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
?CopraRNA 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/RetrieveResults.jsp?jobID=7819033&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicC

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
63 0.004757 0.2539 b1342 ydaN -13.10 0.024145 140 -- 198 7 -- 70 putative Zn(II) transporter  
147 0.01713 0.3828 b3354 yheU -14.93 0.008191 201 -- 276 7 -- 70 UPF0270 family protein  
70 0.005852 0.2791 b3524 yhjG -5.99 0.576071 198 -- 212 7 -- 18 putative inner membrane-anchored periplasmic AsmA family protein  
50 0.003719 0.237 b3705 yidC -9.36 0.163545 61 -- 100 7 -- 65 membrane protein insertase  
127 0.01373 0.3614 b0463 acrA -13.78 0.016343 252 -- 289 8 -- 54 multidrug efflux system  
167 0.01994 0.3993 b1982 amn -7.06 0.411594 174 -- 215 8 -- 54 AMP nucleosidase  
17 0.0007572 0.1438 b2512 bamB -10.25 0.108120 60 -- 97 8 -- 56 BamABCDE complex OM biogenesis lipoprotein  
61 0.004706 0.2539 b3713 chrR -11.93 0.045896 122 -- 163 8 -- 58 chromate reductase Class I flavoprotein  
189 0.02329 0.4145 b1823 cspC -8.37 0.250499 214 -- 248 8 -- 63 stress protein member of the CspA-family  
115 0.0114 0.3326 b2531 iscR -8.61 0.227442 42 -- 64 8 -- 31 isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress- and iron starvation-inducible; autorepressor  

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

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Feeds the job parameters to the input page to resubmit the job.

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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2