Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 7819033

Input and runtime details for job 7819033 (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 7819033 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:25:17 CET 2018
?Processing Started@ Fri Feb 16 15:25:46 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 21:05:24 CET 2018
?Post-Processing Finished@ Fri Feb 16 21:05:32 CET 2018
?Job Completed@ Fri Feb 16 21:05:57 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

The job description you specified

MicC


Output download complete results [zip]

Downloadable files

[csv]
[txt]
[csv]
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[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 0 0 b2215 ompC -25.52 0.000001 134 -- 186 1 -- 70 outer membrane porin protein C  
2 3.183e-05 0.03921 b0889 lrp -15.78 0.004789 150 -- 212 1 -- 70 leucine-responsive global transcriptional regulator  
3 3.498e-05 0.03921 b4255 rraB -13.36 0.020838 142 -- 156 41 -- 54 protein inhibitor of RNase E  
4 6.145e-05 0.05167 b4217 ytfK -14.33 0.011783 150 -- 205 11 -- 68 DUF1107 family protein  
5 0.0001064 0.07159 b1784 yeaH -10.63 0.089613 150 -- 205 1 -- 57 UPF0229 family protein  
6 0.0002023 0.1081 b1884 cheR -8.31 0.257615 184 -- 205 1 -- 21 chemotaxis regulator protein-glutamate methyltransferase  
7 0.0002249 0.1081 b4032 malG -16.06 0.003987 187 -- 221 31 -- 65 maltose transporter subunit  
8 0.0003008 0.1262 b3191 mlaB -9.66 0.142648 16 -- 23 51 -- 58 ABC transporter maintaining OM lipid asymmetry cytoplasmic STAS component  
9 0.0003848 0.1262 b2708 srlQ -10.45 0.097910 5 -- 28 40 -- 60 D-arabinose 5-phosphate isomerase  
10 0.0004066 0.1262 b3429 glgA -9.74 0.137242 173 -- 185 51 -- 64 glycogen synthase  

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)

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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2