Freiburg RNA Tools
CopraRNA - Results
BIF
IFF

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching

CopraRNA 1229462

Input and runtime details for job 1229462 (precomputed example)

Sequence input

? sRNA sequences[.fa]
? Putative target sequences (organism of interest)[.fa]
? Extract sequences aroundstart codon
? nt up (1-300)200
? nt down (1-300)100

CopraRNA parameters

? Consensus prediction off
? p-value combinationno
? p-value filtering (0=off)0

IntaRNA parameters

? Target folding window size150
? Target max. basepair distance100

Job ID 1229462 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:25:41 CET 2018
?CopraRNA Started@ Fri Feb 16 15:25:59 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 20:22:57 CET 2018
?Post-Processing Finished@ Fri Feb 16 20:23:04 CET 2018
?Job Completed@ Fri Feb 16 20:23:29 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

Output download complete results [zip]

Downloadable files

[csv]
[txt]
[csv]
[png] [pdf] [ps]
[png] [pdf] [ps]
[html] [pdf]
[png] [pdf]
[txt] [svg]


heatmap

? Conserved, identified interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Sort by selecting a column name:
Rank CopraRNA p-value CopraRNA fdr value Locus Tag Gene Name Energy [kcal/mol] IntaRNA p-value Position mRNA Position sRNA Annotation Additional homologs
1 2.411e-07 0.0007914 b0889 lrp -21.69 0.000065 168 -- 212 1 -- 64 leucine-responsive global transcriptional regulator  
2 1.932e-06 0.003171 b1243 oppA -16.40 0.003005 12 -- 82 1 -- 59 oligopeptide ABC transporter periplasmic binding protein  
3 3.826e-06 0.004187 b0090 murG -16.88 0.002220 177 -- 235 1 -- 51 N-acetylglucosaminyl transferase  
4 6.512e-06 0.005344 b0929 ompF -18.50 0.000749 185 -- 210 1 -- 33 outer membrane porin 1a (Ia;b;F)  
5 3.022e-05 0.01984 b4553 ysaB -16.91 0.002179 166 -- 209 3 -- 54 uncharacterized protein  
6 0.0001423 0.07172 b3183 obgE -17.58 0.001399 174 -- 220 1 -- 51 GTPase involved in cell partioning and DNA repair  
7 0.0001529 0.07172 b0687 seqA -15.48 0.005290 212 -- 226 5 -- 19 negative modulator of initiation of replication  
8 0.0001978 0.08119 b3391 hofQ -22.13 0.000045 16 -- 73 27 -- 88 DNA catabolic putative fimbrial transporter  
9 0.000223 0.08136 b1826 mgrB -16.34 0.003128 178 -- 244 1 -- 63 regulatory peptide for PhoPQ feedback inhibition  
10 0.0003219 0.1057 b2727 hypB -18.91 0.000562 181 -- 230 1 -- 53 GTP hydrolase involved in nickel liganding into hydrogenases  
11 0.0003561 0.1063 b3857 mobA -16.95 0.002119 239 -- 276 15 -- 59 molybdopterin-guanine dinucleotide synthase  
12 0.000426 0.1165 b2331 smrB -16.71 0.002472 163 -- 205 16 -- 57 putative DNA endonuclease  
13 0.0005091 0.1286 b2062 wza -15.65 0.004784 187 -- 207 5 -- 27 colanic acid export protein; outer membrane auxillary lipoprotein  
14 0.0005823 0.1358 b4348 hsdS -17.02 0.002033 190 -- 210 27 -- 58 specificity determinant for hsdM and hsdR  
15 0.0006204 0.1358 b0652 gltL -11.66 0.043639 269 -- 295 1 -- 25 glutamate/aspartate ABC transporter ATPase  
16 0.0008012 0.1482 b2011 sbcB -16.25 0.003318 186 -- 217 24 -- 52 exodeoxyribonuclease I; exonuclease I  
