Freiburg RNA Tools
CopraRNA - Results
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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
112 0.01125 0.3104 b2515 ispG -10.24 0.110168 132 -- 140 4 -- 12 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase  
101 0.01005 0.3104 b3288 fmt -10.27 0.109217 249 -- 255 5 -- 11 10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase  
169 0.01667 0.3104 b3575 yiaK -9.90 0.125874 198 -- 219 8 -- 29 2 3-diketo-L-gulonate reductase NADH-dependent  
86 0.008729 0.3104 b4213 cpdB -12.03 0.054140 68 -- 81 8 -- 21 2':3'-cyclic-nucleotide 2'-phosphodiesterase  
10 0.0002413 0.08171 b2594 rluD -15.70 0.011720 48 -- 64 5 -- 21 23S rRNA pseudouridine(1911 1915 1917) synthase  
144 0.01383 0.3104 b1135 rluE -11.03 0.080673 174 -- 189 5 -- 20 23S rRNA pseudouridine(2457) synthase  
133 0.01287 0.3104 b3179 rlmE -8.60 0.205247 24 -- 43 1 -- 17 23S rRNA U2552 2'-O-ribose methyltransferase SAM-dependent  
76 0.007084 0.3087 b4214 cysQ -5.34 0.578728 11 -- 17 26 -- 32 3'(2') 5'-bisphosphate nucleotidase  
151 0.01442 0.3104 b1395 paaH -15.43 0.013105 189 -- 216 8 -- 31 3-hydroxyadipyl-CoA dehydrogenase NAD+-dependent  
39 0.002561 0.2224 b3845 fadA -14.30 0.021162 112 -- 126 5 -- 20 3-ketoacyl-CoA thiolase (thiolase I)  

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