# Candidate E. coli sRNA loci, predicted by the QRNA screen # Rivas et al. Curr Biol 11:1369-1373 (2001) # # This file is derived from rivas01.candidates.tbl; see notes therein # for definition of each data column. # # This maps the 275 sRNA candidates from Rivas et al. (2001) onto # current (Jan 2011) E. coli coordinates (NCBI RefSeq NC_000913.2). I # only remapped the candidate sRNA coordinates; I deleted the data # columns for flanking ORF coords, rather than making the effort to # remap those too. # # The original Rivas (2001) predictions were made on the M52 assembly # (NC_000913.1). I did the mapping to the .2 assembly using 100% identity by # megablast. This uniquely mapped 270/275 loci. The remaining ones I # mapped manually. One locus (155>k26) is a repeat element with six # copies in the genome; the locus that QRNA called is unambiguous # (same coords in .2 as .1 assembly). Three loci (1>tpk1, 226>tpke123, # 70>t13) map uniquely to the .2 assembly at 97-99% identity, so some # sequence substitutions have been made at these loci in the .1->.2 # assembly. Finally, one locus (35>tp8) is now two near-identical loci # in the .2 assembly. I annotated both, as 35>tp8.1 and 35>tp8.2. # # Because the 35>tp8 locus is now two loci in the .2 assembly, there # are 276 loci in the data below, for the 275 Rivas et al. candidates. # # SRE, Sat Jan 22 18:25:11 2011 # # number>name start end source bitsc u_gene d_gene C|T other_gene_names # ----------- ------ ----- ------------ ----- ------ ------ ---- ---------------- 57>tke2 257 337 NC_000913.2 15.16 thrL thrA 113>tp27 9193 9306 NC_000913.2 11.06 talB mog 16>tpke11 14081 14169 NC_000913.2 22.33 dnaK dnaJ C 219>tpe88 16979 17095 NC_000913.2 6.95 gefL nhaA 115>pe6 49634 49819 NC_000913.2 11.04 kefC folA 132>pe8 58182 58238 NC_000913.2 10.13 yabH yabP 173>tpe79 75482 75644 NC_000913.2 8.56 tbpA yabN 55>tpe18 83537 83622 NC_000913.2 15.23 leuA leuL 19>tpe6 85320 85516 NC_000913.2 21.63 leuO ilvI T 268>k51 107497 107556 NC_000913.2 5.17 lpxC yacA 9>tp2 122859 123017 NC_000913.2 24.99 pdhR aceE C 83>tpe34 136467 136570 NC_000913.2 13.13 speE yacC 227>tpe90 182320 182440 NC_000913.2 6.62 htrA yaeG 54>t44 189628 189878 NC_000913.2 15.29 map rpsB C 85>tk7 191710 191855 NC_000913.2 13.03 tsf pyrH 14>tpe3 193445 193521 NC_000913.2 23.88 frr yaeM T 251>tp51 201998 202100 NC_000913.2 5.83 lpxD fabZ 243>tk18 219997 220112 NC_000913.2 6.14 rcsF yaeC 193>t47 229006 229164 NC_000913.2 7.56 yaeD yafB 195>pe13 230998 231122 NC_000913.2 7.52 yafC yafD 109>k15 261982 262095 NC_000913.2 11.33 proA b0245 199>k34 309252 309308 NC_000913.2 7.49 yagY yagZ 153>p14 402834 402927 NC_000913.2 9.44 