Freiburg RNA Tools
IntaRNA - Results
BIF
IFF

Main Menu

Freiburg RNA Tools

Interaction Prediction

Seq-Str Alignment

CRISPR

Sequence Design

Splicing

SNP & Mutation

Classification

Gene set extension

MoDPepInt Server

CPSP-Tools Server

Galaxy-FR

CMV server

Teaching

IntaRNA 4596356

Input and runtime details for job 4596356 (precomputed example)

Sequence Parameters

? Query ncRNA (short) in FASTA[.fa]
? Index first query position1
? Target RNA (long) in FASTA[.fa]
? Target NCBI RefSeq IDNC_000913
? All repliconsyes
? Extract sequences aroundstart codon
? nt upstream (1-300)75
? nt downstream (1-300)75
? Index first target position-75

Output Parameters

? Number of interactions per RNA pair1
? Suboptimal interaction overlap can overlap in query
? Max. interaction lengthnot provided
? Max. absolute energy of an interaction0
? Max. delta energy above mfe of an interaction100
? No lonely base pairsyes
? No GU at helix endsyes

Seed Parameters

? Min. number of basepairs in seed7
? Max. Number of mismatches in seed0
? Maximal energy0
? Minimal unpaired probability (per RNA)0
? Seed position (query)not provided
? Seed position (target)not provided
? Ignore seeds with GU base pairsno
? Ignore seeds with GU endsyes

Folding Parameters

? Temperature for energy computation37.0
? Access. query: folding window size150
? Access. query: max. basepair distance100
? Access. target: folding window size150
? Access. target: max. basepair distance100
? Energy parameter set (Vienna package) Turner model, 2004

Job ID 4596356 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:10:48 CET 2020
?IntaRNA Started@ Mon Jan 27 14:13:48 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:14:50 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:16:49 CET 2020
?Job Completed@ Mon Jan 27 14:17:02 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=4596356&toolName=IntaRNA ( 30 days expiry )

Description of the job

FnrS - E. coli

? Output [zip]

Downloadable files

[csv]
[png] [pdf]
[png] [pdf]
[txt]
[html] [pdf] [png]


heatmap

? Identified Interactions for NC_000913 Escherichia coli str. K-12 substr. MG1655

