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.