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]
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[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
1 0 0 b2687 luxS -86.29 0.000000 61 -- 132 1 -- 72 S-ribosylhomocysteine lyase  
4 4.059e-05 0.03436 b2748 ftsB -19.92 0.001892 154 -- 190 1 -- 44 cell division protein  
22 0.001004 0.1545 b0583 entD -18.10 0.004183 41 -- 63 1 -- 22 phosphopantetheinyltransferase component of enterobactin synthase multienzyme complex  
25 0.001519 0.1943 b2817 amiC -17.97 0.004427 110 -- 131 1 -- 21 N-acetylmuramoyl-L-alanine amidase  
59 0.005538 0.3084 b2812 tcdA -16.71 0.007603 29 -- 48 1 -- 19 tRNA threonylcarbamoyladenosine dehydratase; sulfur acceptor for CsdA  
65 0.005951 0.3087 b0064 araC -16.15 0.009664 167 -- 213 8 -- 48 ara regulon transcriptional activator; autorepressor  
14 0.0004057 0.09812 b0886 cydC -15.95 0.010534 194 -- 211 2 -- 21 glutathione/cysteine ABC transporter export permease/ATPase  
2 9.051e-06 0.01532 b2745 truD -15.77 0.011349 54 -- 69 2 -- 17 tRNA(Glu) pseudouridine(13) synthase  
10 0.0002413 0.08171 b2594 rluD -15.70 0.011720 48 -- 64 5 -- 21 23S rRNA pseudouridine(1911 1915 1917) synthase  
7 9.926e-05 0.04801 b1113 ldtC -15.69 0.011765 184 -- 223 1 -- 45 L D-transpeptidase linking Lpp to murein  

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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Results are computed with CopraRNA version 2.1.2