17 0.000872 0.1482 b3940 metL -12.03 0.036099 191 -- 199 51 -- 59 Bifunctional aspartokinase/homoserine dehydrogenase 2  
18 0.0008759 0.1482 b3626 waaR -11.62 0.044565 224 -- 238 11 -- 25 lipopolysaccharide 1 2-glucosyltransferase; UDP-glucose:(glucosyl)LPS alpha-1 2-glucosyltransferase  
19 0.0008973 0.1482 b3964 yijD -17.08 0.001951 152 -- 223 2 -- 55 DUF1422 family inner membrane protein  
20 0.0009027 0.1482 b2696 csrA -13.42 0.017327 268 -- 280 48 -- 60 pleiotropic regulatory protein for carbon source metabolism  
21 0.001002 0.1516 b4045 yjbJ -13.25 0.018991 259 -- 290 28 -- 62 stress-induced protein UPF0337 family  
22 0.001016 0.1516 b0734 cydB -13.57 0.015928 285 -- 300 49 -- 64 cytochrome d terminal oxidase subunit II  
23 0.001279 0.1825 b0199 metN -18.57 0.000714 152 -- 205 7 -- 50 DL-methionine transporter subunit  
24 0.001422 0.1946 b0065 yabI -15.22 0.006192 70 -- 99 1 -- 29 DedA family inner membrane protein  
25 0.00149 0.1957 b4244 pyrI -16.22 0.003374 188 -- 229 11 -- 59 aspartate carbamoyltransferase regulatory subunit  
26 0.001686 0.211 b0091 murC -10.53 0.075719 174 -- 220 1 -- 48 UDP-N-acetylmuramate:L-alanine ligase  
27 0.001735 0.211 b3052 hldE -15.91 0.004078 227 -- 261 1 -- 47 heptose 7-phosphate kinase and heptose 1-phosphate adenyltransferase  
28 0.00198 0.2275 b2821 ptrA -8.02 0.226801 174 -- 191 5 -- 22 protease III  
29 0.00201 0.2275 b1479 maeA -13.16 0.019904 170 -- 200 29 -- 59 malate dehydrogenase decarboxylating NAD-requiring; malic enzyme  
30 0.002455 0.2686 b4551 yheV -11.67 0.043500 186 -- 213 38 -- 63 DUF2387 family putative metal-binding protein  
31 0.00291 0.3081 b1205 ychH -11.03 0.059536 152 -- 163 53 -- 64 DUF2583 family putative inner membrane protein  
32 0.003146 0.3086 b1553 rzpQ -12.95 0.022283 187 -- 223 23 -- 60 Rz-like protein Qin prophage  
33 0.003163 0.3086 b4372 holD -10.86 0.064637 82 -- 98 44 -- 58 DNA polymerase III psi subunit  
34 0.003196 0.3086 b0896 dmsC -10.70 0.070045 189 -- 235 4 -- 59 dimethyl sulfoxide reductase anaerobic subunit C  
35 0.003306 0.3101 b0551 quuD -13.48 0.016718 188 -- 210 3 -- 24 DLP12 prophage; putative antitermination protein  
36 0.003415 0.3114 b1849 purT -10.41 0.080237 8 -- 43 29 -- 56 phosphoribosylglycinamide formyltransferase 2  
37 0.00362 0.3212 b4479 dgoR -15.45 0.005416 239 -- 256 41 -- 57 D-galactonate catabolism operon transcriptional repressor  
38 0.003831 0.3287 b3739 atpI -13.67 0.015109 253 -- 271 1 -- 16 ATP synthase membrane-bound accessory factor  
39 0.003905 0.3287 b3541 dppD -12.54 0.027771 124 -- 154 26 -- 56 dipeptide/heme ABC transporter ATPas  
40 0.004127 0.3349 b1659 ydhB -12.78 0.024485 130 -- 177 1 -- 61 LysR family putative transcriptional regulator  
41 0.004182 0.3349 b3771 ilvD -12.17 0.033695 175 -- 200 14 -- 53 dihydroxyacid dehydratase  
42 0.004307 0.3367 b4051 qorA -12.29 0.031673 118 -- 140 3 -- 26 quinone oxidoreductase NADPH-dependent  
43 0.004693 0.3568 b1395 paaH -8.91 0.157263 246 -- 258 49 -- 61 3-hydroxyadipyl-CoA dehydrogenase NAD+-dependent  
