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
41 0.00276 0.2279 b0889 lrp -10.49 0.100208 207 -- 221 8 -- 21 leucine-responsive global transcriptional regulator  
42 0.002847 0.2296 b1638 pdxH -9.07 0.172497 29 -- 35 5 -- 11 pyridoxine 5'-phosphate oxidase  
43 0.003009 0.2325 b3429 glgA -8.59 0.206361 152 -- 163 7 -- 22 glycogen synthase  
44 0.003062 0.2325 b3847 pepQ -9.98 0.122201 144 -- 157 8 -- 21 proline dipeptidase  
45 0.00309 0.2325 b0584 fepA -13.78 0.026215 91 -- 106 1 -- 17 ferrienterobactin outer membrane transporter  
46 0.003408 0.2484 b2518 ndk -12.77 0.039848 1 -- 16 7 -- 21 multifunctional nucleoside diphosphate kinase and apyrimidinic endonuclease and 3'-phosphodiesterase  
47 0.003448 0.2484 b0614 citX -10.13 0.115098 76 -- 91 4 -- 17 apo-citrate lyase phosphoribosyl-dephospho-CoA transferase  
48 0.00405 0.2857 b0409 secF -13.37 0.031213 166 -- 172 5 -- 11 SecYEG protein translocase auxillary subunit  
49 0.004401 0.299 b0093 ftsQ -10.19 0.112476 259 -- 274 4 -- 20 divisome assembly protein membrane anchored protein involved in growth of wall at septum  
50 0.004415 0.299 b0752 zitB -14.03 0.023662 243 -- 258 5 -- 21 zinc efflux system  

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