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Table 1 Transcriptome and translatome profiles of 115 ncRNAs known from E. coli O157:H7 EDL933

From: Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq – ryhB encodes the regulatory RNA RyhB and a peptide, RyhP

Name Start position in the genome Length Strand Number of transcriptome reads Number of footprint reads RPKM transcriptome RPKM footprints RCV P value* Northern Blot/Shine Dalgarno
DicF_1/Z1327 1255006 52 - 2 7 2 16 8.00 1.55E-11  
STnc70 719959 94 + 47 141 28 182 6.50 4.83E-11  
RyhB 4367464 65 - 92 192 80 359 4.49 1.77E-09  
OmrA-B_2 3766084 82 - 504 844 348 1251 3.59 1.47E-08  
OrzO-P_2 2954314 76 + 5057 8198 3764 13114 3.48 1.97E-08 taaagtggt
STnc100_10 2995675 210 - 496 742 134 430 3.21 4.12E-08 tatgggata
STnc550 2412748 391 - 533 779 77 242 3.14 4.96E-08 caaatagtg
RtT_3 1824178 132 - 22 28 9 26 2.89 1.03E-07  
RprA 2445280 108 + 568 745 297 839 2.82 1.25E-07  
STnc180 2250970 203 - 1225 1534 341 919 2.70 1.86E-07 caagcgggg
GadY 4474223 114 + 213 248 106 264 2.49 3.55E-07  
STnc630 5216481 166 + 502 572 171 419 2.45 4.05E-07 aacggagga
STnc100_1 902843 159 + 1046 1049 372 802 2.16 1.11E-06  
CyaR_RyeE 2912765 86 + 16620 16668 10932 23563 2.16 1.11E-06  
sroE 3426663 92 - 64 63 39 83 2.13 1.22E-06  
Z6077/DicF_4 2325956 52 + 118 112 128 262 2.05 1.64E-06  
C0299 1763522 79 + 1 1 1 2 2.00 1.96E-06  
RtT_2 1824000 132 - 3 2 1 2 2.00 1.96E-06 gaccaaggt
QUAD_7 4002118 150 - 859 791 324 641 1.98 2.12E-06  
tpke11 14107 78 + 59 51 43 79 1.84 3.64E-06  
STnc100_5 1866224 209 + 5038 4068 1364 2366 1.73 5.48E-06  
MicA 3606250 72 + 1500 1180 1178 1992 1.69 6.54E-06  
STnc100_3 1353605 206 + 2403 1688 660 996 1.51 1.41E-05  
sroD 2565135 86 - 94 65 62 92 1.48 1.58E-05  
MicC 2113860 122 - 43 29 20 29 1.45 1.83E-05  
frnS 2168565 118 - 175 106 84 109 1.30 3.70E-05 tcagggcaa
OmrA-B_1 3765887 88 - 696 380 447 525 1.17 6.73E-05  
ArcZ 4160147 108 + 3234 1708 1694 1923 1.14 8.20E-05  
STnc130 1161203 135 - 2 1 1 1 1.00 1.66E-04  
STnc560 1939628 214 + 132 58 35 33 0.94 2.27E-04  
sraL 5161197 141 - 627 265 252 228 0.90 2.81E-04  
RydB 2439675 61 - 280 102 260 203 0.78 5.76E-04  
RtT_4 1824474 131 - 30 10 13 9 0.69 9.91E-04  
sroC 767984 163 - 3945 1269 1369 946 0.69 9.99E-04  
CRISPR-DR4_2 1058550 28 + 3 1 6 4 0.67 1.16E-03  
STnc100_2 1267542 167 + 3718 1129 1259 822 0.65 1.27E-03  
sok_15/sokX 3674872 152 - 93 28 35 22 0.63 1.49E-03 tcaggtata
STnc100_4 1641323 191 + 4486 1215 1329 773 0.58 2.02E-03 positive
GcvB 3732394 206 + 13532 3307 3716 1952 0.53 2.96E-03 negative/tgagccgga
Spot_42/spf 4914606 119 + 323 77 154 79 0.51 3.22E-03 gtagggtac
STnc450 5326800 58 - 20 5 20 10 0.50 3.52E-03  
CRISPR-DR4_1 1058490 28 + 4 1 8 4 0.50 3.52E-03  
STAXI_4 1482887 131 + 4 1 2 1 0.50 3.52E-03  
RybB 1014999 79 - 1953 439 1398 676 0.48 3.95E-03 gcagggcat
sroB 572997 84 + 704 151 474 219 0.46 4.59E-03  
P26 5058572 62 + 261 52 238 102 0.43 5.83E-03  
sok_14 2777459 175 - 1539 298 497 207 0.42 6.35E-03 tgaggccca
sroH 5068058 161 - 606 114 213 86 0.40 6.97E-03  
DicF_2 1881271 52 - 5 1 5 2 0.40 7.16E-03  
rdlD_3 1807675 60 + 58 10 55 20 0.36 9.36E-03  
OrzO-P_1 2953705 74 + 7227 1195 5524 1963 0.36 9.96E-03  
sok_10 1888482 175 + 3663 598 1184 415 0.35 1.03E-02 tgaggctca
ryfA 3444344 305 + 16 3 3 1 0.33 1.18E-02  
IS061 2172064 180 - 10 1 3 1 0.33 1.18E-02  
rdlD_4 4509509 66 + 78 11 67 20 0.30 1.49E-02  
rdlD_2 1807146 60 + 59 8 56 16 0.30 0.02  
