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

[csv]
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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
88 0.004799 0.1855 b2213 ada -9.32 0.185618 222 -- 245 63 -- 86 fused DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase  
87 0.004792 0.1855 b0476 aes -9.71 0.157345 34 -- 55 56 -- 76 acetyl esterase  
134 0.007678 0.1993 b3139 agaC -7.83 0.338422 255 -- 275 57 -- 74 N-acetylgalactosamine-specific enzyme IIC component of PTS  
12 0.0004488 0.1198 b3133 agaV -20.63 0.001136 94 -- 118 64 -- 86 N-acetylgalactosamine-specific enzyme IIB component of PTS  
75 0.003854 0.1809 b0606 ahpF -8.17 0.297536 59 -- 82 64 -- 85 alkyl hydroperoxide reductase F52a subunit FAD/NAD(P)-binding  
171 0.01011 0.2071 b4086 alsC -10.38 0.118114 189 -- 207 53 -- 70 D-allose ABC transporter permease  
149 0.008735 0.2059 b3088 alx -8.37 0.274530 278 -- 288 25 -- 35 putative membrane-bound redox modulator  
106 0.005731 0.1855 b0867 amiD -15.82 0.010089 39 -- 60 64 -- 86 1 6-anhydro-N-acetylmuramyl-L-alanine amidase Zn-dependent; OM lipoprotein  
46 0.002359 0.1727 b4139 aspA -15.43 0.012067 239 -- 273 37 -- 76 aspartate ammonia-lyase  
43 0.002187 0.1727 b2222 atoA -7.38 0.400797 260 -- 273 68 -- 82 acetyl-CoA:acetoacetyl-CoA transferase beta subunit  

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