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
160 0.006309 0.1377 b2602 yfiL -11.97 0.035037 175 -- 199 46 -- 76 lipoprotein  
78 0.001866 0.08273 b2952 yggT -14.70 0.005634 84 -- 104 37 -- 56 putative inner membrane protein; compensates for loss in K+ uptake  
148 0.005829 0.1368 b2962 yggX -8.12 0.280656 21 -- 35 68 -- 81 oxidative damage protective factor for iron-sulfur proteins  
70 0.001371 0.06901 b2989 yghU -9.78 0.124117 251 -- 269 4 -- 23 putative S-transferase  
80 0.001886 0.08273 b3205 yhbJ -9.88 0.117656 21 -- 27 1 -- 7 adaptor protein for GlmZ/GlmY sRNA decay glucosamine-6-phosphate-regulated; NTPase  
113 0.00365 0.1131 b3154 yhbP -10.91 0.065979 249 -- 297 26 -- 85 UPF0306 family protein  
108 0.003432 0.1114 b3159 yhbV -7.84 0.318675 148 -- 178 4 -- 39 U32 peptidase family protein  
139 0.00529 0.1336 b3211 yhcC -9.14 0.172713 199 -- 227 39 -- 75 putative Fe-S oxidoreductase Radical SAM superfamily protein  
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  
93 0.002751 0.1042 b3407 yhgF -15.01 0.004479 248 -- 282 1 -- 31 putative transcriptional accessory protein  

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