Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 6527768

Input and runtime details for job 6527768 (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 6527768 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:24:51 CET 2018
?Processing Started@ Fri Feb 16 15:25:20 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 20:38:58 CET 2018
?Post-Processing Finished@ Fri Feb 16 20:39:05 CET 2018
?Job Completed@ Fri Feb 16 20:39:38 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

The job description you specified

MicA


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
11 0.0003246 0.08948 b2299 yfcD -11.11 0.078371 283 -- 295 5 -- 18 putative NUDIX hydrolase  
12 0.0003263 0.08948 b4036 lamB -12.21 0.050157 189 -- 218 8 -- 32 maltose outer membrane porin (maltoporin)  
13 0.0003435 0.08948 b2551 glyA -14.51 0.019315 147 -- 213 7 -- 69 serine hydroxymethyltransferase  
14 0.0004057 0.09812 b0886 cydC -15.95 0.010534 194 -- 211 2 -- 21 glutathione/cysteine ABC transporter export permease/ATPase  
15 0.000461 0.102 b2140 dusC -12.07 0.053129 194 -- 211 3 -- 22 tRNA-dihydrouridine synthase C  
16 0.0004819 0.102 b0957 ompA -13.00 0.036257 182 -- 195 8 -- 22 outer membrane protein A (3a;II*;G;d)  
17 0.0005644 0.1124 b0949 uup -13.14 0.034258 282 -- 297 4 -- 21 replication regulatory ABC-F family DNA-binding ATPase  
18 0.00061 0.1147 b2126 yehU -11.17 0.076396 235 -- 252 1 -- 18 inner membrane putative sensory kinase in two-component system with YehT  
19 0.0006629 0.1181 b2909 ygfB -11.13 0.077732 186 -- 206 4 -- 22 UPF0149 family protein  
20 0.0008552 0.1448 b4137 cutA -9.23 0.162618 220 -- 236 1 -- 16 divalent-cation tolerance protein copper sensitivity  

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