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
131 0.01264 0.3104 b3412 bioH -11.05 0.080071 12 -- 32 7 -- 31 pimeloyl-ACP methyl ester carboxylesterase  
132 0.01286 0.3104 b3176 glmM -8.35 0.224806 246 -- 258 8 -- 20 phosphoglucosamine mutase  
133 0.01287 0.3104 b3179 rlmE -8.60 0.205247 24 -- 43 1 -- 17 23S rRNA U2552 2'-O-ribose methyltransferase SAM-dependent  
134 0.01294 0.3104 b2234 nrdA -13.57 0.028625 217 -- 231 7 -- 22 ribonucleoside-diphosphate reductase 1 alpha subunit  
135 0.01297 0.3104 b3409 feoB -9.25 0.161231 74 -- 82 5 -- 13 ferrous iron transporter protein B and GTP-binding protein; membrane protein  
136 0.01311 0.3104 b0694 kdpE -14.36 0.020608 275 -- 287 2 -- 14 response regulator in two-component regulatory system with KdpD  
137 0.01327 0.3104 b3858 yihD -10.36 0.105347 5 -- 11 5 -- 11 DUF1040 protein YihD  
138 0.01331 0.3104 b2897 sdhE -11.73 0.060976 261 -- 284 1 -- 21 flavinator of succinate dehydrogenase; antitoxin of CptAB toxin-antitoxin pair  
139 0.01337 0.3104 b1255 yciC -11.25 0.074167 287 -- 299 1 -- 13 UPF0259 family inner membrane protein  
140 0.01344 0.3104 b2388 glk -4.25 0.738023 201 -- 214 10 -- 20 glucokinase  

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