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Table 2 Novel non-coding RNA (ncRNA) candidates (150 in total) based on transcriptome sequencing and ribosomal profiling. ncRNAs are identified by their start position on the genome given in the name (abbreviated as ncR#)

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 Length Max. ORF (nt) Strand Number of transcriptome reads Number of footprint reads RPKM transcriptome RPKM footprints RCV Northern Blot CopraRNA CopraRNA term
ncR1085800 72 - + 11274 532 8857 898 0.1 positive   
ncR1481381 99 9 + 11208 516 6404 634 0.1 positive   
ncR3690952 145 54 - 4898 26 1911 22 0.01 negative 1.18 ecc00620:Pyruvate metabolism
ncR1636218 78 27 - 1034 22 750 34 0.05 negative 1.31a GO:0042364~water-soluble vitamin biosynthetic process
ncR3545929 41 - + 542 2 748 6 0.01    
ncR3665651 109 45 - 1442 2 748 2 0 negative 1.24 GO:0045426~quinone cofactor biosynthetic process
ncR3860554 73 24 - 637 3 494 5 0.01   0.98 2Fe-2S
ncR1088953 37 - + 295 4 451 13 0.03    
ncR3066135 48 - + 354 0 417 0 0    
ncR1484560 42 - + 294 0 396 0 0    
ncR5355946 47 21 - 246 4 296 10 0.04    
ncR16920 36 - - 164 4 258 14 0.05    
ncR165975 49 9 + 216 4 249 10 0.04 negative   
ncR5223290 66 - + 265 3 227 6 0.02    
ncR1641710 114 105 - 430 28 213 30 0.14    
ncR1765944 114 54 + 406 33 201 35 0.18   5.48a membrane
ncR2358348 45 - - 151 1 190 3 0.01    
ncR1888606 46 18 - 147 4 181 11 0.06    
ncR2530362 64 6 - 196 0 173 0 0    
ncR5133665 29 - - 86 0 168 0 0    
ncR2638864 38 - - 100 2 149 6 0.04    
ncR326492 42 - + 110 9 148 26 0.18    
ncR622277 95 63 + 248 1 148 1 0.01 negative   
ncR2549762 59 45 - 150 2 144 4 0.03    
ncR2287 90 45 - 218 8 137 11 0.08    
ncR1019437 57 - - 130 2 129 4 0.03    
ncR1694864 51 18 + 116 1 129 2 0.02    
ncR1864748 174 105 - 370 32 120 22 0.19   4.00a cell membrane
ncR3526958 96 45 - 193 9 114 11 0.1   2.92a ecd00190:Oxidative phosphorylation
ncR867065 45 21 - 76 1 96 3 0.03    
ncR1079732 27 - - 41 2 86 9 0.11    
ncR3020266 116 57 + 168 9 82 9 0.12    
ncR1328373 40 21 - 55 1 78 3 0.04    
ncR3094200 36 9 + 47 3 74 10 0.14    
ncR774709 58 39 + 74 1 72 2 0.03    
ncR3725111 44 - - 52 1 67 3 0.04    
ncR451977 43 21 - 50 3 66 8 0.13    
ncR4881271 105 75 + 123 7 66 8 0.12   1.70a GO:0022900~electron transport chain
ncR4922734 44 27 + 49 2 63 6 0.09    
ncR1748457 38 9 - 40 0 60 0 0    
ncR4393950 74 - - 78 5 60 8 0.14    
ncR5324582 92 24 + 94 4 58 5 0.09    
ncR1847082 38 - + 38 1 57 3 0.06    
ncR2820623 107 66 - 105 9 56 10 0.18   1.89a lipoprotein
ncR1114186 94 60 - 91 3 55 4 0.07    
ncR3583650 35 - - 34 1 55 3 0.06    
ncR1509794 96 60 - 91 5 54 6 0.12    
ncR4391372 28 - - 26 2 53 9 0.17    
ncR4546182 36 12 - 34 2 53 7 0.13    
ncR612919 36 - + 32 0 50 0 0    
ncR426804 47 - + 41 3 49 8 0.16    
ncR3164662 66 9 + 56 3 48 6 0.12    
ncR2585184 44 - + 36 1 46 3 0.06    
ncR2930972 38 6 - 30 2 45 6 0.14    
ncR3527530 119 51 - 95 4 45 4 0.09   1.97a GO:0046395~carboxylic acid catabolic process
ncR4520884 50 24 + 40 3 45 7 0.16    
ncR2498369 53 33 - 41 1 44 2 0.05    
ncR4161484 42 39 + 33 1 44 3 0.07    
ncR2699447 35 18 + 26 1 42 3 0.08    
ncR5210782 28 18 + 21 0 42 0 0    
ncR205409 74 45 - 53 0 41 0 0   1.02 IPR014021:Helicase, superfamily 1 and 2, ATP-binding
ncR1868696 103 30 - 72 6 40 7 0.18    
ncR3915561 37 - - 26 2 40 7 0.17    
ncR1462015 40 21 - 27 0 38 0 0    
ncR1475353 73 - - 48 4 37 7 0.18    
ncR397399 68 - - 44 0 37 0 0    
ncR4645569 57 15 - 36 0 36 0 0    
ncR1239030 54 - + 33 1 35 2 0.07    
ncR1645154 42 - - 26 1 35 3 0.08    
ncR3553461 57 33 + 35 1 35 2 0.06    
ncR4853400 65 15 + 40 3 35 6 0.16    
ncR1143400 43 18 + 25 2 33 6 0.17    
ncR2693045 49 6 - 29 2 33 5 0.15    