44 0.004782 0.3568 b3243 aaeR -11.65 0.043804 4 -- 44 1 -- 57 transcriptional regulator for aaeXAB operon  
45 0.005107 0.3601 b0435 bolA -10.01 0.096403 160 -- 209 3 -- 59 stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC  
46 0.00512 0.3601 b2012 yeeD -13.46 0.016912 185 -- 206 3 -- 23 putative TusA family sulfurtransferase  
47 0.005156 0.3601 b2614 grpE -12.03 0.036099 152 -- 179 1 -- 26 heat shock protein  
48 0.005342 0.3653 b3380 yhfW -15.20 0.006283 218 -- 233 1 -- 15 phosphopentomutase-related metalloenzyme superfamily protein  
49 0.00563 0.3739 b2239 glpQ -9.17 0.140723 61 -- 103 1 -- 49 periplasmic glycerophosphodiester phosphodiesterase  
50 0.005695 0.3739 b1086 rluC -13.13 0.020232 139 -- 168 28 -- 55 23S rRNA pseudouridine(955 2504 2580) synthase  
51 0.006039 0.3887 b3822 recQ -9.34 0.130811 192 -- 200 50 -- 58 ATP-dependent DNA helicase  
52 0.0063 0.3902 b1473 yddG -8.84 0.162012 257 -- 264 2 -- 9 aromatic amino acid exporter  
53 0.006355 0.3902 b2916 argP -17.11 0.001913 217 -- 267 1 -- 51 transcriptional regulator for arginine transport and DNA replication genes; replication initiation inhibitor  
54 0.006418 0.3902 b0946 zapC -14.33 0.010402 184 -- 201 47 -- 63 FtsZ stabilizer  
55 0.006796 0.4056 b3192 mlaC -12.17 0.033659 167 -- 226 1 -- 57 ABC transporter maintaining OM lipid asymmetry periplasmic binding protein  
56 0.007094 0.4159 b1242 ychE -10.14 0.091024 67 -- 90 1 -- 23 UPF0056 family inner membrane protein  
57 0.007764 0.4472 b0585 fes -12.40 0.029926 182 -- 237 1 -- 55 enterobactin/ferrienterobactin esterase  
58 0.008338 0.4523 b2280 nuoJ -13.62 0.015495 7 -- 16 55 -- 64 NADH:ubiquinone oxidoreductase membrane subunit J  
59 0.008416 0.4523 b0566 envY -9.46 0.123665 249 -- 263 50 -- 64 porin thermoregulatory transcriptional activator b1499 b0564 b3515 b4116 b3516
60 0.008489 0.4523 b3912 cpxR -10.34 0.082729 218 -- 229 5 -- 16 response regulator in two-component regulatory system with CpxA  
61 0.008575 0.4523 b3464 ftsY -13.38 0.017655 71 -- 119 2 -- 50 Signal Recognition Particle (SRP) receptor  
62 0.008588 0.4523 b1746 astD -15.44 0.005443 188 -- 231 17 -- 59 succinylglutamic semialdehyde dehydrogenase  
63 0.008816 0.4523 b3600 mtlD -11.23 0.053963 184 -- 208 1 -- 23 mannitol-1-phosphate dehydrogenase NAD-dependent  
64 0.008913 0.4523 b4231 yjfF -11.33 0.051476 106 -- 140 1 -- 41 putative sugar ABC transporter permease  
65 0.009342 0.4523 b0871 poxB -9.00 0.151653 248 -- 256 51 -- 59 pyruvate dehydrogenase thiamine triphosphate-binding FAD-binding  
66 0.009484 0.4523 b4034 malE -12.98 0.021943 73 -- 123 2 -- 55 maltose transporter subunit  
67 0.009794 0.4523 b2823 ppdC -12.40 0.029910 245 -- 275 3 -- 28 putative prepilin peptidase-dependent protein  
68 0.00983 0.4523 b1321 ycjX -10.80 0.066674 34 -- 41 55 -- 62 DUF463 family protein puatative P-loop NTPase  
69 0.009861 0.4523 b0879 macB -12.35 0.030572 144 -- 182 1 -- 59 macrolide ABC transporter peremase/ATPase  
70 0.01004 0.4523 b1658 purR -15.06 0.006831 174 -- 223 1 -- 65 transcriptional repressor hypoxanthine-binding  
