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
?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
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  
92 0.004229 0.1596 stm0669 phoL -19.39 0.022083 221 -- 286 36 -- 89 putative phosphate starvation-inducible protein ATP-binding  
93 0.004254 0.1596 stm0408 secF -18.22 0.034847 7 -- 64 39 -- 91 protein-export membrane protein SecF  
94 0.0043 0.1596 stm3866 atpG -16.85 0.058909 206 -- 253 35 -- 80 F0F1 ATP synthase subunit gamma  
95 0.004301 0.1596 stm4114 pflD -11.77 0.360092 46 -- 100 34 -- 88 formate C-acetyltransferase stm0843
96 0.004303 0.1596 stm4243 yjbN -11.74 0.363864 272 -- 280 155 -- 163 tRNA dihydrouridine(20/20a) synthase DusA  
97 0.004849 0.1728 stm0832 ybiF -11.58 0.382043 25 -- 72 45 -- 91 threonine/homoserine exporter RhtA  
98 0.004857 0.1728 stm2811 proX -15.53 0.097032 195 -- 224 56 -- 84 glycine betaine ABC transporter substrate-binding protein  
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  
100 0.00495 0.1728 stm1879 ptrB -19.83 0.018631 144 -- 223 40 -- 120 oligopeptidase B  

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