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Table 27 Top classification hits in E. coli

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

R Start End Strand Upstream operon Dist. to upstream Uracil Dist. to downstream Downstream operon Probability
1 384006 384105 forward insC-1,insCD-1,insD-1 -2154 0.52 402 tauA,tauB,tauC,tauD 0.942
2 237185 237284 forward aspV -129 0.47 102 yafT 0.934
3 2777119 2777218 forward yfjX,yfjY,yfjZ,ypjF,ypjJ -1266 0.38 7252 ygaQ_1,ygaQ_2 0.925
4 2304856 2304955 forward eco -2392 0.45 6202 micF 0.923
5 83968 84067 forward setA,sgrS,sgrT -5120 0.49 352 leuO 0.92
6 2902496 2902595 reverse queE -224 0.48 4249 ygcW 0.918
7 294815 294914 forward yagJ -3311 0.43 7352 yagU 0.914
8 4554566 4554665 forward uxuR -1145 0.48 402 iraD 0.913
9 405479 405578 forward yaiI 16 0.45 102 aroL,aroM,yaiA 0.908
10 4570237 4570336 forward yjiS -250 0.38 152 yjiT 0.906
11 754000 754099 forward nei,ybgI,ybgJ,ybgK,ybgL -8002 0.4 352 sdhA1 0.905
12 2054653 2054752 reverse asnW -1349 0.44 3349 yeeL_1,yeeL_2 0.905
13 2202241 2202340 reverse yehS -7458 0.44 10099 mrp 0.903
14 330995 331094 forward betT -226 0.52 552 yahA 0.9
15 3183291 3183390 reverse glgS -6421 0.44 599 ribB,sroG 0.9
16 384056 384155 forward insC-1,insCD-1,insD-1 -2204 0.43 352 tauA,tauB,tauC,tauD 0.898
17 4570187 4570286 forward yjiS -200 0.42 202 yjiT 0.898
18 557285 557384 forward cysS -2017 0.35 102 sfmA 0.894
19 3190062 3190161 reverse sibD -2632 0.37 149 glgS 0.893
20 1543575 1543674 forward nhoA -10633 0.45 1802 fdnG,fdnH,fdnI 0.89
21 2190295 2190394 reverse yehE -193 0.46 99 yehA,yehB,yehC,yehD 0.89
22 3181507 3181606 reverse ribB,sroG -279 0.43 1099 ygiD 0.89
23 3834703 3834802 reverse nlpA -2446 0.37 799 yicI,yicJ 0.889
24 1753166 1753265 reverse ynhG -2530 0.45 49 ydhZ 0.888
25 819916 820015 forward ybhL -56 0.41 52 ybhM 0.887
26 2901746 2901845 reverse queE -974 0.51 3499 ygcW 0.887
27 651208 651307 forward ybdR -8610 0.49 202 dpiA,dpiB 0.886
28 584973 585072 forward appY -1271 0.57 9802 cusA,cusB,cusC,cusF 0.886
29 2362398 2362497 reverse ais -593 0.48 149 yfaZ 0.886
30 1596214 1596313 forward osmC -41085 0.39 3252 lsrA,lsrB,lsrC,lsrD,lsrF,lsrG,tam 0.882
31 522335 522434 forward ybbA,ybbP -232 0.39 102 rhsD,ybbC,ybbD,ylbH 0.881
32 3490420 3490519 reverse php,yhfS,yhfT,yhfU,yhfW,yhfX -12488 0.39 149 ppiA 0.88
33 1986023 1986122 reverse yecH -1203 0.45 49 isrB 0.879
34 3217299 3217398 reverse ygjH -1589 0.42 249 aer 0.878
35 2714626 2714725 forward eamB -545 0.45 102 ung 0.877
36 3984255 3984354 forward aslB -1990 0.42 152 glmZ 0.877
37 2651611 2651710 reverse sseB -519 0.5 99 C0614 0.877
38 4516300 4516399 forward insO-2,yjhV,yjhW -8095 0.39 202 insA-7 0.876
39 3886253 3886352 reverse purP -6993 0.31 4549 dnaA,dnaN,recF 0.876
40 1577414 1577513 forward osmC -22285 0.41 22052 lsrA,lsrB,lsrC,lsrD,lsrF,lsrG,tam 0.875
41 776349 776448 reverse zitB -6707 0.39 11299 mngR 0.874
42 1543625 1543724 forward nhoA -10683 0.46 1752 fdnG,fdnH,fdnI 0.871
43 29201 29300 forward dapB 43 0.49 402 carA,carB 0.871
44 1542975 1543074 forward nhoA -10033 0.39 2402 fdnG,fdnH,fdnI 0.871
45 3768179 3768278 reverse yibH,yibI -38 0.41 8249 yibF 0.871
46 3631114 3631213 forward yhhI -7528 0.4 1702 yhiM 0.87
47 2166486 2166585 forward cyaR -1213 0.41 202 yegS 0.87
48 4578972 4579071 forward symR -989 0.38 5952 mrr 0.869
49 522235 522334 forward ybbA,ybbP -132 0.39 202 rhsD,ybbC,ybbD,ylbH 0.869
50 2383795 2383894 reverse yfbN -1888 0.48 99 yfbK 0.869
51 4577258 4577357 forward yjiV -2331 0.36 552 symR 0.868
52 153855 153954 forward yadD -5936 0.37 8202 hrpB 0.868