71 0.01035 0.4523 b3365 nirB -13.52 0.016420 166 -- 211 14 -- 63 nitrite reductase large subunit NAD(P)H-binding  
72 0.01058 0.4523 b3458 livK -8.91 0.157650 183 -- 215 28 -- 63 leucine transporter subunit  
73 0.01069 0.4523 b1949 fliQ -11.32 0.051762 219 -- 228 2 -- 11 flagellar biosynthesis protein  
74 0.0107 0.4523 b3385 gph -12.85 0.023515 41 -- 77 8 -- 48 phosphoglycolate phosphatase  
75 0.01076 0.4523 b4291 fecA -8.60 0.179326 183 -- 193 2 -- 12 TonB-dependent outer membrane ferric citrate transporter and signal transducer; ferric citrate extracelluar receptor; FecR-interacting protein  
76 0.01084 0.4523 b3990 thiH -9.70 0.111440 16 -- 25 55 -- 64 tyrosine lyase involved in thiamine-thiazole moiety synthesis  
77 0.01108 0.4523 b2099 yegU -9.55 0.118747 1 -- 10 2 -- 11 ADP-ribosylglycohydrolase family protein  
78 0.01113 0.4523 b2678 proW -13.08 0.020853 190 -- 200 49 -- 59 glycine betaine/proline ABC transporter permease  
79 0.01117 0.4523 b1593 ynfK -13.04 0.021217 188 -- 210 1 -- 21 putative dethiobiotin synthetase  
80 0.01119 0.4523 b0241 phoE -11.22 0.054424 189 -- 234 2 -- 43 outer membrane phosphoporin protein E  
81 0.01129 0.4523 b1718 infC -12.35 0.030679 105 -- 150 1 -- 56 translation initiation factor IF-3  
82 0.0113 0.4523 b3747 kup -9.05 0.148352 64 -- 70 53 -- 59 potassium transporter  
83 0.0117 0.4626 b1071 flgM -8.58 0.180603 153 -- 179 1 -- 25 anti-sigma factor for FliA (sigma 28)  
84 0.01184 0.4627 b3101 yqjF -11.66 0.043663 211 -- 235 1 -- 23 putative quinol oxidase subunit  
85 0.01268 0.4896 b1827 kdgR -11.91 0.038409 291 -- 299 56 -- 64 KDG regulon transcriptional repressor  
86 0.013 0.4962 b0451 amtB -9.48 0.122870 5 -- 23 1 -- 22 ammonium transporter  
87 0.01323 0.4992 b1951 rcsA -11.40 0.049597 149 -- 196 25 -- 65 transcriptional regulator of colanic acid capsular biosynthesis  
88 0.01388 0.5059 b3809 dapF -7.53 0.274407 192 -- 207 1 -- 17 diaminopimelate epimerase  
89 0.01433 0.5059 b0636 rlmH -12.18 0.033475 189 -- 207 1 -- 19 23S rRNA m(3)Psi1915 pseudouridine methyltransferase SAM-dependent  
90 0.01478 0.5059 b0740 tolB -11.20 0.054749 186 -- 207 1 -- 21 periplasmic protein  
91 0.01489 0.5059 b3805 hemC -12.98 0.021909 168 -- 195 24 -- 52 hydroxymethylbilane synthase  
92 0.01497 0.5059 b1902 ftnB -10.62 0.072498 12 -- 36 1 -- 25 ferritin B putative ferrous iron reservoir  
93 0.0151 0.5059 b1675 ydhZ -8.81 0.164498 185 -- 226 5 -- 54 uncharacterized protein  
94 0.01566 0.5059 b3918 cdh -10.38 0.081442 225 -- 238 1 -- 14 CDP-diacylglycerol phosphotidylhydrolase  
95 0.01574 0.5059 b2714 ascG -10.13 0.091468 184 -- 220 14 -- 55 asc operon transcriptional repressor; prpBC operon repressor  
96 0.01578 0.5059 b3283 yrdD -12.59 0.027007 10 -- 20 2 -- 12 ssDNA-binding protein function unknown  
97 0.01584 0.5059 b0116 lpd -10.63 0.072174 157 -- 204 5 -- 49 dihydrolipoyl dehydrogenase; E3 component of pyruvate and 2-oxoglutarate dehydrogenases complexes; glycine cleavage system L protein; dihydrolipoamide dehydrogenase  
98 0.01586 0.5059 b1860 ruvB -8.95 0.154425 184 -- 211 1 -- 30 ATP-dependent DNA helicase component of RuvABC resolvasome  
