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
131 0.007315 0.1966 b3824 rhtB -9.48 0.174149 77 -- 100 63 -- 87 homoserine homoserine lactone and S-methyl-methionine efflux pump  
132 0.007501 0.1993 b1947 fliO -6.89 0.474041 212 -- 250 53 -- 93 flagellar biosynthesis protein  
133 0.007533 0.1993 b2194 ccmH -11.64 0.067570 191 -- 199 1 -- 9 heme lyase CcmH subunit  
134 0.007678 0.1993 b3139 agaC -7.83 0.338422 255 -- 275 57 -- 74 N-acetylgalactosamine-specific enzyme IIC component of PTS  
135 0.007679 0.1993 b0096 lpxC -11.14 0.084212 289 -- 298 76 -- 85 UDP-3-O-acyl N-acetylglucosamine deacetylase  
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  
138 0.007886 0.2012 b3991 thiG -13.21 0.033127 237 -- 259 64 -- 85 thiamine biosynthesis ThiGH complex subunit  
139 0.008022 0.2031 b0311 betA -9.91 0.144745 36 -- 54 64 -- 80 choline dehydrogenase a flavoprotein  
140 0.008117 0.2031 b3221 yhcH -13.19 0.033484 158 -- 212 34 -- 73 DUF386 family protein cupin superfamily  

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