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
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  
52 0.001934 0.1324 stm0653 ybeL -17.18 0.051878 262 -- 299 155 -- 188 similar to E. coli putative alpha helical protein (AAC73744.1); Blastp hit to AAC73744.1 (160 aa) 91% identity in aa 1 - 160  
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  
70 0.003306 0.1596 stm2688 smpB -12.25 0.308628 191 -- 230 36 -- 77 SsrA-binding protein  
113 0.005549 0.1728 stm2948 cysJ -13.61 0.194760 269 -- 298 56 -- 85 sulfite reductase [NADPH] flavoprotein subunit alpha  
176 0.009613 0.1945 stm3378 N/A -14.56 0.138793 155 -- 243 45 -- 125 sulfoxide reductase heme-binding subunit YedZ  
73 0.003444 0.1596 stm1437 ydhM -18.33 0.033340 6 -- 47 35 -- 81 TetR family transcriptional regulator  
97 0.004849 0.1728 stm0832 ybiF -11.58 0.382043 25 -- 72 45 -- 91 threonine/homoserine exporter RhtA  
104 0.005232 0.1728 stm0744 ybgC -16.85 0.058772 132 -- 175 54 -- 90 tol-pal system-associated acyl-CoA thioesterase  
127 0.006343 0.1774 stm1751 hns -12.42 0.292757 1 -- 14 147 -- 162 transcriptional regulator  

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