99 0.01587 0.5059 b2155 cirA -12.92 0.022646 275 -- 290 1 -- 16 colicin IA outer membrane receptor and translocator; ferric iron-catecholate transporter  
100 0.01591 0.5059 b0531 sfmC -11.86 0.039421 211 -- 227 6 -- 22 putative periplasmic pilus chaperone b4316
101 0.01605 0.5059 b3360 pabA -8.89 0.158482 100 -- 107 55 -- 62 aminodeoxychorismate synthase subunit II  
102 0.01618 0.5059 b3306 rpsH -10.04 0.095208 179 -- 210 1 -- 36 30S ribosomal subunit protein S8  
103 0.01627 0.5059 b3527 yhjJ -12.72 0.025178 191 -- 250 1 -- 59 putative periplasmic M16 family chaperone  
104 0.01633 0.5059 b3057 bacA -10.04 0.095309 188 -- 194 54 -- 60 undecaprenyl pyrophosphate phosphatase  
105 0.01645 0.5059 b0454 ybaZ -8.45 0.190978 84 -- 93 47 -- 56 excision repair protein alkyltransferase-like protein ATL  
106 0.01645 0.5059 b2416 ptsI -13.93 0.013056 96 -- 143 1 -- 59 PEP-protein phosphotransferase of PTS system (enzyme I)  
107 0.01649 0.5059 b0830 gsiB -12.67 0.025954 282 -- 298 1 -- 18 glutathione ABC transporter periplasmic binding protein  
108 0.01698 0.5123 b0078 ilvH -10.97 0.061484 141 -- 180 1 -- 51 acetolactate synthase 3 small subunit valine-sensitive  
109 0.01701 0.5123 b2075 mdtB -10.10 0.092694 6 -- 26 38 -- 56 multidrug efflux system subunit B  
110 0.01732 0.5155 b1800 dmlA -11.31 0.051964 127 -- 183 1 -- 58 D-malate oxidase NAD-dependent; putative tartrate dehydrogenase  
111 0.01748 0.5155 b4012 yjaB -9.42 0.126217 155 -- 212 1 -- 59 GNAT-family putative N-acetyltransferase; acetyl coenzyme A-binding protein  
112 0.01793 0.5155 b1418 cybB -10.08 0.093429 125 -- 145 33 -- 57 cytochrome b561  
113 0.01802 0.5155 b3910 yiiM -13.90 0.013248 191 -- 239 40 -- 92 6-N-hydroxylaminopurine resistance protein  
114 0.01806 0.5155 b3033 yqiB -9.53 0.119911 174 -- 206 15 -- 50 DUF1249 protein YqiB  
115 0.01846 0.5155 b4483 tatD -10.31 0.084235 251 -- 265 1 -- 13 quality control of Tat-exported FeS proteins; Mg-dependent cytoplasmic DNase  
116 0.01846 0.5155 b3349 slyD -11.19 0.055067 245 -- 274 8 -- 47 FKBP-type peptidyl prolyl cis-trans isomerase (rotamase)  
117 0.01855 0.5155 b3011 yqhD -12.43 0.029448 82 -- 109 34 -- 64 aldehyde reductase NADPH-dependent  
118 0.01863 0.5155 b0738 tolR -11.80 0.040697 190 -- 199 50 -- 59 membrane spanning protein in TolA-TolQ-TolR complex  
119 0.019 0.5155 b0904 focA -10.20 0.088413 192 -- 208 1 -- 18 formate channel  
120 0.01923 0.5155 b4004 zraR -8.11 0.219313 234 -- 248 1 -- 12 fused DNA-binding response regulator in two-component regulatory system with ZraS: response regulator/sigma54 interaction protein b2220
121 0.01924 0.5155 b0074 leuA -11.43 0.049038 243 -- 261 39 -- 56 2-isopropylmalate synthase  
122 0.01943 0.5155 b1842 holE -10.27 0.085496 209 -- 257 4 -- 63 DNA polymerase III theta subunit  
123 0.01951 0.5155 b0032 carA -10.10 0.092857 258 -- 264 55 -- 61 carbamoyl phosphate synthetase small subunit glutamine amidotransferase  
124 0.01977 0.5155 b1920 fliY -11.21 0.054671 192 -- 201 49 -- 58 cystine transporter subunit  