sok_7 1480784 158 + 2602 366 932 282 0.29 0.02  
RyeB 2600241 100 - 2380 314 1346 382 0.28 0.02  
QUAD_1 2898598 149 + 358 47 136 38 0.28 0.02  
MicF 3117339 94 + 1059 132 637 171 0.27 0.02  
STnc100_6 1893978 190 + 6373 703 1897 450 0.24 0.03  
OxyS 5033797 110 - 106 11 55 12 0.22 0.03  
arrS 4467416 69 - 266 22 201 36 0.18 0.04  
istR 4712705 130 - 99 8 43 7 0.16 0.05  
SraB 1590770 169 + 511 38 171 27 0.16 0.05  
QUAD_6 4001742 150 - 771 54 291 44 0.15 0.06  
DsrA 2725072 87 - 82 6 53 8 0.15 0.06  
StyR-44_7 5087479 109 + 1784 125 926 139 0.15 0.06  
QUAD_5 3861645 151 + 1621 113 607 91 0.15 0.06  
StyR-44_5 4902290 109 + 1846 127 958 142 0.15 0.06  
QUAD_4 3861252 151 + 2395 153 897 123 0.14 0.07  
StyR-44_4 4806012 109 + 1761 112 914 125 0.14 0.07  
StyR-44_1 228975 109 + 1908 111 990 124 0.13 0.08  
STnc240 2830003 75 - 112 6 84 10 0.12 0.08  
Bacteria_small_SRP /ffs 542524 97 + 230378 12741 134343 15969 0.12 0.08 positive
STnc100_9 2773346 167 - 3475 184 1177 134 0.11 0.09  
GlmZ_SraJ_2 4848834 207 + 7351 364 2009 214 0.11 0.10 positive
SraC_RyeA 2600138 145 + 2011 91 784 76 0.10 0.12  
GlmY_tke1_2 4848836 149 + 7310 323 2775 264 0.10 0.12  
StyR-44_6 5046470 109 + 4004 161 2078 180 0.09 0.14  
STnc100_8 2314989 167 - 706 23 239 17 0.07 0.19  
RtT_1 867059 143 + 3357 102 1328 87 0.07 0.21  
C4_2 2673794 88 + 108363 3042 69654 4203 0.06 0.23  
sok_6 1389612 175 - 934 22 302 15 0.05 0.29  
STnc100_7 2145571 190 - 327 7 97 4 0.04 0.35  
CsrB 3714213 360 - 43044 748 6763 253 0.04 0.38  
CsrC 4915753 254 + 25764 425 5738 203 0.04 0.40  
RydC 2079463 64 + 1636 27 1446 51 0.04 0.40  
RNaseP_bact_a /rnpB 4077043 377 - 39359 640 5905 206 0.03 0.40  
GlmZ_SraJ_1 3481543 185 - 7668 122 2345 80 0.03 0.41  
GlmY_tke1_1 3481544 148 - 7634 119 2918 98 0.03 0.42  
6S/ssrS 3860420 184 + 470148 7239 144532 4783 0.03 0.42  
QUAD_3 2899260 144 + 3436 44 1350 37 0.03 0.47  
symR 5467620 77 + 726 6 533 9 0.02 0.60  
sRNA-Xcc1 1392052 89 - 40293 290 25609 396 0.02 0.62  
rdlD_1 1806611 66 + 2090 8 1791 15 0.01 0.76  
StyR-44_3 4229125 109 - 2523 2 1309 2 0.00 0.96  
StyR-44_2 3519339 109 - 2499 1 1297 1 0.00 0.97  
HPnc0260 2421623 163 - 1 0 0 0 N/A N/A  
rseX 2733408 90 + 4 0 3 0 N/A N/A  
sok_12 2152486 125 - 13 0 6 0 N/A N/A  
SraG 4120940 172 + 1 0 0 0 N/A N/A  
STAXI_1 1087216 64 + 6 0 5 0 N/A N/A  
STAXI_2 1087280 131 + 2 0 1 0 N/A N/A  
STAXI_3 1482823 64 + 3 0 3 0 N/A N/A  
STnc100_11 3553828 189 - 387 0 116 0 N/A N/A  
STnc410 4777710 158 + 3 0 1 0 N/A N/A  
tp2 127504 114 - 1 0 0 0 N/A N/A  
sraA 524870 96 - 0 0 0 0 N/A N/A  
STnc480 635390 67 + 0 0 0 0 N/A N/A  
sar 1661162 67 - 0 0 0 0 N/A N/A  
group-II-D1D4-2 2037712 118 - 0 0 0 0 N/A N/A  
DicF_3 2159230 56 + 0 0 0 0 N/A N/A  
C0465 2649880 76 + 0 0 0 0 N/A N/A  
STnc430 5118969 150 - 0 0 0 0 N/A N/A  
  1. *; The P values give the probability that the RCV of the given RNA is similar to / results from the RCV distribution of the tRNAs. Thus, RNAs with high P values are probably not translated and vice versa
  2. Annotated ncRNAs which are not independent of translation (e.g. leader peptides or ribosomal RNAs, etc.) are not shown (see text). The genome position (start) of each ncRNA is indicated, the ncRNAs are sorted according to their RCV. Transcripts examined via Northern blots are indicated and putative Shine-Dalgarno sequences are shown. An overview of all data for the 115 known ncRNAs is found in Additional file 8: Table S6