Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1654565

Input and runtime details for job 1654565 (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 1654565 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:23:36 CET 2018
?CopraRNA Started@ Fri Feb 16 15:24:05 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 22:25:53 CET 2018
?Post-Processing Finished@ Fri Feb 16 22:26:01 CET 2018
?Job Completed@ Fri Feb 16 22:26:34 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1654565&toolName=CopraRNA ( 30 days expiry )

Description of the job

FnrS

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
196 0.008885 0.1548 b3052 hldE -13.36 0.014255 113 -- 160 38 -- 93 heptose 7-phosphate kinase and heptose 1-phosphate adenyltransferase  
151 0.005924 0.1368 b3248 yhdE -13.35 0.014399 2 -- 41 1 -- 42 dTTP/UTP pyrophosphatase; m(5)UTP/m(5)CTP/pseudo-UTP pyrophosphatase  
143 0.005544 0.1363 b2936 loiP -13.30 0.014839 83 -- 152 1 -- 41 Phe-Phe periplasmic metalloprotease OM lipoprotein; low salt-inducible; Era-binding heat shock protein  
129 0.00462 0.126 b1795 yeaQ -13.29 0.014930 139 -- 150 70 -- 81 UPF0410 family protein  
69 0.001222 0.06239 b0699 ybfA -13.19 0.016050 183 -- 205 37 -- 62 DUF2517 family protein  
172 0.007014 0.1437 b3430 glgC -13.14 0.016567 21 -- 80 1 -- 39 glucose-1-phosphate adenylyltransferase  
125 0.004538 0.1258 b0951 pqiB -12.90 0.019327 185 -- 205 37 -- 57 paraquat-inducible SoxRS-regulated MCE domain protein  
198 0.008909 0.1548 b2205 napG -12.90 0.019402 153 -- 203 39 -- 89 ferredoxin-type protein  
27 0.0001238 0.01616 b0081 mraZ -12.77 0.021128 157 -- 196 45 -- 91 RsmH methytransferase inhibitor  
7 8.167e-06 0.003921 b1531 marA -12.70 0.022098 183 -- 204 40 -- 62 multiple antibiotic resistance transcriptional 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