125 0.01993 0.5155 b2347 yfdC -8.10 0.220050 281 -- 291 15 -- 25 putative inner membrane protein  
126 0.01995 0.5155 b2452 eutH -9.16 0.141344 190 -- 206 5 -- 22 ethanolamine transporter  
127 0.01998 0.5155 b2922 yggE -8.69 0.172995 232 -- 253 1 -- 26 oxidative stress defense protein  
128 0.0201 0.5155 b2782 mazF -10.78 0.067406 32 -- 50 1 -- 23 mRNA interferase toxin antitoxin is MazE b4225
129 0.02061 0.5217 b0633 rlpA -9.57 0.117965 261 -- 273 1 -- 12 septal ring protein suppressor of prc minor lipoprotein  
130 0.02079 0.5217 b3455 livG -10.98 0.060940 96 -- 122 4 -- 29 branched-chain amino acid ABC transporter ATPase  
131 0.02082 0.5217 b2038 rfbC -12.83 0.023839 249 -- 268 2 -- 18 dTDP-4-deoxyrhamnose-3 5-epimerase  
132 0.0212 0.526 b2455 eutE -9.17 0.140915 224 -- 235 1 -- 12 aldehyde oxidoreductase ethanolamine utilization protein  
133 0.02154 0.526 b1105 lpoB -10.17 0.089721 187 -- 196 50 -- 59 OM lipoprotein stimulator of MrcB transpeptidase  
134 0.02184 0.526 b0034 caiF -11.03 0.059446 251 -- 259 1 -- 9 cai operon transcriptional activator  
135 0.02191 0.526 b1342 ydaN -17.19 0.001818 129 -- 197 1 -- 58 putative Zn(II) transporter  
136 0.02238 0.526 b1883 cheB -10.46 0.078180 185 -- 206 1 -- 23 fused chemotaxis regulator: protein-glutamate methylesterase in two-component regulatory system with CheA  
137 0.02279 0.526 b1739 osmE -8.84 0.162198 202 -- 246 21 -- 65 osmotically-inducible lipoprotein  
138 0.02287 0.526 b0081 mraZ -12.90 0.022954 180 -- 193 52 -- 64 RsmH methytransferase inhibitor  
139 0.0229 0.526 b3958 argC -10.25 0.086580 11 -- 36 23 -- 56 N-acetyl-gamma-glutamylphosphate reductase NAD(P)-binding  
140 0.02319 0.526 b3615 waaH -10.58 0.073933 178 -- 212 1 -- 47 LPS(HepIII)-glucuronic acid glycosyltransferase  
141 0.0236 0.526 b3339 tufA -10.69 0.070202 69 -- 84 1 -- 19 translation elongation factor EF-Tu 1 b3980
142 0.02395 0.526 b0192 nlpE -14.44 0.009771 167 -- 226 1 -- 55 lipoprotein involved with copper homeostasis and adhesion  
143 0.02405 0.526 b3292 zntR -11.17 0.055543 275 -- 285 1 -- 12 zntA gene transcriptional activator  
144 0.02445 0.526 b3441 yhhY -11.04 0.059403 187 -- 218 22 -- 53 aminoacyl nucleotide detoxifying acetyltransferase  
145 0.02447 0.526 b4518 ymdF -10.96 0.061577 258 -- 296 23 -- 64 KGG family protein  
146 0.02455 0.526 b0491 fetB -8.60 0.179526 114 -- 156 14 -- 57 iron export ABC transporter permease; peroxide resistance protein  
147 0.02463 0.526 b2830 rppH -8.72 0.170707 205 -- 218 1 -- 14 RNA pyrophosphohydrolase  
148 0.02477 0.526 b2262 menB -9.56 0.118602 261 -- 300 25 -- 56 dihydroxynaphthoic acid synthetase  
149 0.02481 0.526 b2108 yehA -13.80 0.014025 228 -- 241 1 -- 14 putative fimbrial-like adhesin protein  
150 0.02489 0.526 b2088 insE1 -9.25 0.136086 235 -- 276 1 -- 55 IS3 transposase A b0298 b0373 b0540 b1027
151 0.02491 0.526 b3575 yiaK -7.81 0.245984 13 -- 22 1 -- 10 2 3-diketo-L-gulonate reductase NADH-dependent  
152 0.02492 0.526 b3665 adeD -5.38 0.553104 121 -- 181 3 -- 52 cryptic adenine deaminase b4328
153 0.02513 0.526 b2745 truD -9.91 0.100940 94 -- 116 1 -- 24 tRNA(Glu) pseudouridine(13) synthase  
