Freiburg RNA Tools
CopraRNA - Results
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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]
[txt]
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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
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  
132 0.006673 0.1774 stm2677 ffh -17.54 0.045291 232 -- 275 38 -- 86 4.5S-RNP protein  
133 0.006689 0.1774 stm0831 dps -13.05 0.236755 141 -- 176 159 -- 184 DNA starvation/stationary phase protection protein Dps  
134 0.006725 0.1774 stm0546 fimD -17.45 0.046766 176 -- 200 37 -- 60 outer membrane usher protein stm0301 stm0175 stm4593 stm3638 stm0023
135 0.006796 0.1774 stm1044 sodC -14.39 0.147293 208 -- 244 43 -- 78 Gifsy-2 prophage superoxide dismutase precursor (Cu-Zn) stm1440 stm0924
136 0.006805 0.1774 stm2812 N/A -16.76 0.060981 84 -- 153 36 -- 90 MFS transporter  
137 0.006825 0.1774 stm1196 acpP -14.14 0.161333 197 -- 223 36 -- 60 acyl carrier protein  
138 0.007086 0.182 stm0624 citC -16.00 0.081371 136 -- 192 38 -- 93 [citrate (pro-3S)-lyase] ligase stm0058
139 0.007115 0.182 stm0826 ybiN -18.61 0.029895 232 -- 282 36 -- 90 23S rRNA (adenine(1618)-N(6))-methyltransferase  
140 0.007169 0.182 stm3126 N/A -18.02 0.037639 66 -- 114 39 -- 91 putative amino acid transporter  

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