psiF yaiC 224>tp47 418413 418609 NC_000913.2 6.71 phoR brnQ 144>pe11 420136 420210 NC_000913.2 9.73 brnQ b0402 249>p27 434786 434858 NC_000913.2 5.96 nusB b0417 270>tp55 450836 451032 NC_000913.2 5.16 cyoA ampG 101>tpe43 451113 451294 NC_000913.2 11.80 cyoA ampG T 10>t2 454015 454261 NC_000913.2 24.93 bolA tig T 3>te1 455657 455865 NC_000913.2 32.63 tig clpP T 81>t15 457926 458112 NC_000913.2 13.41 clpX lon - sraA 94>t22 460468 460675 NC_000913.2 12.20 lon hupB 189>t45 460949 461092 NC_000913.2 7.80 hupB b0441 163>e8 463012 463120 NC_000913.2 8.86 b0441 b0442 102>t24 463535 463601 NC_000913.2 11.71 b0442 b0443 272>k52 484845 484985 NC_000913.2 5.09 acrA acrR 64>pk1 502518 502700 NC_000913.2 14.54 ybaL fsr 206>k38 594691 594813 NC_000913.2 7.31 b0571 b0572 111>pe5 617278 617336 NC_000913.2 11.20 entF fepE 192>k32 643240 643378 NC_000913.2 7.56 rnk rna 93>tk8 661867 661975 NC_000913.2 12.21 ybeD dacA 204>k36 668153 668345 NC_000913.2 7.40 ybeB phpB 122>tp28 709961 710158 NC_000913.2 10.62 fur fldA 114>p12 711192 711261 NC_000913.2 11.06 b0685 b0686 256>e17 719685 719844 NC_000913.2 5.66 speF kdpE 254>k48 764274 764375 NC_000913.2 5.72 sucD farR 73>tpe29 773827 773975 NC_000913.2 13.84 ybgE ybgC 135>tk12 808482 808566 NC_000913.2 10.09 bioA bioB 252>e16 829880 830077 NC_000913.2 5.82 ybiH rhlE 242>p25 887194 887357 NC_000913.2 6.15 b0846 b0847 - rybB 236>tk16 892670 892870 NC_000913.2 6.35 b0853 potF 21>k2 914218 914570 NC_000913.2 21.47 b0874 aqpZ T 72>tk5 921522 921589 NC_000913.2 13.88 b0879 cspD 260>t70 925385 925443 NC_000913.2 5.57 clpA infA 30>t6 932314 932446 NC_000913.2 19.45 lrp ftsK T 237>k45 938568 938651 NC_000913.2 6.34 ycaJ serS 147>k25 950305 950479 NC_000913.2 9.64 pflA pflB 117>t25 960253 960424 NC_000913.2 10.97 b0909 cmk 11>tpe1 962893 963051 NC_000913.2 24.75 rpsA himD T 137>pe10 963339 963394 NC_000913.2 10.02 himD ycaI 233>k43 982119 982278 NC_000913.2 6.43 ycbB b0926 158>tpke118 984934 985118 NC_000913.2 9.14 aspC ompF T 205>t51 986207 986403 NC_000913.2 7.35 ompF asnS 146>t30 1005016 1005137 NC_000913.2 9.65 pyrD b0946 217>p23 1014688 1014884 NC_000913.2 6.99 b0952 rmf 45>e3 1018167 1018227 NC_000913.2 16.21 ycbG ompA 79>k10 1080042 1080191 NC_000913.2 13.52 putP b1016 220>t56 1121839 1121932 NC_000913.2 6.90 pyrC yceB 194>t48 1140213 1140293 NC_000913.2 7.55 flgL rne 151>pke2 1145858 1146016 NC_000913.2 9.50 yceF yceD - sraB 214>t54 1146775 1146874 NC_000913.2 7.03 rpmF plsX 269>t74 1152418 1152520 NC_000913.2 5.17 fabF pabC 240>t62 1156799 1156996 NC_000913.2 6.23 ycfH ptsG 100>t23 1158528 1158585 NC_000913.2 11.81 ptsG fhuE 46>tpk6 1165110 1165308 NC_000913.2 16.16 b1108 ndh 209>e13 1195607 