154 0.02518 0.526 b1602 pntB -9.01 0.150855 190 -- 197 52 -- 59 pyridine nucleotide transhydrogenase beta subunit  
155 0.02521 0.526 b4208 cycA -8.71 0.171102 175 -- 207 24 -- 51 D-alanine/D-serine/glycine transporter  
156 0.02543 0.526 b2805 fucR -9.08 0.146396 128 -- 135 52 -- 59 l-fucose operon activator  
157 0.02559 0.526 b2057 wcaC -8.75 0.168472 165 -- 205 16 -- 58 putative glycosyl transferase  
158 0.0258 0.526 b3738 atpB -11.34 0.051140 75 -- 89 1 -- 15 F0 sector of membrane-bound ATP synthase subunit a  
159 0.02583 0.526 b2572 rseA -12.83 0.023837 184 -- 236 1 -- 63 anti-sigma factor  
160 0.02589 0.526 b3297 rpsK -10.33 0.083340 178 -- 193 52 -- 64 30S ribosomal subunit protein S11  
161 0.02632 0.526 b3670 ilvN -9.27 0.134814 179 -- 196 49 -- 65 acetolactate synthase 1 small subunit  
162 0.02632 0.526 b1886 tar -10.00 0.096892 244 -- 251 53 -- 60 methyl-accepting chemotaxis protein II  
163 0.02649 0.526 b3156 yhbS -11.68 0.043230 178 -- 217 16 -- 53 GNAT family putative N-acetyltransferase  
164 0.02654 0.526 b3993 thiE -11.45 0.048376 123 -- 151 37 -- 65 thiamine phosphate synthase (thiamine phosphate pyrophosphorylase)  
165 0.02655 0.526 b2388 glk -7.68 0.259430 184 -- 233 1 -- 52 glucokinase  
166 0.02659 0.526 b1580 rspB -9.76 0.108040 184 -- 209 1 -- 29 putative Zn-dependent NAD(P)-binding oxidoreductase  
167 0.02708 0.531 b3705 yidC -10.20 0.088356 85 -- 115 24 -- 58 membrane protein insertase  
168 0.02737 0.531 b1385 feaB -11.89 0.038862 180 -- 210 1 -- 28 phenylacetaldehyde dehydrogenase  
169 0.02775 0.531 b2110 yehC -5.87 0.481945 191 -- 199 20 -- 28 putative periplasmic pilin chaperone  
170 0.02787 0.531 b3184 yhbE -10.77 0.067448 1 -- 31 11 -- 53 EamA family inner membrane putative transporter  
171 0.02792 0.531 b2754 ygbF -9.28 0.134010 284 -- 290 53 -- 59 CRISPR adaptation ssRNA endonuclease  
172 0.02805 0.531 b1912 pgsA -10.33 0.083391 160 -- 169 52 -- 61 phosphatidylglycerophosphate synthetase  
173 0.02817 0.531 b0952 pqiC -7.60 0.267291 63 -- 71 1 -- 9 DUF330 family putative lipoprotein  
174 0.02825 0.531 b2154 yeiG -9.96 0.098977 140 -- 169 15 -- 51 S-formylglutathione hydrolase  
175 0.0283 0.531 b2048 cpsG -16.42 0.002969 89 -- 138 17 -- 58 phosphomannomutase  
176 0.02871 0.5353 b0518 fdrA -11.39 0.049925 288 -- 297 6 -- 15 putative NAD(P)-binding acyl-CoA synthetase b0320
177 0.02886 0.5353 b2206 napA -7.95 0.233634 77 -- 89 1 -- 13 nitrate reductase periplasmic large subunit  
178 0.02931 0.5406 b3858 yihD -11.25 0.053413 186 -- 232 8 -- 55 DUF1040 protein YihD  
179 0.02973 0.5424 b2812 tcdA -11.60 0.044907 209 -- 228 1 -- 28 tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA  
180 0.02979 0.5424 b4217 ytfK -6.46 0.400721 35 -- 83 12 -- 56 DUF1107 family protein  
181 0.02995 0.5424 b0601 ybdM -11.52 0.046768 198 -- 207 55 -- 64 Spo0J family protein ParB-like nuclease domain  
182 0.03007 0.5424 b3131 agaR -10.52 0.076061 148 -- 177 28 -- 59 transcriptional repressor of the aga regulon  
183 0.03025 0.5427 b0999 cbpM -7.72 0.255487 289 -- 296 53 -- 60 modulator of CbpA co-chaperone  
