Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 6793193

Input and runtime details for job 6793193 (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 6793193 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:27:03 CET 2018
?Processing Started@ Fri Feb 16 15:27:32 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 21:26:02 CET 2018
?Post-Processing Finished@ Fri Feb 16 21:26:10 CET 2018
?Job Completed@ Fri Feb 16 21:26:45 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=6793193&toolName=CopraRNA ( 30 days expiry )

The job description you specified

RprA


Output download complete results [zip]

Downloadable files

[csv]
[txt]
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[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 5.015e-10 1.765e-06 b0680 glnS -23.71 0.000006 155 -- 198 34 -- 77 glutamyl-tRNA synthetase  
2 1.464e-07 0.0002576 b2741 rpoS -16.90 0.006155 67 -- 107 33 -- 71 RNA polymerase sigma S (sigma 38) factor  
3 3.356e-06 0.003937 b3724 phoU -15.84 0.012477 157 -- 192 43 -- 78 negative regulator of PhoR/PhoB two-component regulator  
4 8.9e-06 0.006694 b3281 aroE -13.87 0.039990 230 -- 259 45 -- 75 dehydroshikimate reductase NAD(P)-binding  
5 9.512e-06 0.006694 b4006 purH -17.40 0.004319 188 -- 204 31 -- 46 IMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase  
6 1.32e-05 0.00774 b0475 hemH -21.46 0.000115 123 -- 162 34 -- 75 ferrochelatase  
7 1.819e-05 0.009142 b1849 purT -22.68 0.000026 168 -- 199 33 -- 74 phosphoribosylglycinamide formyltransferase 2  
8 3.984e-05 0.01752 b2752 cysD -11.53 0.128779 103 -- 132 45 -- 74 sulfate adenylyltransferase subunit 2  
9 4.743e-05 0.01855 b1204 pth -17.38 0.004387 162 -- 190 43 -- 74 peptidyl-tRNA hydrolase  
10 6.564e-05 0.0231 b3458 livK -17.14 0.005196 153 -- 196 35 -- 71 leucine transporter subunit  

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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Results are computed with CopraRNA version 2.1.2