Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 6527768

Input and runtime details for job 6527768 (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 6527768 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:24:51 CET 2018
?Processing Started@ Fri Feb 16 15:25:20 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 20:38:58 CET 2018
?Post-Processing Finished@ Fri Feb 16 20:39:05 CET 2018
?Job Completed@ Fri Feb 16 20:39:38 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=6527768&toolName=CopraRNA ( 30 days expiry )

The job description you specified

MicA


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
161 0.01501 0.3104 b1709 btuD -8.32 0.227073 129 -- 137 1 -- 9 vitamin B12 ABC transporter ATPase  
162 0.01506 0.3104 b0871 poxB -6.02 0.481603 228 -- 255 23 -- 53 pyruvate dehydrogenase thiamine triphosphate-binding FAD-binding  
163 0.0151 0.3104 b1517 lsrF -8.60 0.205199 166 -- 179 8 -- 21 putative autoinducer-2 (AI-2) aldolase  
164 0.0157 0.3104 b1735 chbR -6.99 0.357617 139 -- 145 6 -- 12 repressor of chb operon for N N'-diacetylchitobiose utilization  
165 0.01591 0.3104 b4393 trpR -12.13 0.051953 230 -- 246 5 -- 21 transcriptional repressor tryptophan-binding  
166 0.01595 0.3104 b3560 glyQ -10.24 0.110293 22 -- 29 7 -- 14 glycine tRNA synthetase alpha subunit  
167 0.01599 0.3104 b4220 tamA -9.57 0.142740 193 -- 207 4 -- 21 translocation and assembly module for autotransporter export outer membrane subunit  
168 0.01645 0.3104 b3720 bglH -8.64 0.202347 15 -- 28 9 -- 22 carbohydrate-specific outer membrane porin cryptic  
169 0.01667 0.3104 b3575 yiaK -9.90 0.125874 198 -- 219 8 -- 29 2 3-diketo-L-gulonate reductase NADH-dependent  
170 0.01687 0.3104 b0033 carB -11.35 0.071227 1 -- 15 5 -- 17 carbamoyl-phosphate synthase large 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