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]
[txt]
[csv]
[png] [pdf] [ps]
[png] [pdf] [ps]
[html] [pdf]
[png] [pdf]
[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
111 0.01125 0.3104 b0102 zapD -10.07 0.117779 99 -- 113 8 -- 22 FtsZ stabilizer  
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  
113 0.01159 0.3104 b1279 yciS -9.20 0.164515 90 -- 101 6 -- 18 DUF1049 family inner membrane protein function unknown  
114 0.01161 0.3104 b3392 hofP -8.60 0.204995 138 -- 147 1 -- 11 DNA catabolic protein  
115 0.01182 0.3104 b3367 nirC -10.39 0.104055 218 -- 233 4 -- 19 nitrite transporter  
116 0.01184 0.3104 b1218 chaC -12.45 0.045440 10 -- 29 8 -- 30 cation transport regulator  
117 0.01191 0.3104 b2137 yohF -11.08 0.079147 231 -- 259 5 -- 35 putative oxidoreductase  
118 0.01199 0.3104 b2573 rpoE -10.72 0.091300 77 -- 87 8 -- 18 RNA polymerase sigma E factor  
119 0.01215 0.3104 b3691 dgoT -8.17 0.239341 58 -- 68 8 -- 21 D-galactonate transporter  
120 0.01222 0.3104 b0916 ycaQ -9.32 0.156865 225 -- 243 1 -- 17 DUF1006 family protein with C-terminal wHTH domain  

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)

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:
Feeds the job parameters to the input page to resubmit the job.

de.NBI usability assessment

Please support us by filling this short quality survey for evaluating this de.NBI service.

When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2