Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1786318

Input and runtime details for job 1786318 (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 1786318 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:20:27 CET 2018
?Processing Started@ Fri Feb 16 15:20:56 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 22:01:46 CET 2018
?Post-Processing Finished@ Fri Feb 16 22:01:53 CET 2018
?Job Completed@ Fri Feb 16 22:02:22 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

The job description you specified

ArcZ


Output download complete results [zip]

Downloadable files

[csv]
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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
48 0.002388 0.1727 b2198 ccmD -12.59 0.043972 250 -- 282 36 -- 77 cytochrome c biogenesis protein; heme export ABC transporter holo-CcmE release factor  
16 0.0007867 0.1666 b2178 yejB -12.57 0.044336 179 -- 196 66 -- 82 microcin C ABC transporter permease  
23 0.001421 0.1727 b1234 rssA -12.55 0.044848 179 -- 192 61 -- 74 putative patatin-like family phospholipase  
19 0.001118 0.1727 b2455 eutE -12.39 0.048028 37 -- 59 68 -- 89 aldehyde oxidoreductase ethanolamine utilization protein  
116 0.006112 0.1855 b1260 trpA -12.39 0.048115 172 -- 199 63 -- 89 tryptophan synthase alpha subunit  
169 0.01004 0.2071 b2384 ypdE -12.38 0.048278 93 -- 137 31 -- 75 aminopeptidase b4305 b3898
35 0.001921 0.1727 b1849 purT -12.35 0.048961 166 -- 192 67 -- 88 phosphoribosylglycinamide formyltransferase 2  
63 0.003148 0.1727 b0131 panD -12.33 0.049519 276 -- 291 70 -- 84 aspartate 1-decarboxylase  
109 0.005919 0.1855 b3807 cyaY -12.33 0.049473 23 -- 64 29 -- 73 iron-dependent inhibitor of iron-sulfur cluster formation; frataxin; iron-binding and oxidizing protein  
74 0.003792 0.1804 b2520 yfhM -12.28 0.050623 263 -- 298 53 -- 91 bacterial alpha2-macroglobulin colonization factor ECAM; anti-host protease defense factor; periplasmic inner membrane-anchored lipoprotein  

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