1195705 NC_000913.2 7.21 icdA b1137 250>t64 1210669 1210859 NC_000913.2 5.91 mcrA b1160 263>k49 1227965 1228023 NC_000913.2 5.46 b1180 b1181 82>tp21 1255837 1255942 NC_000913.2 13.34 b1202 ychF 150>p13 1268489 1268737 NC_000913.2 9.59 kdsA chaA 181>tpe83 1269024 1269272 NC_000913.2 8.09 kdsA chaA 246>tpe95 1269546 1269836 NC_000913.2 6.04 kdsA chaA 203>k35 1300839 1300923 NC_000913.2 7.44 oppA oppB 200>k33 1318464 1318648 NC_000913.2 7.49 trpC trpE 149>t31 1331692 1331743 NC_000913.2 9.61 topA cysB 141>t29 1415412 1415512 NC_000913.2 9.79 recE racC 258>t68 1416267 1416417 NC_000913.2 5.58 ydaD sieB 245>tke8 1435054 1435279 NC_000913.2 6.07 b1377 b1378 38>te3 1553785 1553846 NC_000913.2 17.63 sfcA rpsV 172>te18 1643052 1643143 NC_000913.2 8.59 rem relF 273>p31 1687778 1687872 NC_000913.2 5.05 manA b1614 191>pk4 1712299 1712401 NC_000913.2 7.63 b1634 gst 62>tpe20 1733277 1733402 NC_000913.2 14.61 b1655 sodB 136>e6 1753526 1753722 NC_000913.2 10.03 b1675 pykF 198>t50 1755137 1755334 NC_000913.2 7.50 pykF lpp 15>t3 1755683 1755734 NC_000913.2 23.48 lpp b1678 T 22>tpe7 1762685 1762875 NC_000913.2 21.30 b1684 b1685 C rydB 50>tp13 1793178 1793272 NC_000913.2 15.52 btuC himA 164>te16 1797175 1797248 NC_000913.2 8.85 pheS pheM 182>tke6 1797296 1797417 NC_000913.2 8.06 pheM rplT 95>pk2 1798025 1798120 NC_000913.2 12.18 rpmI infC 39>p5 1823032 1823156 NC_000913.2 16.94 b1742 b1743 T 87>t17 1860602 1860795 NC_000913.2 12.85 b1778 gapA 103>tpk13 1861792 1861849 NC_000913.2 11.64 gapA b1780 234>p24 1886017 1886085 NC_000913.2 6.42 rnd fadD 98>tp25 1896332 1896421 NC_000913.2 11.84 sdaA b1815 166>t37 1902772 1902825 NC_000913.2 8.82 manZ b1820 128>tp29 1903368 1903613 NC_000913.2 10.32 b1820 b1821 138>e7 1905163 1905250 NC_000913.2 9.97 yebH cspC 75>tp18 1910602 1910788 NC_000913.2 13.83 htpX prc 86>te5 1918171 1918241 NC_000913.2 12.95 b1834 b1835 99>tpke79 1921027 1921308 NC_000913.2 11.82 b1838 b1839 - sraC,ryeA,ryeB 248>k46 1932701 1932856 NC_000913.2 5.96 edd zwf 175>p18 1938219 1938322 NC_000913.2 8.50 msbB yebA 231>k41 1944003 1944069 NC_000913.2 6.50 ruvA yebB 143>tp30 1975165 1975290 NC_000913.2 9.75 motA flhC 118>te10 1976232 1976427 NC_000913.2 10.96 flhD insB_5 90>tpe40 1994068 1994123 NC_000913.2 12.29 yecF sdiA 120>te11 2111238 2111448 NC_000913.2 10.73 rfbB galF 48>tp11 2151249 2151594 NC_000913.2 15.88 b2073 b2074 - ryeC,ryeD 129>tpe60 2151625 2151868 NC_000913.2 10.20 b2073 b2074 - ryeC,ryeD 140>k24 2157704 2157903 NC_000913.2 9.90 b2075 b2077 196>t49 2163583 2163691 NC_000913.2 7.51 b2080 b2081 8>tpe2 2190333 2190528 NC_000913.2 25.48 yehD yehE T 24>k3 2227057 2227436 NC_000913.2 20.83 yohH yohI T 123>k21 