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Table 24 Top entropy hits in B. subtilis filtered for GC-comp. and uracil-comp.

From: Secondary structural entropy in RNA switch (Riboswitch) identification

B. subtilis Start End Strand Upstream operon Upstream gene Dist. to upstream MFE MFE p. Val. GC RND RND p. Val. Uracil Dist. to downstream Downstream gene Downstream operon Probability
157 nt 191850 192006 forward BSU01590 ybaS -12186 -54.16 0.01 0.4904 94.7470016 0.0359 0.3057 2277 trnSL-Glu2 BSU_tRNA_75 0.8561704159
157 nt 749147 749303 forward BSU06780 yeeC -3069 -49.19 - 0.4458 94.8936005 0.0310 0.3630 550 yeeG BSU06820 0.8463344574
157 nt 665425 665581 forward BSU06130 ydjC -677 -51.50 - 0.4968 95.6813965 0.0169 0.3439 1963 gutB BSU06150 0.8462108970
157 nt 1017114 1017270 forward BSU09400 spoVR 18 -53.10 - 0.4968 94.5084991 0.0412 0.3376 1806 lytE BSU09420 0.8305525184
157 nt 823013 823169 forward BSU07480 yfmG -604 -48.60 - 0.5032 94.2139969 0.0507 0.2866 4161 yfmA BSU07540 0.7458834648
157 nt 3421066 3421222 reverse BSU33340 sspJ -320 -49.40 - 0.4713 97.1984024 0.0049 0.3312 79 lysP BSU33330 0.8851321340
157 nt 3158851 3159007 reverse BSU30890 ytxO -328 -48.50 - 0.4395 95.1657028 0.0250 0.3630 3376 ytdA BSU30850 0.8522043228
157 nt 736435 736591 reverse BSU06740 yefB -2481 -50.51 - 0.4904 95.0205994 0.0279 0.3376 3690 yerO BSU06700 0.8204180002
157 nt 201248 201404 reverse BSU01800 alkA -1220 -49.46 - 0.4968 95.0683975 0.0269 0.2930 7301 ybbK BSU01720 0.8003951907
157 nt 4129689 4129845 reverse BSU40200 yydD -810 -48.40 - 0.4904 94.8125000 0.0332 0.3567 2120 yydF BSU40180 0.7834032774
150 nt 4134601 4134750 forward BSU40190 fbp -4483 -50.91 - 0.4733 91.2214966 - 0.3800 677 yycS BSU40240 0.8779885173
150 nt 3359819 3359968 forward BSU32650 yurS -5258 -46.80 - 0.4600 92.3918991 - 0.3600 12677 yuzL BSU32849 0.8770275712
150 nt 749175 749324 forward BSU06780 yeeC -3102 -46.50 - 0.4600 92.0363998 - 0.3867 527 yeeG BSU06820 0.8652582169
150 nt 1958237 1958386 forward BSU18190 yngC -9899 -48.30 - 0.4733 90.9682007 - 0.3533 44327 iseA BSU18380 0.8436317444
150 nt 1540761 1540910 forward BSU14680 ykzC -1995 -46.42 - 0.4333 90.3455963 - 0.3400 1052 ylaA BSU14710 0.8428211212
150 nt 3199841 3199990 forward BSU31170 yulF -1875 -47.20 - 0.4467 89.9530029 - 0.3733 12677 tgl BSU31270 0.8267914653
150 nt 3421066 3421215 reverse BSU33340 sspJ -325 -49.40 - 0.4800 93.4540024 - 0.3333 74 lysP BSU33330 0.9072541595
150 nt 933665 933814 reverse BSU08620 yfhP -718 -49.54 - 0.4600 89.9813995 - 0.3733 5474 sspK BSU08550 0.8426564932
200 nt 3359769 3359968 forward BSU32650 yurS -5183 -66.40 - 0.4600 123.4530029 - 0.3450 12702 yuzL BSU32849 0.9236087203
200 nt 339225 339424 forward BSU03130 nadE -20 -63.60 - 0.4700 121.1809998 - 0.3250 702 aroK BSU03150 0.8414211273
200 nt 1678852 1679051 reverse BSU17060 ymzD -101667 -62.81 - 0.4750 122.0299988 - 0.3300 7299 ylqB BSU15960 0.8517054319
200 nt 3717398 3717597 reverse BSU36100 ywrD -1637 -51.30 - 0.3650 130.8540039 - 0.3950 399 cotH BSU36060 0.9702541828
200 nt 198226 198425 reverse BSU01800 alkA -4222 -30.81 - 0.3750 130.7449951 - 0.5150 4299 ybbK BSU01720 0.8267450333
157 nt 235800 235956 reverse BSU02180 ybfE -2285 -54.99 - 0.3312 66.4815979 01 0.3439 550 glpT BSU02140 0.0401644297
200 nt 3236257 3236456 forward BSU31500 yuxK 61 -82.70 - 0.4200 93.3933029 02 0.2650 802 yufL BSU31520 0.0853443071
  1. Significant hits of the forward and reverse strands of the B. subtilis intergenic regions having significantly high RND entropy (p-Val. <0.0500), significantly low (p.Val. <0.050), GC and uracil compositions within the range of those for known riboswitches Threshold values and their corresponding p-values have been calculated separately for each genome-wide test. No overlap used for 157 nt scan (28340 segments). 175 nt overlap used for 150 nt scan (60204 segments). 100 nt overlap used for 200 nt scan (44847 segments). Distance from upstream and downstream operons are the distance from the center of the hit to the stop and start codons of upstream and downstream operons, respectively. Probability denotes the multinomial regression likelihood of being a riboswitch under the LMFEGCRND model. Negative values indicate distance to upstream operon. Columns Upsream/Downstream Operon show gene ID within the operon.
  2. 1Table 24: The entropy of this sequence is the lowest within the test. The significance of this value is also shown in Figure 5 as the lowest blue point on the graph.
  3. 2Table 24: The entropy of this sequence is the lowest within the test.