	`TGATGA`	`GGAAGCCGTTCCAGA`	`CTGA`	`GGAAAGAAAA`
sR23	`TCCTATTAAG`	`ATGATGA`	`ATCTGGAGCCCC`	`CTGA`	`TCGG`	`TGATGA`	`TCAGTCTGCGGAG`	`CTGA`	`TAACATGATT`
sR24	`AAGTTACCCT`	`ATGATGA`	`GAGAGCTGTTAA`	`ATGA`	`G`	`CGGTGA`	`TTAAAGGATGGCTGG`	`CTGA`	`GGGTGAGATA`
sR25	`TGAAGGTTCA`	`ATGATGA`	`AAACTCCCTGAT`	`CTGA`	`AAAATAAA`	`TGATGA`	`AGACCGGTTCA`	`CTGA`	`GATTTCTGCT`
sR26	`TAAAAAGGCG`	`ATGATGA`	`GTGATGGGCGAA`	`CTGA`	`AAACA`	`TGATGA`	`AGGTAGGTGATCT`	`CTGA`	`GCTATCATCG`
sR27	`TAGCTTCAGA`	`GTGATGA`	`GCCCGCGCAGCG`	`CTGA`	`TAGA`	`TGATGA`	`AGATTTTAAGTG`	`CTGA`	`CTTCTAACCT`
sR28	`ATACTTAGGA`	`ATGATGA`	`CCGGTTTCGGGA`	`CTGA`	`ACGA`	`TGATGA`	`CACCAGCTATCG`	`CTGA`	`CCTTGTCTAA`
sR29	`TTGTGGGCGG`	`ATGATGA`	`TCCTTGCCCAGC`	`CTGA`	`GGAG`	`TGATGA`	`AGTCGGTATTAG`	`CTGA`	`CGCTGTGTTT`
sR30	`ATTATTGTGG`	`ATGATGA`	`GTAGTCGGAAGG`	`CTGA`	`GCTGA`	`TGATGA`	`AGGACGCCCATGT`	`CTGA`	`TCCTTATCTT`
sR31	`GGGATTAAAG`	`ATGATGA`	`ACTCGGCAGGTC`	`CTGA`	`TTCG`	`TGATGA`	`GGATCTTGAGTG`	`CTGA`	`TTTACCTTAC`
sR32	`TAAAATGGAG`	`ATGATGA`	`GCTTGGCCGCTAC`	`CCGA`	`G`	`TGATGA`	`GGGCCAAACTCCGGTG`	`CTGA`	`TCACATTGCA`
sR33	`CCTCTTTGAC`	`GTGATGA`	`GGAATCGGGGAG`	`CTGA`	`AGCTA`	`TGATGA`	`GATCCGCCAACG`	`CTGA`	`TTTTCCAAAT`
sR34	`ATCCAAGCCG`	`ATGAGGA`	`TCGTTAGCCACG`	`CTGA`	`GGA`	`TGATGA`	`TAAGAGGGTTAG`	`CCGA`	`GGCTTATTTT`
sR35	`AGACGAAAAA`	`ATGATGA`	`GTACGGGGCCAC`	`CTGA`	`GCGG`	`TGATGA`	`GGTTTCTCCCAAGT`	`CTGA`	`TTACCTAACC`
sR36	`GGTTTGGTGG`	`ATGAAGA`	`GAGGGTAGGTAG`	`CTGA`	`TCTG`	`TGATGA`	`ACTAATCGGCCC`	`CTGA`	`CACGGGGTGA`
sR37	`GGTTAGAGCG`	`ATGATGT`	`AGATTAGCCCCGA`	`CTGA`	`GCGG`	`TGATGA`	`GGCTGGCCCATCG`	`CTGA`	`GTCCCAAAAA`
sR38	`GGAGTAGGCG`	`ATGATTT`	`GACTCCGGAAAAG`	`CTGA`	`ATGA`	`TGATGA`	`AGTCCAGCCCGA`	`ATGA`	`GCCGGGGTGA`
sR39	`AAAGGGGGTG`	`ATGAGGA`	`AAATTTCGCTAG`	`CTGA`	`AGTGAAAGA`	`TGATGA`	`ATACCCTCGCAA`	`CCGA`	`GCCTATTTTA`