Sort by selecting a column name.
Target Start(T) End(T) Query Start(Q) End(Q) Energy p-value fdr gene annotation
b0483 -56 -16 FnrS 51 91 -15.77 0.0002842 0.5665147 ybaQ putative DNA-binding transcriptional regulator
b1847 -25 -11 FnrS 72 87 -15.67 0.0003127 0.5665147 yebF extracellular Colicin M immunity family protein
b1841 -43 4 FnrS 38 76 -15.32 0.000434 0.5665147 yobA CopC family protein
b0123 -50 -21 FnrS 1 31 -14.36 0.0010196 0.9422174 cueO multicopper oxidase (laccase)
b4002 -29 -18 FnrS 43 54 -13.88 0.0015278 0.9422174 zraP Zn-dependent periplasmic chaperone
b2501 -6 31 FnrS 55 94 -13.4 0.0022581 0.9422174 ppk polyphosphate kinase component of RNA degradosome
b2552 -31 24 FnrS 20 85 -13.23 0.0025851 0.9422174 hmp fused nitric oxide dioxygenase/dihydropteridine reductase 2
b0585 18 28 FnrS 46 56 -13.23 0.0025851 0.9422174 fes enterobactin/ferrienterobactin esterase
b2936 -58 -49 FnrS 1 10 -13.18 0.0026891 0.9422174 loiP Phe-Phe periplasmic metalloprotease OM lipoprotein low salt-inducible Era-binding heat shock protein
b2078 -48 -8 FnrS 53 92 -13.16 0.0027318 0.9422174 baeS sensory histidine kinase in two-component regulatory system with BaeR
b1943 -11 45 FnrS 4 56 -12.74 0.003784 0.9422174 fliK flagellar hook-length control protein
b1196 57 71 FnrS 42 55 -12.72 0.0038423 0.9422174 ycgY uncharacterized protein
b4236 56 68 FnrS 37 49 -12.7 0.0039014 0.9422174 cybC pseudogene truncated cytochrome b562 cytochrome b(562)
b4040 -14 8 FnrS 34 59 -12.6 0.0042095 0.9422174 ubiA p-hydroxybenzoate octaprenyltransferase
b2777 -4 8 FnrS 66 77 -12.41 0.0048567 0.9422174 queE 7-carboxy-7-deazaguanine synthase queosine biosynthesis
b1112 -36 -15 FnrS 1 22 -12.35 0.0050791 0.9422174 bhsA biofilm cell surface and signaling protein
b0699 -18 5 FnrS 37 62 -12.33 0.0051553 0.9422174 ybfA DUF2517 family protein
b3935 -3 27 FnrS 4 34 -12.15 0.0058894 0.9422174 priA Primosome factor n' (replication factor Y)
b1813 -10 28 FnrS 15 54 -12.15 0.0058894 0.9422174 nudL putative CoA pyrophosphohydrolase weak 3-phosphohydroxypyruvate phosphatase
b2513 -21 5 FnrS 37 63 -12.12 0.0060206 0.9422174 yfgM ancillary SecYEG translocon subunit putative anti-RcsB factor
b1478 -34 -5 FnrS 51 77 -12.07 0.0062452 0.9422174 adhP ethanol-active dehydrogenase/acetaldehyde-active reductase
b3441 -6 15 FnrS 41 58 -12.05 0.0063372 0.9422174 yhhY aminoacyl nucleotide detoxifying acetyltransferase
b1654 -13 6 FnrS 35 56 -11.95 0.0068158 0.9422174 grxD glutaredoxin-4
b0356 59 74 FnrS 4 20 -11.93 0.0069153 0.9422174 frmA alcohol dehydrogenase class III glutathione-dependent formaldehyde dehydrogenase
b1557 -63 -40 FnrS 69 91 -11.89 0.0071184 0.9422174 cspB Qin prophage cold shock protein
b3068 29 49 FnrS 66 90 -11.87 0.007222 0.9422174 mug G/U mismatch-specific DNA glycosylase xanthine DNA glycosylase
b1531 -18 2 FnrS 42 62 -11.77 0.0077608 0.9422174 marA multiple antibiotic resistance transcriptional regulator
b2210 -40 -33 FnrS 1 8 -11.75 0.0078728 0.9422174 mqo malate dehydrogenase FAD/NAD(P)-binding domain
b1869 66 73 FnrS 1 8 -11.72 0.0080437 0.9422174 yecN MAPEG family inner membrane protein
b3847 -56 4 FnrS 38 89 -11.7 0.0081594 0.9422174 pepQ proline dipeptidase
b0753 -64 -55 FnrS 1 10 -11.69 0.0082179 0.9422174 ybgS putative periplasmic protein
b3260 39 72 FnrS 3 35 -11.66 0.0083955 0.9422174 dusB tRNA-dihydrouridine synthase B
b1685 66 74 FnrS 1 9 -11.63 0.0085766 0.9422174 ydiH uncharacterized protein
b2531 -14 1 FnrS 44 57 -11.6 0.0087612 0.9422174 iscR isc operon transcriptional repressor suf operon transcriptional activator oxidative stress- and iron starvation-inducible autorepressor
b2279 -65 -31 FnrS 43 92 -11.54 0.0091414 0.9422174 nuoK NADH:ubiquinone oxidoreductase membrane subunit K
b2152 1 42 FnrS 4 41 -11.51 0.009337 0.9422174 yeiB DUF418 family putative inner membrane protein
b1476 -31 -17 FnrS 42 57 -11.48 0.0095365 0.9422174 fdnI formate dehydrogenase-N cytochrome B556 (gamma) subunit nitrate-inducible
b2819 30 72 FnrS 4 42 -11.41 0.010017 0.9422174 recD exonuclease V (RecBCD complex) alpha chain
b0404 15 22 FnrS 1 8 -11.4 0.0100874 0.9422174 acpH acyl carrier protein (ACP) phosphodiesterase ACP hydrolyase
b0846 -67 -52 FnrS 43 61 -11.38 0.0102296 0.9422174 rcdA transcriptional regulator of csgD and ybiJI autoregulator
b3928 -21 10 FnrS 40 76 -11.36 0.0103736 0.9422174 zapB FtsZ stabilizer septal ring assembly factor cell division stimulator
b1925 -52 -18 FnrS 40 91 -11.29 0.0108921 0.9422174 fliS flagellar protein potentiates polymerization
