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
171 0.01687 0.3104 b1512 lsrR -11.43 0.068975 231 -- 262 7 -- 31 lsr operon transcriptional repressor b4295
172 0.01719 0.3104 b0678 nagB -13.42 0.030481 5 -- 26 1 -- 17 glucosamine-6-phosphate deaminase  
173 0.0173 0.3104 b0145 dksA -10.49 0.099910 175 -- 187 5 -- 21 transcriptional regulator of rRNA transcription; DnaK suppressor protein  
174 0.01734 0.3104 b3470 tusA -9.03 0.174990 268 -- 281 8 -- 22 mnm(5)-s(2)U34-tRNA 2-thiolation sulfurtransferase  
175 0.01743 0.3104 b0921 smtA -12.81 0.039244 146 -- 164 2 -- 20 putative S-adenosyl-L-methionine-dependent methyltransferase  
176 0.01748 0.3104 b0435 bolA -9.78 0.131850 202 -- 220 4 -- 22 stationary-phase morphogene transcriptional repressor for mreB; also regulator for dacA dacC and ampC  
177 0.01751 0.3104 b2900 yqfB -9.18 0.165418 52 -- 70 1 -- 17 UPF0267 family protein  
178 0.01756 0.3104 b2017 yefM -12.99 0.036476 219 -- 231 5 -- 18 antitoxin of the YoeB-YefM toxin-antitoxin system  
179 0.01766 0.3104 b0377 sbmA -9.49 0.147268 6 -- 15 3 -- 12 peptide antibiotic transporter b1496
180 0.01774 0.3104 b0593 entC -14.03 0.023631 112 -- 128 4 -- 19 isochorismate synthase 1  

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