ncR3735643 69 45 + 40 2 33 4 0.11    
ncR3991822 44 9 - 26 0 33 0 0    
ncR4714439 67 6 - 39 2 33 4 0.11    
ncR1960332 35 - + 20 1 32 3 0.11   1.96a GO:0034660~ncRNA metabolic process
ncR2885483 44 - - 25 1 32 3 0.09    
ncR4463425 63 12 - 36 1 32 2 0.06    
ncR501481 70 21 + 39 0 32 0 0    
ncR963596 50 9 - 28 1 32 2 0.08    
ncR1152534 90 51 + 50 4 31 5 0.17   0.84 ecq00052:Galactose metabolism
ncR2602372 62 12 - 34 2 31 4 0.13    
ncR2062548 38 - + 20 0 30 0 0    
ncR4770438 40 12 + 21 1 30 3 0.1    
ncR865067 103 51 - 54 1 30 1 0.04    
ncR11537 73 48 + 37 2 29 3 0.12    
ncR3040352 77 18 - 40 3 29 5 0.16    
ncR4249267 64 9 + 33 2 29 4 0.13    
ncR1592436 48 9 - 24 1 28 3 0.09    
ncR3583545 40 - - 20 1 28 3 0.11    
ncR725615 61 - + 30 2 28 4 0.14    
ncR1066434 66 21 - 32 1 27 2 0.07    
ncR4163613 125 45 + 59 5 27 5 0.18   1.29 antibiotic resistance
ncR15950 44 18 + 20 0 26 0 0    
ncR2452385 45 18 - 21 0 26 0 0    
ncR2841773 79 18 + 37 0 26 0 0    
ncR3320428 75 51 + 34 1 26 2 0.06    
ncR2903620 140 33 - 61 3 25 3 0.11    
ncR3042903 164 57 - 69 3 24 2 0.09    
ncR543583 67 51 + 29 0 24 0 0    
ncR1585703 88 48 + 36 2 23 3 0.12    
ncR1999946 51 15 + 21 0 23 0 0    
ncR5077759 50 6 - 20 1 23 2 0.11    
ncR1640190 56 - - 22 2 22 4 0.2    
ncR1752346 64 - + 25 0 22 0 0    
ncR3074598 54 36 - 21 0 22 0 0    
ncR3320341 85 18 + 33 0 22 0 0    
ncR3330508 57 - - 22 0 22 0 0    
ncR4096595 60 - - 23 2 22 4 0.19    
ncR4137844 268 195 - 102 7 22 3 0.15    
ncR4414172 53 - - 21 0 22 0 0    
ncR492696 51 - - 20 0 22 0 0    
ncR1215540 74 21 + 28 2 21 3 0.15    
ncR2254917 76 - + 28 2 21 3 0.15    
ncR2902855 104 - - 39 3 21 4 0.17    
ncR752395 172 66 + 64 2 21 1 0.07    
ncR283226 71 27 + 25 0 20 0 0    
ncR1049002 77 48 - 26 1 19 2 0.08   1.84a GO:0050890~cognition
ncR1216838 100 12 - 33 1 19 1 0.07    
ncR4829752 78 - - 26 1 19 2 0.08    
ncR1483108 77 63 + 23 1 17 2 0.09    
ncR155024 78 18 + 23 0 17 0 0    
ncR4156147 78 - - 23 1 17 2 0.09   1.75a GO:0032196~transposition
ncR4788281 97 78 - 30 0 17 0 0   0.99 topological domain:Periplasmic
ncR1854285 91 48 - 25 1 16 1 0.09    
ncR1942672 85 - + 24 1 16 1 0.09   2.09a GO:0015031~protein transport
ncR2614043 86 57 - 25 0 16 0 0    
ncR4741832 75 30 - 21 0 16 0 0    
ncR484751 94 51 - 27 2 16 3 0.16    
ncR5283975 98 84 - 28 0 16 0 0   2.14a GO:0009386~translational attenuation
ncR1314229 101 48 + 26 2 15 2 0.17    
ncR1893573 187 87 - 48 4 15 3 0.18    
ncR3609575 74 - + 20 0 15 0 0   1.72a eum00660:C5-Branched dibasic acid metabolism
ncR3724967 105 42 - 28 0 15 0 0    
ncR4245110 118 48 + 30 1 14 1 0.07    
ncR866957 79 42 - 20 0 14 0 0    
ncR336953 96 27 + 22 2 13 3 0.2    
ncR3997954 104 81 + 23 2 13 2 0.19    
ncR411208 99 6 - 22 2 13 2 0.2   2.64a GO:0015980~energy derivation by oxidation of organic compounds
ncR1736783 100 57 - 22 1 12 1 0.1    
ncR745748 107 54 + 23 1 12 1 0.09    
ncR3609372 201 - + 38 1 11 1 0.06    Rfam match: tRNA RF00005b
ncR3890479 104 51 - 20 1 11 1 0.11    
ncR1087411 224 135 + 41 2 10 1 0.11    
ncR3874837 127 48 - 22 2 10 2 0.2    
ncR4187491 122 9 - 22 0 10 0 0    
ncR769665 198 102 + 34 2 10 1 0.13    
ncR5157894 218 114 + 33 3 9 2 0.2    
ncR196880 135 81 - 20 1 8 1 0.11   1.23 ecc00330:Arginine and proline metabolism
  1. aDAVID enrich. score; signif. ≥ 1.3. btRNA
  2. The longest potential ORF is indicated for each ncRNA. RPKM values of transcriptome and translatome are shown, as well as the ribosome coverage value (RCV). A transcript is considered non-coding if it has at least 20 reads in the transcriptome data and the RCV is below 0.197 (α = 0.01). Transcripts examined via Northern blots are indicated and CopraRNA functional enrichments are shown