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Table 1 List of high scoring clusters

From: Identification of cyanobacterial non-coding RNAs by comparative genome analysis

CLID Sequence number Strain Alignment length Z Z rev Exp Comment Reference
   MED SS1 MIT WH8       
194 3 3 - - - 201 -6.28 -12.94 + yfr2, yfr3, yfr4 This paper
5 3 - 1 1 1 345 -7.58 -10.18 NT rplCD operon leader, corresponds to Escherichia coli S10 r-operon [61, 62]
92 5 1 1 1 2 756 -4.47 -9.9 NT rrn operon leader [63, 64]
112 2 2 - - - 1129 -8.15 -9.15 NT Reciprocal coverage of 7.9%, artifact due to low-complexity sequences -
229 2 - - 1 1 161 -7.98 -4.90 NT Hghly similar sequences, putative ncRNAs This paper
227 2 - - 1 1 229 -7.38 -7.32 NT rplJ operon leader, corresponds to E. coli β r-operon [65]
84 1 - 1 - - 122 -6.27 -5.54 + Yfr2 This paper
101 3 - 1 1 1 152 -5.77 -5.61 NT Putative Cobalamin riboswitch [39, 66]
226 2 - - 1 1 142 -5.29 -5.28 NT Possible bi-directional terminator of the rplKAJL operon Predicted by TransTerm [67]
9 6 - 1 1 4 397 -4.38 -4.95 NT No conserved position, no significant BLASTN hit to MED4 This paper
51 2 1 1 - - 146 -0.84 -4.92 + yfr7 This paper
53 9 2 2 1 4 697 -3.26 -4.59 + yfr6 in MED4 and SS120 and a subgroup of 5' UTR regions to annotated genes and putative unannotated genes in all four strains This paper
245 2 - - 1 1 259 -3.7 -4.53 - rpoBC operon leader, corresponds to E. coli attenuator separating the rpl genes from rpoBC in the rplKAJLrpoBC gene cluster [37, 68]
217 1 1 - - - 153 -1.63 -4.28 - Located between genes for a two-component sensor histidine kinase and a conserved hypothetical protein This paper
87 2 - - 1 1 336 -4.24 -3.64 NT Region upstream of the rbcLS cluster containing conserved promoter [51]
228 2 - - 1 1 106 -0.67 -4.00 NT Rpl11 operon leader, corresponds to E. coli L11 r-operon [69, 70]
257 2 - - 1 1 176 -3.42 -3.97 + Yfr1 This paper
2 3 - 1 1 1 197 -3.93 -2.94 NT Putative TPP riboswitch in front of thiC [38]
  1. RNA elements were predicted according to the scheme shown in Figure 2. The total number of sequences in each cluster and the distribution within the four compared genomes plus the total alignment length are given. The elements are ordered according to the lowest score in either forward (Z) or reverse (Z rev) orientation (in bold letters). The lower the Z-score the higher the support for structural conservation. Exp (experimental testing): +, tested positively by Northern hybridisation; NT, not tested. The cluster identities (CLID) were also used in Table 2. For further details and exact positions of sequences see Table 2 and [34].