Freiburg RNA Tools
CopraRNA - Results
BIF
IFF
CopraRNA 1765463

Input and runtime details for job 1765463 (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 1765463 (server version trunk)

?Job Submitted & Queued@ Fri Feb 16 15:41:59 CET 2018
?CopraRNA Started@ Fri Feb 16 15:42:13 CET 2018
?CopraRNA Finished & Post-Processing@ Fri Feb 16 19:57:45 CET 2018
?Post-Processing Finished@ Fri Feb 16 19:57:53 CET 2018
?Job Completed@ Fri Feb 16 19:58:19 CET 2018
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1765463&toolName=CopraRNA ( 30 days expiry )

Description of the job

5 ChiX sequences

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
118 0.0238 0.6177 b3321 rpsJ -9.75 0.046314 151 -- 177 30 -- 55 30S ribosomal subunit protein S10  
152 0.03059 0.6177 b2609 rpsP -6.70 0.186060 187 -- 203 23 -- 53 30S ribosomal subunit protein S16  
173 0.03478 0.6177 b1234 rssA -4.70 0.418234 181 -- 188 43 -- 50 putative patatin-like family phospholipase  
163 0.03345 0.6177 b1235 rssB -5.20 0.346272 186 -- 195 44 -- 55 PcnB-degradosome interaction factor; response regulator  
161 0.03295 0.6177 b1630 rsxD -5.86 0.265655 34 -- 42 49 -- 57 SoxR iron-sulfur cluster reduction factor component; putative membrane protein of electron transport complex  
182 0.03771 0.6177 b0397 sbcC -11.00 0.025718 84 -- 100 39 -- 56 exonuclease dsDNA ATP-dependent  
112 0.02248 0.6177 b2796 sdaC -8.62 0.078257 115 -- 131 34 -- 50 putative serine transporter  
143 0.02773 0.6177 b0409 secF -7.84 0.111773 181 -- 195 43 -- 55 SecYEG protein translocase auxillary subunit  
138 0.02658 0.6177 b2331 smrB -9.17 0.060779 224 -- 232 45 -- 53 putative DNA endonuclease  
98 0.0193 0.6177 b2705 srlD -10.75 0.028892 101 -- 114 40 -- 53 sorbitol-6-phosphate dehydrogenase  

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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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2