2265735 2265825 NC_000913.2 10.60 yeiQ yeiR 68>t12 2268579 2268651 NC_000913.2 14.11 b2175 b2176 67>k7 2280828 2280901 NC_000913.2 14.16 rplY yejK 159>t36 2309561 2309650 NC_000913.2 9.13 yojL ompC 244>p26 2378546 2378744 NC_000913.2 6.12 menF b2266 184>k30 2403507 2403694 NC_000913.2 7.95 nuoA lrhA 78>tp19 2410637 2410699 NC_000913.2 13.64 b2294 b2295 69>tpe27 2412696 2412769 NC_000913.2 13.99 ackA pta 167>tp35 2430970 2431034 NC_000913.2 8.74 folC accD 201>e12 2434673 2434737 NC_000913.2 7.49 usg pdxB 168>tp36 2458496 2458671 NC_000913.2 8.71 b2342 b2343 275>p32 2465736 2465822 NC_000913.2 5.03 yfdB b2350 92>tpke70 2494651 2495085 NC_000913.2 12.32 b2378 b2379 C 187>e10 2496319 2496477 NC_000913.2 7.86 b2379 b2380 25>tp5 2508910 2509021 NC_000913.2 20.55 b2389 b2390 T 179>k29 2528200 2528257 NC_000913.2 8.14 lig b2412 65>tpk8 2531404 2531603 NC_000913.2 14.45 cysK ptsH 124>tk11 2618184 2618263 NC_000913.2 10.47 uraA upp 239>tpe92 2635422 2635496 NC_000913.2 6.31 b2511 b2512 121>k20 2638656 2638708 NC_000913.2 10.65 hisS gcpE 53>tp14 2651364 2651557 NC_000913.2 15.30 sseA sseB - ryfA 4>tp1 2651804 2652176 NC_000913.2 29.07 sseA sseB C ryfA 29>tke1 2689185 2689396 NC_000913.2 19.53 b2556 purL C 112>tpke37 2702137 2702356 NC_000913.2 11.11 rnc llepB T 171>k27 2720644 2720746 NC_000913.2 8.61 b2584 pssA 216>t55 2729426 2729619 NC_000913.2 7.00 kgtP clpB 208>tp44 2735519 2735618 NC_000913.2 7.22 yfiA pheL 177>k28 2742139 2742202 NC_000913.2 8.37 yfiB rplS 127>tpke89 2744209 2744457 NC_000913.2 10.34 rpsP ffh T 232>k42 2753977 2754154 NC_000913.2 6.49 smpB intA 261>t71 2809325 2809448 NC_000913.2 5.55 emrR emrA 61>t11 2815884 2816081 NC_000913.2 14.64 b2690 csrA 266>tp54 2821793 2821871 NC_000913.2 5.32 recA ygaD 59>p7 2847873 2847981 NC_000913.2 14.84 hycB hycA 161>tpe75 2870844 2871029 NC_000913.2 9.09 b2748 ygbE 222>pke3 2922553 2922757 NC_000913.2 6.77 b2792 syd 188>e11 2937334 2937389 NC_000913.2 7.83 fucU fucR 52>tpk7 2940603 2940902 NC_000913.2 15.35 gcvA b2809 - gcvB 274>t77 2969166 2969275 NC_000913.2 5.05 b2832 b2833 223>t59 2974125 2974323 NC_000913.2 6.72 aas galR - sraE,rygA,rygB 155>k26 2995624 2995711 NC_000913.2 9.41 yi21_4 b2862 190>k31 3034306 3034385 NC_000913.2 7.74 prfB recJ 202>tpe85 3044129 3044190 NC_000913.2 7.44 ygfF gcvP 131>e5 3048691 3048918 NC_000913.2 10.14 gcvT visC 133>t27 3054822 3055043 NC_000913.2 10.12 ygfA serA - rygC 210>t52 3071715 3071957 NC_000913.2 7.12 epd yggC 148>tpke85 3081833 3081949 NC_000913.2 9.64 speB speA T 63>k6 3087703 3087777 NC_000913.2 14.60 galP sprT 125>tpk16 3107239 3107413 NC_000913.2 10.39 speC b2966 185>tk15 3151449 3151585 NC_000913.2 7.95 metC yghB 119>pke1 