Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 5172788

Input and runtime details for job 5172788 (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 5172788 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:22:27 CET 2018
?CopraRNA Started@ Fri Feb 16 15:22:50 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 20:35:14 CET 2018
?Post-Processing Finished@ Fri Feb 16 20:35:22 CET 2018
?Job Completed@ Fri Feb 16 20:35:53 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5172788&toolName=CopraRNA ( 30 days expiry )

Description of the job

CyaR

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
42 0.000828 0.06626 b2129 yehX -13.83 0.023625 55 -- 85 15 -- 47 putative ABC transporter ATPase  
40 0.0008246 0.06626 b4019 metH -11.44 0.086775 244 -- 271 15 -- 42 homocysteine-N5-methyltetrahydrofolate transmethylase B12-dependent  
43 0.0008959 0.07003 b3068 mug -12.52 0.050096 232 -- 248 1 -- 17 G/U mismatch-specific DNA glycosylase; xanthine DNA glycosylase  
44 0.0009392 0.07174 b3453 ugpB -12.21 0.059079 239 -- 268 1 -- 32 sn-glycerol-3-phosphate ABC transporter periplasmic binding protein  
47 0.001093 0.07744 b0128 yadH -6.67 0.521304 272 -- 286 25 -- 36 putative ABC transporter permease  
45 0.001037 0.07744 b0857 potI -11.49 0.084883 37 -- 88 3 -- 46 putrescine ABC transporter permease  
53 0.001234 0.07744 b0884 infA -13.12 0.035785 57 -- 86 2 -- 40 translation initiation factor IF-1  
54 0.001244 0.07744 b1874 cutC -11.77 0.073856 3 -- 15 22 -- 35 copper homeostasis protein  
51 0.001198 0.07744 b2174 lpxT -10.53 0.132559 260 -- 270 31 -- 41 lipid A 1-diphosphate synthase; undecaprenyl pyrophosphate:lipid A 1-phosphate phosphotransferase  
52 0.001222 0.07744 b2217 rcsB -14.74 0.013297 68 -- 91 9 -- 38 response regulator in two-component regulatory system with RcsC and YojN  

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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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