Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 5882223

Input and runtime details for job 5882223 (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 5882223 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:29:59 CET 2018
?CopraRNA Started@ Fri Feb 16 20:39:56 CET 2018
?CopraRNA Finished & Post-Processing@ Sat Feb 17 03:02:39 CET 2018
?Post-Processing Finished@ Sat Feb 17 03:02:47 CET 2018
?Job Completed@ Sat Feb 17 03:03:15 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5882223&toolName=CopraRNA ( 30 days expiry )

Description of the job

Spot42

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
49 0.0005477 0.03933 b2715 ascF -9.59 0.059292 173 -- 180 1 -- 8 cellobiose/arbutin/salicin-specific PTS enzymes IIB and IC components  
75 0.001328 0.06227 b1748 astC -8.39 0.124654 121 -- 127 1 -- 7 succinylornithine transaminase PLP-dependent  
157 0.006279 0.1407 b0312 betB -8.02 0.153308 1 -- 12 52 -- 63 betaine aldehyde dehydrogenase NAD-dependent  
54 0.0007615 0.04961 b0313 betI -7.44 0.209816 47 -- 68 32 -- 57 choline-inducible betIBA-betT divergent operon transcriptional repressor  
23 0.0001777 0.02687 b0774 bioA -12.72 0.005870 209 -- 228 5 -- 24 7 8-diaminopelargonic acid synthase PLP-dependent  
45 0.0004826 0.03773 b4133 cadC -9.27 0.072737 38 -- 110 5 -- 66 cadBA operon transcriptional activator  
190 0.008456 0.1558 b0036 caiD -8.40 0.123663 110 -- 117 1 -- 8 carnitinyl-CoA dehydratase  
128 0.004347 0.1195 b3690 cbrA -9.56 0.060736 197 -- 211 17 -- 31 colicin M resistance protein; FAD-binding protein putative oxidoreductase  
121 0.004045 0.1176 b1738 chbB -6.64 0.311906 2 -- 15 34 -- 50 N N'-diacetylchitobiose-specific enzyme IIB component of PTS  
47 0.0005047 0.03778 b1888 cheA -10.26 0.037926 179 -- 191 53 -- 66 fused chemotactic sensory histidine kinase in two-component regulatory system with CheB and CheY: sensory histidine kinase/signal sensing protein  

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

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Feeds the job parameters to the input page to resubmit the job.

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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2