3154542 3154761 NC_000913.2 10.95 b3011 b3012 160>te14 3161505 3161696 NC_000913.2 9.11 plsC parC 71>k8 3184115 3184209 NC_000913.2 13.91 ygiL yi21_5 35>tp8.1 3193088 3193339 NC_000913.2 18.34 b3051 b3052 C rygD 35>tp8.2 3192711 3192922 NC_000913.2 18.34 b3051 b3052 C rygD 162>p16 3208607 3208803 NC_000913.2 8.91 ygjD rpsU 186>te20 3209026 3209120 NC_000913.2 7.94 rpsU dnaG 1>tpk1 3236329 3236596 NC_000913.2 46.77 ygjR ygjT C sraF 110>k17 3244562 3244659 NC_000913.2 11.21 exuT exuR 235>tp50 3246848 3246976 NC_000913.2 6.36 yqjB yqjC 212>pe14 3256093 3256284 NC_000913.2 7.10 yhaO yhaP 178>p19 3274877 3274949 NC_000913.2 8.20 yhaG sohA 142>tp31 3301393 3301470 NC_000913.2 9.75 yhbV yhbW 271>t75 3303845 3303993 NC_000913.2 5.14 mtr deaD 267>e19 3306948 3307055 NC_000913.2 5.32 yhbM pnp 26>p3 3309261 3309437 NC_000913.2 20.24 pnp rpsO T sraG 106>p11 3309708 3309848 NC_000913.2 11.55 rpsO truB 139>k23 3319990 3320093 NC_000913.2 9.95 yhbX secG 215>te21 3326110 3326261 NC_000913.2 7.02 yhbY greA 36>tk1 3330760 3330884 NC_000913.2 17.89 yhbE rpmA 60>tp16 3344484 3344600 NC_000913.2 14.79 yhbH ptsN 88>t18 3375718 3375837 NC_000913.2 12.63 sspA rpsI 238>k44 3376675 3376886 NC_000913.2 6.34 rplM yhcM 255>pe16 3382528 3382725 NC_000913.2 5.70 mdh argR 97>tk9 3405292 3405397 NC_000913.2 12.00 accC yhdT 31>k4 3436467 3436663 NC_000913.2 19.34 mscL yhdM C 57>tp15 3437538 3437638 NC_000913.2 15.03 yhdN rplQ 34>t8 3440495 3440640 NC_000913.2 18.39 rpsM rpmJ T 28>tp6 3446173 3446336 NC_000913.2 19.62 rplN rpsQ T 108>tpk14 3451294 3451526 NC_000913.2 11.37 rpsJ pinO 37>tpke31 3468117 3468167 NC_000913.2 17.66 yheB tufA T 51>t10 3469353 3469422 NC_000913.2 15.42 tufA fusA 91>t21 3472576 3472700 NC_000913.2 12.28 rpsL yheL T 74>tpk9 3474476 3474627 NC_000913.2 13.84 b3346 fkpA 152>t32 3479192 3479311 NC_000913.2 9.47 yheR yheS 84>p8 3494910 3494977 NC_000913.2 13.12 nirD nirC 228>tp48 3517372 3517479 NC_000913.2 6.56 aroK hofQ 170>tp37 3535313 3535506 NC_000913.2 8.68 greB yhgF 213>k40 3577671 3577785 NC_000913.2 7.09 yhhW yhhX 259>tp53 3597740 3597855 NC_000913.2 5.57 livJ rpoH 207>tpe86 3598854 3599051 NC_000913.2 7.30 rpoH ftsX 42>tk2 3604407 3604474 NC_000913.2 16.69 b3468 b3469 218>tp46 3679988 3680184 NC_000913.2 6.96 yhjJ dctA 77>k9 3718384 3718650 NC_000913.2 13.73 cspA yi5A 197>tpke122 3720147 3720337 NC_000913.2 7.50 yi5B glyS T 265>p30 3770015 3770304 NC_000913.2 5.37 yibI mtlA 229>tp49 3775144 3775326 NC_000913.2 6.54 yibL lldP 225>t60 3788153 3788341 NC_000913.2 6.68 yibD tdh 47>tp10 3809177 3809273 NC_000913.2 16.00 mutM rpmG 23>t4 3809713 3809910 NC_000913.2 21.27 rpmB radC T 126>te12 3813795 3813886 NC_000913.2 