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
71 0.003339 0.1596 stm0105 yabI -14.10 0.163814 151 -- 168 141 -- 162 similar to E. coli orf hypothetical protein (AAC73176.1); Blastp hit to AAC73176.1 (254 aa) 89% identity in aa 1 - 253  
91 0.004202 0.1596 stm0387 yaiI -16.26 0.073758 5 -- 45 23 -- 58 similar to E. coli orf hypothetical protein (AAC73490.1); Blastp hit to AAC73490.1 (192 aa) 89% identity in aa 41 - 191  
31 0.0007673 0.08814 stm0403 yajB -17.88 0.039643 23 -- 70 41 -- 90 ACP phosphodiesterase  
169 0.009276 0.1945 stm0495 ybaK -13.73 0.186840 16 -- 30 44 -- 58 aminoacyl-tRNA deacylase  
112 0.005549 0.1728 stm0602 ybdH -14.01 0.169356 159 -- 193 39 -- 79 oxidoreductase  
99 0.004942 0.1728 stm0604 ybdM -18.77 0.028138 203 -- 249 36 -- 81 similar to E. coli orf hypothetical protein (AAC73702.1); Blastp hit to AAC73702.1 (209 aa) 77% identity in aa 5 - 209  
191 0.01055 0.1967 stm0634 ybeF -18.83 0.027435 210 -- 262 35 -- 82 putative LysR family transcriptional regulator  
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  
102 0.005164 0.1728 stm0668 ybeY -18.23 0.034693 146 -- 193 37 -- 81 rRNA maturation RNase YbeY  
104 0.005232 0.1728 stm0744 ybgC -16.85 0.058772 132 -- 175 54 -- 90 tol-pal system-associated acyl-CoA thioesterase  

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