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Table 1 Selected Synechocystis sRNAs for two-step RT-PCR analysis and relative abundance (ranked by sRNA abundance)

From: Systematic and functional identification of small non-coding RNAs associated with exogenous biofuel stress in cyanobacterium Synechocystis sp. PCC 6803

sRNA Location Dir* G (kcal/mol) 5′ gene Annotation Distance (bp) 3′ gene Annotation Distance (bp) Relative abundance E24 E48  
nc64 1,832,231–1,832,345 <>> −40.6 sll1382 Ferredoxin 302 slr1474 Hypothetical protein 15 Nc64 (4.5S rRNA) 1.01 0.51  
nc18 552,943–553,017 <<< −16.8 sll1635 FAD-dependent thymidylate synthase 76 sml0005 Photosystem II reaction center protein K 48 Nc18 (Ncl0200) 0.965 0.837  
nc1 2948–3061 <>< −14.1 sll0558 Hypothetical protein 75 sll1214 Magnesium-protoporphyrin IX monomethyl ester cyclase 131 Nc1 0.881 1.274  
nc121 3,316,752–3,317,151 ><< −108.3 slr1464 Hypothetical protein 17 ssl2667 NifU protein 212 Nc121 (tmRNA) 1.315 0.646  
nc81 2,250,490–2,250,580 ><> −34.9 ssr3307 Preprotein translocase subunit SecG 16 slr1946 Hypothetical protein 131 Nc81 1.133 3.577  
nc110 3,138,648–3,138,738 <<< −18.2 sll0737 Hypothetical protein 44 sll0048 Hypothetical protein 179 Nc110 (SyR5) 1.19 2.171  
nc26 842,648–842,758 <<> −40.5 sll1799 50S ribosomal protein L3 35 slr1894 Hypothetical protein 347 Nc26 1.201 0.635  
nc41 1,190,736–1,190,822 <>> −22.2 sll1783 Hypothetical protein 353 slr1852 Hypothetical protein 45 Nc41 (Ncr0480) 0.678 1.053  
nc70 1,886,895–1,887,070 >>< −47.8 slr1288 Hypothetical protein 158 sll1166 Hypothetical protein 89 Nc70 (6S rRNA) 0.743 0.701  
nc7 219,563–219,783 <<< −66.9 sll1029 Carbon dioxide concentrating mechanism protein CcmK 46 sll1027 NADH-glutamate synthase small subunit 196 Nc7 1.303 0.632  
nc122 3,323,090–3,323,230 <>> −25.8 sll0629 Photosystem I subunit X 327 slr0653 RNA polymerase sigma factor RpoD 45 Nc122 (Ncr1650) 1.042 0.848  
nc60 1,748,923–1,749,070 <<> −44.8 sll1247 Hypothetical protein 30 slr1351 UDP-N-acetylmuramoylalanyl-d-glutamyl-2,6-diamino-pimelate-d-alanyl-d-alanine ligase 76 Nc60 (SyR7) 0.912 1.229  
nc117 3,250,549–3,250,647 >>> −10.1 slr0550 Dihydrodipicolinate synthase 262 slr0551 Hypothetical protein 353 Nc117 (Ncr1600) 1.519 1.67  
nc33 1,004,885–1,005,121 <<< −40.2 sll1454 Nitrate reductase 108 sll1453 Nitrate transport protein NrtD 60 Nc33 1.607 0.815  
nc85 2,383,750–2,383,875 >>< −42.3 slr0381 Hypothetical protein 114 sll0330 3-Ketoacyl-ACP reductase 74 Nc85 1.13 2.111  
nc65 1,840,822–1,840,980 <>< −25.4 sll1376 Bifunctional sterol desaturase/short chain dehydrogenase 331 sll1374 Melibiose carrier protein 76 Nc65 1.068 1.089  
sRNA E72 B24 B48 B72 H24 H48 H72 S24 S48 S72 N24 N48 N72
nc64 1.519 1.254 0.709 2.69 1.387 0.609 1.572 2.061 1.09 2.143 0.674 0.387 1.131
nc18 0.834 1.289 1.001 0.596 0.972 0.634 0.221 0.366 0.298 0.278 0.111 0.048 0.05
nc1 0.858 0.927 1.584 0.804 0.72 0.844 0.548 0.642 0.993 0.748 0.189 0.188 0.115
nc121 0.853 1.452 0.36 1.469 2.311 0.544 1.534 1.107 0.853 1.626 0.888 0.768 3.146
nc81 0.882 1.641 7.166 1.058 1.326 1.784 0.381 0.691 1.021 0.261 2.293 4.651 1.237
nc110 1.04 1.335 2.358 1.799 3.616 1.22 0.647 1.097 1.398 0.538 1.276 3.595 3.599
nc26 0.64 0.852 0.76 0.653 0.75 0.813 0.489 2.159 1.544 1.709 0.587 0.225 0.163
nc41 0.973 0.959 0.955 0.665 0.969 1.249 0.619 0.207 0.314 0.296 0.319 0.209 0.149
nc70 1.635 0.896 0.465 1.346 1.511 0.577 1.472 1.005 0.865 1.809 1.086 0.876 2.212
nc7 1.178 1.08 0.454 0.981 1.001 0.572 1.259 1.193 1.054 2.444 0.398 0.311 1.158
nc122 1.031 0.864 0.968 0.823 0.723 0.875 1.059 0.58 0.768 0.677 1.531 1.263 1.962
nc60 1.078 0.504 0.73 0.506 0.979 0.512 0.365 0.179 0.201 0.26 1.438 0.965 0.573
nc117 1.293 1.743 1.623 1.035 1.101 0.851 0.866 2.083 1.12 1.12 0.875 1.061 1.404
nc33 1.282 2.254 0.773 1.172 1.239 0.905 0.788 4.606 2.041 3.843 3.152 3.674 4.558
nc85 1.39 1.305 2.13 1.212 0.898 0.964 0.472 1.077 1.402 0.769 4.358 4.151 3.34
nc65 0.927 1.165 1.148 0.987 1.223 0.99 0.857 1.044 1.129 0.94 1.392 1.526 1.364
  1. * Direction of sRNA and adjacent genes