10.37 pyrE rph 230>e15 3845192 3845328 NC_000913.2 6.53 uhpT uhpC 130>tpe62 3850809 3850913 NC_000913.2 10.19 ilvB b3672 247>t63 3864928 3865032 NC_000913.2 5.97 hslS hslT 2>k1 3903639 3903751 NC_000913.2 41.61 bglF bglG T 134>pe9 3925032 3925178 NC_000913.2 10.10 asnC asnA 96>k12 3935195 3935302 NC_000913.2 12.04 rbsB rbsK 145>cc4\_13 3948445 3948584 NC_000913.2 9.68 ilvL ilvG_1 T 107>k14 3951443 3951532 NC_000913.2 11.45 ilvE ilvD 174>e9 3980836 3980897 NC_000913.2 8.54 yifK aslB 116>k19 3984465 3984709 NC_000913.2 11.02 aslA hemY - sraJ,ryiA 169>tpke120 3999150 3999449 NC_000913.2 8.69 yigE corA 41>cc4\_14 3999453 3999822 NC_000913.2 16.80 yigE corA T 211>k39 4003824 4003881 NC_000913.2 7.11 pldA recQ 6>tpk2 4049102 4049369 NC_000913.2 26.06 b3865 byihI C sraK,ryiB 7>p1 4049881 4050062 NC_000913.2 25.68 yihI hemN T 12>tpk3 4056084 4056430 NC_000913.2 24.68 glnA yihK T 262>p29 4104347 4104492 NC_000913.2 5.54 b3914 yiiP 264>te23 4112497 4112589 NC_000913.2 5.38 fpr glpX 66>tp17 4113604 4113689 NC_000913.2 14.22 glpX glpK 154>t33 4118379 4118439 NC_000913.2 9.43 menA hslU 183>t43 4120312 4120403 NC_000913.2 8.05 hslV ftsN 253>pe15 4156333 4156513 NC_000913.2 5.74 argH oxyR 5>t1 4173582 4173696 NC_000913.2 26.36 b3975 tufB T 20>tp4 4175153 4175381 NC_000913.2 21.48 tufB secE T 226>tpke123 4176314 4176470 NC_000913.2 6.66 nusG rplK 18>tpk4 4178950 4179218 NC_000913.2 21.77 rplL rpoB T 165>p17 4183298 4183373 NC_000913.2 8.83 rpoB rpoC 76>tpke51 4225536 4225648 NC_000913.2 13.79 metH yjbB 49>tpke51 4225651 4225767 NC_000913.2 15.79 metH yjbB T 241>tk17 4261107 4261271 NC_000913.2 6.20 yjbO qor 221>t57 4277864 4278003 NC_000913.2 6.79 yjcD yjcE 180>tp40 4328267 4328511 NC_000913.2 8.12 yjcZ proP 44>tp9 4339769 4339915 NC_000913.2 16.31 melR melA 43>k5 4354436 4354492 NC_000913.2 16.41 b4130 cadA 80>tp20 4363381 4363492 NC_000913.2 13.50 cutA dcuA 58>tke3 4370697 4370798 NC_000913.2 14.91 mopA b4144 156>p15 4381646 4381795 NC_000913.2 9.38 yjeA yjeM 104>te8 4402330 4402409 NC_000913.2 11.59 hflC b4176 13>p2 4404011 4404207 NC_000913.2 24.15 purA yjeB T 89>t19 4408041 4408156 NC_000913.2 12.50 yjfH yjfI 257>p28 4422414 4422539 NC_000913.2 5.58 b4198 yjfY 40>e1 4437818 4437892 NC_000913.2 16.84 ytfK ytfL 157>t34 4465463 4465647 NC_000913.2 9.32 treR mgtA 32>t7 4526008 4526133 NC_000913.2 19.11 yjhL yjhM T 33>tpke10 4531814 4532310 NC_000913.2 18.64 yjhQ yjhR T 27>tpke10 4532011 4532320 NC_000913.2 19.66 yjhQ yjhR T 17>tpe4 4556320 4556376 NC_000913.2 22.29 yjiE iadA T 105>pe4 4566576 4566830 NC_000913.2 11.58 yjiO yjiP 70>t13 4609036 4609121 NC_000913.2 13.98 prfC osmY 176>tpe80 4610026 4610434 NC_000913.2 8.46 osmY yjjU