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
141 0.01345 0.3104 b3311 rpsQ -8.13 0.242987 140 -- 150 8 -- 18 30S ribosomal subunit protein S17  
142 0.01346 0.3104 b0729 sucD -11.71 0.061414 39 -- 57 3 -- 21 succinyl-CoA synthetase NAD(P)-binding alpha subunit  
143 0.01362 0.3104 b3284 smg -7.50 0.302399 64 -- 82 5 -- 21 DUF494 family putative periplasmic protein  
144 0.01383 0.3104 b1135 rluE -11.03 0.080673 174 -- 189 5 -- 20 23S rRNA pseudouridine(2457) synthase  
145 0.01404 0.3104 b0721 sdhC -10.79 0.088833 202 -- 215 9 -- 22 succinate dehydrogenase membrane subunit binds cytochrome b556  
146 0.01406 0.3104 b3831 udp -7.35 0.318150 153 -- 161 1 -- 9 uridine phosphorylase  
147 0.01411 0.3104 b0441 ppiD -10.51 0.099467 81 -- 98 3 -- 21 periplasmic folding chaperone has an inactive PPIase domain  
148 0.01421 0.3104 b2379 alaC -8.54 0.209762 290 -- 297 5 -- 12 glutamate-pyruvate aminotransferase; glutamic-pyruvic transaminase (GPT); alanine transaminase  
149 0.01422 0.3104 b0415 ribE -7.20 0.333957 258 -- 265 4 -- 11 riboflavin synthase beta chain  
150 0.01436 0.3104 b3951 pflD -11.87 0.057659 67 -- 75 5 -- 13 putative glycine radical domain-containing pyruvate formate-lyase b0823

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