sR40	`TCCAGAGGCC`	`ATGAGGA`	`TAGGCGGGTTTG`	`CTGA`	`CCTCGGGGCG`	`TGATGA`	`ACCTTTGGAGCC`	`CCGA`	`GGGCCGGAGA`
sR41	`TTGAAGGCGG`	`ATGATGA`	`AGGCTAATTT`	`CGGA`	`TTGG`	`TGAAGA`	`GCCCTATGAGCG`	`CTGA`	`CGCTATGATT`
sR42	`CTACTTTGTG`	`ATGATGA`	`TCTTCACGGTACC`	`CTGA`	`GAGGCGCTCGA`	`TGATGA`	`GCCCCCTCTCAA`	`CTGA`	`TCATAGCTTT`
sR43	`AGTAATTGAG`	`ATGAAGA`	`AAAAGCACCTCCA`	`CTGA`	`GTGA`	`TGATGA`	`CACGCCCACGGT`	`CTGA`	`TCAAACTGTT`
sR44	`CGTCAAGGCG`	`ATGAGGA`	`GATCGGTCTTGT`	`CTGA`	`AGAA`	`TGATGA`	`AAGTGGTCACCG`	`CTGA`	`GCCTTAAGAA`
sR45	`AAAAAACGGG`	`ATGAGGA`	`AGCCGAGGACAC`	`CTGA`	`AGGA`	`TGATGA`	`CTCTTCGCTTCG`	`CCGA`	`CCGGCGGTGA`
sR46	`TCAAAAGGCA`	`ATGAGGA`	`ATGAATCCAATG`	`CTGA`	`GCTTAGG`	`CAATGA`	`TTGGCCCCAGAGTGG`	`CCGA`	`GCCTTCATAT`
sR47	`AGTTCAACCG`	`ATGAAGA`	`GCCTTTTGGGCC`	`CTGA`	`GAGA`	`TGATGA`	`AAGCCCCCCTAT`	`CTGA`	`GGGGGATAAA`
sR49	`TTCCTGGGCG`	`ATGAAGA`	`ACTGGATCCGAG`	`CTGA`	`TCTCA`	`TGATGA`	`AGGAGGTTTAAC`	`CTGA`	`GCCTCCATGA`
sR53	`AGTCCGGCCG`	`ATGACGA`	`AGGTGGGCACTCT`	`CCGA`	`TT`	`TGATGA`	`GGATGTGGGGCGAGGAGC`	`CAGA`	`GGCTTTATAA`
sR54	`ATTAGTTGGG`	`ATGATGA`	`AGTTCGCTAGAA`	`CTGA`	`GAGG`	`TGATGA`	`CGCCCAGGGTAT`	`CTGA`	`CTTTTCCAAT`
sR55	`TTGTAAACCG`	`ATGATGT`	`GTGTCATCCCTG`	`CTGA`	`AAGGGGTCGA`	`TGATGA`	`TGTTTTGATCCCCAT`	`CTGA`	`GGTGCTGGAA`
sR58	`AGAAAGCCCG`	`ATGATTG`	`GAAGTGGAGTGAG`	`CTGA`	`TGCA`	`TGATGA`	`CCGACTTCCCT`	`CTGA`	`GGGCTTTTTA`
sR59	`TCTAAGGGCG`	`ATGATGT`	`AGGGTGGCGTCC`	`CTGA`	`CATA`	`TGATGA`	`AGCCTGCGATGG`	`CTGA`	`GCAAATTATT`
sR60	`TATCATCGGG`	`ATGAGGA`	`GTTCAGCCTAAG`	`CTGA`	`GACA`	`TGATGA`	`GGGAGTGACGGA`	`CTGA`	`CCGTTGGCTA`

None of the Pho predictions 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). The gaps in numbering for sR48, sR50, sR51, and sR52 are intentional (no Pho homologs were found). sR58-sR60 were first described by Gaspin et al. as sR38, sR34, sR39.