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

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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
21 0.0009524 0.1536 b0241 phoE -11.39 0.070016 174 -- 180 5 -- 11 outer membrane phosphoporin protein E b0929 b2215 b1377
22 0.001004 0.1545 b0583 entD -18.10 0.004183 41 -- 63 1 -- 22 phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex  
23 0.001384 0.1943 b0399 phoB -10.33 0.106753 53 -- 63 8 -- 18 response regulator in two-component regulatory system with PhoR  
24 0.001508 0.1943 b0150 fhuA -11.07 0.079438 192 -- 210 5 -- 21 ferrichrome outer membrane transporter  
25 0.001519 0.1943 b2817 amiC -17.97 0.004427 110 -- 131 1 -- 21 N-acetylmuramoyl-L-alanine amidase  
26 0.001545 0.1943 b1678 ldtE -10.42 0.102915 208 -- 217 2 -- 11 murein L D-transpeptidase  
27 0.001549 0.1943 b0440 hupB -11.81 0.059023 134 -- 149 5 -- 20 HU DNA-binding transcriptional regulator beta subunit  
28 0.001743 0.2094 b2308 hisQ -15.00 0.015715 1 -- 16 7 -- 21 histidine ABC transporter permease  
29 0.001844 0.2094 b2047 wcaJ -13.26 0.032615 200 -- 222 7 -- 21 colanic biosynthesis UDP-glucose lipid carrier transferase  
30 0.001906 0.2094 b0616 citE -12.56 0.043465 103 -- 116 8 -- 21 citrate lyase citryl-ACP lyase (beta) 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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Feeds the job parameters to the input page to resubmit the job.

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Results are computed with CopraRNA version 2.1.2