53 3665704 3665803 reverse yhjA -61 0.42 149 gadA,gadW,gadX 0.868
54 3651672 3651771 reverse hdeA,hdeB,yhiD -1557 0.45 499 insH-11 0.868
55 4619642 4619741 forward deoA,deoB,deoC,deoD 32 0.38 102 yjjJ 0.867
56 1645875 1645974 reverse ynfP -4828 0.45 49 dicC,ydfW,ydfX 0.867
57 4554516 4554615 forward uxuR -1095 0.42 452 iraD 0.866
58 4539860 4539959 forward fimB -229 0.41 152 fimE 0.866
59 1588711 1588810 reverse hipA,hipB -118 0.4 199 yneL 0.866
60 3181557 3181656 reverse ribB,sroG -229 0.33 1149 ygiD 0.865
61 269657 269756 reverse insH-1 -3619 0.45 299 perR 0.864
62 3925028 3925127 forward cbrB,cbrC -28347 0.47 102 asnA 0.863
63 4538580 4538679 forward yjhR -4477 0.43 352 fimB 0.863
64 4077095 4077194 reverse fdhE,fdoG,fdoH,fdoI -1178 0.39 5549 yihS,yihT,yihU 0.863
65 1210379 1210478 reverse iraM -475 0.42 1549 stfE,tfaE 0.862
66 4213351 4213450 forward metA -70 0.37 102 aceA,aceB,aceK 0.861
67 578853 578952 forward essD,rrrD,rzpD -1013 0.49 202 ybcW 0.861
68 3755951 3756050 reverse selA,selB -40 0.33 149 yiaY 0.861
69 924768 924867 forward clpA 44 0.36 7002 lrp 0.86
70 2520650 2520749 reverse xapA,xapB -52 0.42 199 xapR 0.86
71 582454 582553 forward tfaX -122 0.44 402 appY 0.859
72 1049984 1050083 forward insA-4,insAB-4,insB-4 -182 0.38 652 cspG 0.859
73 3767704 3767803 forward yibG -994 0.36 2552 mtlA,mtlD,mtlR 0.859
74 2383745 2383844 reverse yfbN -1938 0.45 49 yfbK 0.859
75 1005025 1005124 forward pyrD 25 0.46 102 zapC 0.858
76 157105 157204 forward yadD -9186 0.34 4952 hrpB 0.858
77 1669567 1669666 reverse mdtI,mdtJ -1228 0.46 1999 ynfL 0.858
78 3800263 3800362 forward rfaD,waaC,waaF,waaL -3984 0.35 6252 coaD,waaA 0.856
79 2784960 2785059 reverse ygaU -9350 0.41 1149 ileY 0.856
80 2468130 2468229 reverse yfdK,yfdL,yfdM,yfdN,yfdO -920 0.49 5149 mlaA 0.855
81 2991883 2991982 reverse ygeK,ygeL -550 0.39 3549 yqeK 0.855
82 2859337 2859436 reverse nlpD,rpoS -5195 0.42 99 ygbI 0.855
83 3490370 3490469 reverse php,yhfS,yhfT,yhfU,yhfW,yhfX -12538 0.32 99 ppiA 0.854
84 4220501 4220600 forward aceA,aceB,aceK -2097 0.37 1302 metH 0.853
85 715871 715970 reverse potE,speF -249 0.37 99 ybfG,ybfH 0.853
86 2461957 2462056 reverse mlaA -268 0.45 3049 yfcZ 0.852
87 2876502 2876601 reverse cas1,cas2,casA,casB,casC,casD,casE -40 0.34 2199 cysC,cysD,cysN 0.851
88 4084875 4084974 forward fdhD 46 0.42 102 yiiG 0.85
89 4535630 4535729 forward yjhR -1527 0.31 3302 fimB 0.849
90 1635392 1635491 reverse gnsB -192 0.42 1049 nohA,tfaQ,ydfN 0.849
91 3497220 3497319 reverse php,yhfS,yhfT,yhfU,yhfW,yhfX -5688 0.33 6949 ppiA 0.849
92 3266938 3267037 reverse garK,garL,garP,garR,rnpB -1251 0.35 1899 tdcA,tdcB,tdcC,tdcD,tdcE,tdcF,tdcG 0.848
93 2267568 2267667 reverse yejG -8298 0.34 4299 yeiW 0.848
94 3580990 3581089 reverse ggt -2065 0.4 1999 ryhB 0.848
95 1811219 1811318 reverse cedA -177 0.5 99 ydjO 0.845
96 583210 583309 reverse envY,ompT -644 0.4 1299 ybcY 0.845
97 3576850 3576949 reverse yhhW -74 0.33 149 gntK,gntR,gntU 0.844
98 3266488 3266587 reverse garK,garL,garP,garR,rnpB -1701 0.43 1449 tdcA,tdcB,tdcC,tdcD,tdcE,tdcF,tdcG 0.843
99 2055603 2055702 reverse asnW -399 0.33 4299 yeeL_1,yeeL_2 0.843
100 2739273 2739372 reverse rimM,rplS,rpsP,trmD -2883 0.3 149 aroF,tyrA 0.842
  1. Top 50 hits of the forward and reverse strands of the E. coli intergenic regions using 50 nt-overlap 100 nt window and under the LMFEGCRND model. The ranking of each hit is denoted in column R. 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. Positions are according to gbU00096.2 version of E. coli and not gbU00096.3 version.
  2. 1Table 27: Complete list of genes in this operon is sdhA,sdhB,sdhC,sdhD,sucA,sucB,sucC,sucD.