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
?CopraRNA 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: https://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3202356&toolName=CopraRNA ( 30 days expiry )

Description of the job

GcvB

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_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
4 5.758e-05 0.04123 stm3564 livK -17.90 0.039430 157 -- 215 37 -- 90 leucine ABC transporter subunit substrate-binding protein LivK  
90 0.004161 0.1596 stm1124 putA -17.89 0.039481 159 -- 201 125 -- 168 trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase  
31 0.0007673 0.08814 stm0403 yajB -17.88 0.039643 23 -- 70 41 -- 90 ACP phosphodiesterase  
131 0.006551 0.1774 stm3217 aer -17.88 0.039631 254 -- 298 36 -- 77 senses cellular redox state or proton motive force; similar to E. coli aerotaxis sensor receptor flavoprotein (AAC76107.1); Blastp hit to AAC76107.1 (506 aa) 83% identity in aa 1 - 506  
6 7.515e-05 0.04123 stm0665 gltI -17.87 0.039793 157 -- 199 35 -- 81 glutamate/aspartate transporter  
170 0.009347 0.1945 stm0477 acrR -17.70 0.042454 229 -- 246 74 -- 91 DNA-binding transcriptional repressor AcrR  
2 2.663e-05 0.04123 stm2355 argT -17.69 0.042680 144 -- 202 34 -- 91 histidine ABC transporter substrate-binding protein HisJ  
123 0.006073 0.1758 stm4355 yjeS -17.69 0.042665 80 -- 140 31 -- 90 putative Fe-S protein  
26 0.0006768 0.08814 stm1365 ydiJ -17.55 0.045121 78 -- 116 57 -- 91 similar to E. coli putative oxidase (AAC74757.1); Blastp hit to AAC74757.1 (1018 aa) 88% identity in aa 1 - 1017  
132 0.006673 0.1774 stm2677 ffh -17.54 0.045291 232 -- 275 38 -- 86 4.5S-RNP 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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When using CopraRNA please cite :

Results are computed with CopraRNA version 2.1.2