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
121 0.01226 0.3104 b3209 elbB -12.57 0.043302 225 -- 240 4 -- 18 isoprenoid biosynthesis protein with amidotransferase-like domain  
122 0.01233 0.3104 b3599 mtlA -8.56 0.208645 247 -- 281 4 -- 32 mannitol-specific PTS enzyme: IIA IIB and IIC components  
123 0.01235 0.3104 b0097 secM -7.65 0.286972 189 -- 203 7 -- 21 regulator of secA translation  
124 0.0124 0.3104 b1860 ruvB -8.20 0.236824 252 -- 265 8 -- 20 ATP-dependent DNA helicase component of RuvABC resolvasome  
125 0.01241 0.3104 b0002 thrA -8.21 0.235915 191 -- 205 9 -- 21 Bifunctional aspartokinase/homoserine dehydrogenase 1  
126 0.01241 0.3104 b4379 yjjW -11.82 0.058804 207 -- 217 8 -- 18 putative pyruvate formate lyase activating enzyme  
127 0.01249 0.3104 b2964 nupG -12.57 0.043346 150 -- 164 1 -- 16 nucleoside transporter b2406
128 0.01258 0.3104 b0677 nagA -7.18 0.336330 272 -- 297 1 -- 22 N-acetylglucosamine-6-phosphate deacetylase  
129 0.01261 0.3104 b3025 qseB -10.92 0.084347 141 -- 152 5 -- 17 quorum sensing DNA-binding response regulator in two-component regulatory system with QseC  
130 0.01263 0.3104 b1952 dsrB -7.17 0.338083 230 -- 240 7 -- 18 uncharacterized 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)

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Results are computed with CopraRNA version 2.1.2