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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[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
28 0.001743 0.2094 b2308 hisQ -15.00 0.015715 1 -- 16 7 -- 21 histidine ABC transporter permease  
46 0.003408 0.2484 b2518 ndk -12.77 0.039848 1 -- 16 7 -- 21 multifunctional nucleoside diphosphate kinase and apyrimidinic endonuclease and 3'-phosphodiesterase  
105 0.01074 0.3104 b3791 wecE -13.91 0.024834 1 -- 12 7 -- 18 TDP-4-oxo-6-deoxy-D-glucose transaminase  
170 0.01687 0.3104 b0033 carB -11.35 0.071227 1 -- 15 5 -- 17 carbamoyl-phosphate synthase large subunit  
82 0.007621 0.3104 b3388 damX -7.48 0.304490 3 -- 13 8 -- 18 cell division protein that binds to the septal ring  
137 0.01327 0.3104 b3858 yihD -10.36 0.105347 5 -- 11 5 -- 11 DUF1040 protein YihD  
172 0.01719 0.3104 b0678 nagB -13.42 0.030481 5 -- 26 1 -- 17 glucosamine-6-phosphate deaminase  
179 0.01766 0.3104 b0377 sbmA -9.49 0.147268 6 -- 15 3 -- 12 peptide antibiotic transporter b1496
197 0.01929 0.3104 b2185 rplY -8.58 0.206984 8 -- 20 7 -- 19 50S ribosomal subunit protein L25  
116 0.01184 0.3104 b1218 chaC -12.45 0.045440 10 -- 29 8 -- 30 cation transport regulator  

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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Results are computed with CopraRNA version 2.1.2