Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1229462

Input and runtime details for job 1229462 (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 1229462 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:25:41 CET 2018
?CopraRNA Started@ Fri Feb 16 15:25:59 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 20:22:57 CET 2018
?Post-Processing Finished@ Fri Feb 16 20:23:04 CET 2018
?Job Completed@ Fri Feb 16 20:23:29 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1229462&toolName=CopraRNA ( 30 days expiry )

Description of the job

MicF

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
1 2.411e-07 0.0007914 b0889 lrp -21.69 0.000065 168 -- 212 1 -- 64 leucine-responsive global transcriptional regulator  
2 1.932e-06 0.003171 b1243 oppA -16.40 0.003005 12 -- 82 1 -- 59 oligopeptide ABC transporter periplasmic binding protein  
3 3.826e-06 0.004187 b0090 murG -16.88 0.002220 177 -- 235 1 -- 51 N-acetylglucosaminyl transferase  
4 6.512e-06 0.005344 b0929 ompF -18.50 0.000749 185 -- 210 1 -- 33 outer membrane porin 1a (Ia;b;F)  
5 3.022e-05 0.01984 b4553 ysaB -16.91 0.002179 166 -- 209 3 -- 54 uncharacterized protein  
6 0.0001423 0.07172 b3183 obgE -17.58 0.001399 174 -- 220 1 -- 51 GTPase involved in cell partioning and DNA repair  
7 0.0001529 0.07172 b0687 seqA -15.48 0.005290 212 -- 226 5 -- 19 negative modulator of initiation of replication  
8 0.0001978 0.08119 b3391 hofQ -22.13 0.000045 16 -- 73 27 -- 88 DNA catabolic putative fimbrial transporter  
9 0.000223 0.08136 b1826 mgrB -16.34 0.003128 178 -- 244 1 -- 63 regulatory peptide for PhoPQ feedback inhibition  
10 0.0003219 0.1057 b2727 hypB -18.91 0.000562 181 -- 230 1 -- 53 GTP hydrolase involved in nickel liganding into hydrogenases  

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