Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1786318

Input and runtime details for job 1786318 (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 1786318 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:20:27 CET 2018
?Processing Started@ Fri Feb 16 15:20:56 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 22:01:46 CET 2018
?Post-Processing Finished@ Fri Feb 16 22:01:53 CET 2018
?Job Completed@ Fri Feb 16 22:02:22 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=1786318&toolName=CopraRNA ( 30 days expiry )

The job description you specified

ArcZ


Output download complete results [zip]

Downloadable files

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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
81 0.004478 0.1855 b3327 gspF -8.77 0.233220 243 -- 251 26 -- 34 general secretory pathway component cryptic  
104 0.005642 0.1855 b1476 fdnI -8.74 0.236866 280 -- 291 51 -- 62 formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible  
64 0.003238 0.1727 b2578 eamB -8.70 0.240388 240 -- 262 70 -- 85 cysteine and O-acetylserine exporter  
162 0.009519 0.2068 b4167 nnr -8.70 0.240671 167 -- 176 76 -- 85 bifunctional NAD(P)H-hydrate repair enzyme; C-terminal domain ADP-dependent (S)-NAD(P)H-hydrate dehydratase and N-terminal domain NAD(P)H-hydrate epimerase  
101 0.005473 0.1855 b1129 phoQ -8.66 0.244665 211 -- 219 79 -- 87 sensory histidine kinase in two-component regulatory system with PhoP  
136 0.007706 0.1993 b2188 yejM -8.60 0.250530 107 -- 119 70 -- 83 essential inner membrane DUF3413 domain-containing protein; lipid A production and membrane permeability factor  
137 0.007754 0.1993 b4024 lysC -8.53 0.257132 131 -- 141 73 -- 85 lysine-sensitive aspartokinase 3  
147 0.008705 0.2059 b0071 leuD -8.42 0.269085 76 -- 114 1 -- 54 3-isopropylmalate dehydratase small subunit  
107 0.005754 0.1855 b3447 ggt -8.41 0.270031 252 -- 270 52 -- 70 gamma-glutamyltranspeptidase  
149 0.008735 0.2059 b3088 alx -8.37 0.274530 278 -- 288 25 -- 35 putative membrane-bound redox modulator  

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)

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Results are computed with CopraRNA version 2.1.2