Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 3202356

Input and runtime details for job 3202356 (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 3202356 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:24:02 CET 2018
?Processing Started@ Fri Feb 16 15:24:35 CET 2018
?CopraRNA Finished & Post-Processing@ Sat Feb 17 02:03:47 CET 2018
?Post-Processing Finished@ Sat Feb 17 02:03:55 CET 2018
?Job Completed@ Sat Feb 17 02:04:28 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de:80/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

The job description you specified

GcvB


Output download complete results [zip]

Downloadable files

[csv]
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heatmap

? Conserved, identified interactions for NC_003197 NC_003277 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2

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
151 0.00796 0.1845 stm2365 folC -10.71 0.491716 269 -- 300 50 -- 78 bifunctional tetrahydrofolate synthase/dihydrofolate synthase  
152 0.008087 0.1845 stm0213 dapD -12.65 0.271269 222 -- 289 49 -- 104 2 3 4 5-tetrahydropyridine-2 6-dicarboxylate N-succinyltransferase  
153 0.008123 0.1845 stm2512 xseA -14.57 0.138273 215 -- 252 42 -- 82 exodeoxyribonuclease VII large subunit  
154 0.008185 0.1845 stm3738 yigC -11.16 0.433331 228 -- 246 55 -- 74 similar to E. coli orf hypothetical protein (AAC76670.1); Blastp hit to AAC76670.1 (223 aa) 94% identity in aa 19 - 223  
155 0.008213 0.1845 stm3112 mltC -21.66 0.009126 170 -- 198 62 -- 90 murein transglycosylase C  
156 0.008228 0.1845 stm1715 yciN -28.69 0.000575 104 -- 163 36 -- 90 similar to E. coli orf hypothetical protein (AAC74355.1); Blastp hit to AAC74355.1 (83 aa) 92% identity in aa 1 - 83  
157 0.008234 0.1845 stm0693 fur -16.04 0.080078 199 -- 253 31 -- 90 ferric iron uptake transcriptional regulator  
158 0.00827 0.1845 stm1712 acnA -14.47 0.143385 236 -- 294 48 -- 104 aconitate hydratase 1  
159 0.008305 0.1845 stm3625 yhjV -13.06 0.235438 203 -- 240 55 -- 86 transporter  
160 0.008331 0.1845 stm0002 thrA -15.10 0.113872 18 -- 81 44 -- 90 bifunctional aspartate kinase/homoserine dehydrogenase I  

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