184 0.03077 0.549 b1101 ptsG -13.95 0.012872 39 -- 58 1 -- 19 fused glucose-specific PTS enzymes: IIB component/IIC component  
185 0.03096 0.5492 b1686 menI -12.09 0.035132 263 -- 300 22 -- 58 1 4-dihydroxy-2-naphthoyl-CoA hydrolase  
186 0.03152 0.5492 b0922 mukF -11.29 0.052395 27 -- 43 42 -- 57 chromosome condensin MukBEF kleisin-like subunit binds calcium  
187 0.03165 0.5492 b2717 hycI -9.48 0.123006 243 -- 251 1 -- 9 protease involved in processing C-terminal end of HycE  
188 0.03165 0.5492 b3247 rng -10.28 0.085420 187 -- 220 10 -- 64 ribonuclease G  
189 0.03168 0.5492 b1533 eamA -9.19 0.139150 178 -- 226 1 -- 49 cysteine and O-acetyl-L-serine efflux system  
190 0.03178 0.5492 b2266 elaB -7.52 0.274944 163 -- 222 3 -- 61 putative membrane-anchored DUF883 family ribosome-binding protein  
191 0.03238 0.5507 b0445 ybaE -8.08 0.221556 124 -- 136 4 -- 16 putative ABC transporter periplasmic binding protein  
192 0.03268 0.5507 b3532 bcsB -10.41 0.080313 186 -- 199 1 -- 12 regulator of cellulose synthase cyclic di-GMP binding  
193 0.03268 0.5507 b2513 yfgM -8.78 0.166450 282 -- 288 52 -- 58 ancillary SecYEG translocon subunit; putative anti-RcsB factor  
194 0.03269 0.5507 b2049 cpsB -9.94 0.099932 179 -- 235 1 -- 54 mannose-1-phosphate guanyltransferase  
195 0.03271 0.5507 b3213 gltD -10.79 0.067022 188 -- 211 38 -- 59 glutamate synthase 4Fe-4S protein small subunit  
196 0.0332 0.554 b0128 yadH -11.13 0.056665 104 -- 121 39 -- 55 putative ABC transporter permease  
197 0.03325 0.554 b4139 aspA -12.92 0.022631 26 -- 66 25 -- 59 aspartate ammonia-lyase  
198 0.03373 0.5555 b3915 fieF -7.92 0.235762 278 -- 297 1 -- 19 ferrous iron and zinc transporter  
199 0.03375 0.5555 b3860 dsbA -9.14 0.142422 273 -- 281 48 -- 56 periplasmic protein disulfide isomerase I  
200 0.03384 0.5555 b0316 yahB -11.86 0.039401 41 -- 57 47 -- 61 putative DNA-bindng transcriptional regulator b0504

Details of Selected Interaction Download Interaction Details 

mRNA

sRNA


		

		

		

		
		

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
			

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
			

		
 
		
		

		
		

		
		
		
		
Evolutionary conservation of mRNA targets
			(alignment generated with
			Jalview)

		
		
		
Evolutionary conservation of sRNA
			(alignment generated with
			Jalview)

		
		
		

		
	

	
	
	

	
	
	




			 
	





	
Job resubmission

	

		

			Use the following button if you want to resubmit the job with
			altered input or parameterization:
		

		

			
			Feeds the job parameters to the input page to resubmit the job.
			
		

	


	





	
de.NBI 
		usability assessment

	

		

			
				
				
			 
		

		

			Please 
			support us 
			by filling this 
			short quality survey 
			for evaluating this
			de.NBI
			service.
		

	





	





	
	
		 
		
When using CopraRNA please cite :







		 
	
	
	
		 
		



Results are computed with CopraRNA version 2.1.2



		 
	

			





	About this web server
	  | 
	version 5.0.9
	  | 
	Copyright © 2012 - 2024 Bioinformatics Group Freiburg
	  | 
	de.NBI
	  | 
	Imprint and Disclaimer