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
61 0.005608 0.3084 b2174 lpxT -9.09 0.171357 170 -- 179 1 -- 10 lipid A 1-diphosphate synthase; undecaprenyl pyrophosphate:lipid A 1-phosphate phosphotransferase  
62 0.005646 0.3084 b1242 ychE -13.92 0.024785 141 -- 151 1 -- 11 UPF0056 family inner membrane protein  
63 0.0059 0.3087 b3834 ubiJ -8.76 0.193647 289 -- 295 4 -- 10 aerobic ubiquinone synthesis protein SCP2 family protein  
64 0.005939 0.3087 b3237 argR -9.39 0.153279 85 -- 104 1 -- 19 l-arginine-responsive arginine metabolism regulon transcriptional regulator  
65 0.005951 0.3087 b0064 araC -16.15 0.009664 167 -- 213 8 -- 48 ara regulon transcriptional activator; autorepressor  
66 0.006019 0.3087 b0223 yafJ -7.05 0.351504 68 -- 78 1 -- 10 type 2 glutamine amidotransferase family protein  
67 0.006163 0.3087 b0773 ybhB -10.36 0.105479 214 -- 228 7 -- 20 kinase inhibitor homolog UPF0098 family b0545
68 0.006348 0.3087 b1202 ycgV -6.40 0.429936 233 -- 244 4 -- 18 putative adhesin b2647
69 0.006491 0.3087 b3347 fkpA -11.66 0.062814 96 -- 113 4 -- 22 FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase)  
70 0.006501 0.3087 b3301 rplO -9.96 0.122936 194 -- 206 8 -- 20 50S ribosomal subunit protein L15  

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