b0233 1 16 FnrS 58 73 -11.29 0.0108921 0.9422174 yafO mRNA interferase toxin of the YafO-YafN toxin-antitoxin system
b4216 -29 -22 FnrS 1 8 -11.27 0.0110445 0.9422174 ytfJ putative transcriptional regulator
b1809 -51 -5 FnrS 43 81 -11.21 0.0115135 0.9422174 yoaB putative reactive intermediate deaminase
b4552 21 44 FnrS 38 61 -11.14 0.0120834 0.9422174 yrhC pseudogene fragment
b1795 -61 -51 FnrS 70 80 -11.14 0.0120834 0.9422174 yeaQ UPF0410 family protein
b1452 -49 -5 FnrS 50 88 -11.13 0.0121669 0.9422174 yncE ATP-binding protein periplasmic function unknown
b4656 -62 -55 FnrS 1 8 -11.13 0.0121669 0.9422174 yjhY pseudogene zinc finger protein family
b3282 -40 -26 FnrS 37 52 -11.08 0.0125922 0.9422174 tsaC tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein threonine-dependent ADP-forming ATPase
b3136 -57 -18 FnrS 4 49 -11.04 0.012942 0.9422174 agaS tagatose-6-phosphate ketose/aldose isomerase
b3226 42 50 FnrS 1 9 -10.93 0.0139501 0.9422174 nanR sialic acid-inducible nan operon repressor
b0657 32 43 FnrS 1 12 -10.92 0.0140451 0.9422174 lnt apolipoprotein N-acyltransferase
b1048 23 35 FnrS 64 78 -10.89 0.0143339 0.9422174 opgG OPG biosynthetic periplasmic beta-16 branching glycosyltransferase
b2676 -72 -66 FnrS 1 7 -10.89 0.0143339 0.9422174 nrdF ribonucleoside-diphosphate reductase 2 beta subunit ferritin-like protein
b0946 -48 -3 FnrS 45 92 -10.89 0.0143339 0.9422174 zapC FtsZ stabilizer
b0546 11 20 FnrS 45 54 -10.86 0.014628 0.9422174 ybcM DLP12 prophage putative DNA-binding transcriptional regulator
b2085 51 75 FnrS 44 80 -10.85 0.0147273 0.9422174 yegR uncharacterized protein
b2650 -30 4 FnrS 40 76 -10.84 0.0148271 0.9422174 ypjC pseudogene
b3770 -75 -56 FnrS 1 24 -10.78 0.0154393 0.9422174 ilvE branched-chain amino acid aminotransferase
b0642 -72 -63 FnrS 68 77 -10.63 0.017071 0.9422174 leuS leucyl-tRNA synthetase
b1049 3 41 FnrS 21 54 -10.56 0.0178846 0.9422174 opgH OPG biosynthetic ACP-dependent transmembrane UDP-glucose beta-12 glycosyltransferase nutrient-dependent cell size regulator FtsZ assembly antagonist
b3306 -14 6 FnrS 35 55 -10.56 0.0178846 0.9422174 rpsH 30S ribosomal subunit protein S8
b1266 10 29 FnrS 61 89 -10.53 0.0182438 0.9422174 yciV PHP domain protein
b4648 -45 -29 FnrS 60 76 -10.5 0.0186096 0.9422174 ysaC pseudogene
b2019 28 36 FnrS 68 76 -10.49 0.018733 0.9422174 hisG ATP phosphoribosyltransferase
b0353 -31 -22 FnrS 1 10 -10.49 0.018733 0.9422174 mhpT 3-hydroxyphenylpropionic transporter
b1206 -51 -43 FnrS 1 9 -10.45 0.019234 0.9422174 dauA C4-dicarboxylic acid transporter
b4141 -71 -55 FnrS 73 88 -10.44 0.0193611 0.9422174 yjeH putative transporter
b1526 -16 3 FnrS 71 89 -10.44 0.0193611 0.9422174 yneJ putative DNA-binding transcriptional regulator
b0802 -20 -13 FnrS 1 8 -10.42 0.0196176 0.9422174 ybiJ DUF1471 family putative periplasmic protein
b4020 15 22 FnrS 1 8 -10.42 0.0196176 0.9422174 yjbB putative Na+/Pi-cotransporter
b4602 -44 -10 FnrS 53 92 -10.3 0.0212222 0.9422174 ynhF stress response membrane
b0889 -28 -4 FnrS 41 61 -10.3 0.0212222 0.9422174 lrp leucine-responsive global transcriptional regulator
b0006 15 23 FnrS 1 9 -10.3 0.0212222 0.9422174 yaaA peroxide resistance protein lowers intracellular iron
b3195 -12 7 FnrS 35 54 -10.22 0.0223567 0.9422174 mlaF ABC transporter maintaining OM lipid asymmetry ATP-binding protein
b2592 55 62 FnrS 1 8 -10.21 0.0225023 0.9422174 clpB protein disaggregation chaperone
b1817 -75 -47 FnrS 57 88 -10.21 0.0225023 0.9422174 manX fused mannose-specific PTS enzymes: IIA component/IIB component
b2101 -13 4 FnrS 38 56 -10.2 0.0226488 0.9422174 yegW putative DNA-binding transcriptional regulator
b3892 -16 -1 FnrS 31 49 -10.14 0.0235457 0.9422174 fdoI formate dehydrogenase-O cytochrome b556 subunit
b0227 53 74 FnrS 1 22 -10.14 0.0235457 0.9422174 yafL putative lipoprotein and C40 family peptidase
b3106 -28 -17 FnrS 48 59 -10.14 0.0235457 0.9422174 yhaK redox-sensitive bicupin
b3429 -28 -16 FnrS 44 55 -10.14 0.0235457 0.9422174 glgA glycogen synthase
b4638 -20 38 FnrS 41 89 -10.14 0.0235457 0.9422174 ttcC pseudogene prophage Rac integration site ttcA duplicationPhage or Prophage Related
b0451 68 74 FnrS 1 7 -10.12 0.0238516 0.9422174 amtB ammonium transporter
b3689 63 70 FnrS 1 8 -10.12 0.0238516 0.9422174 yidR DUF3748 family protein
b4032 48 55 FnrS 1 8 -10.11 0.024006 0.9422174 malG maltose transporter subunit
b1759 58 71 FnrS 21 36 -10.11 0.024006 0.9422174 nudG CTP pyrophosphohydrolase also hydrolyzes 2-hydroxy-dATP 8-hydroxy-dGTP 5-hydroxy-CTP dCTP and 5-methyl-dCTP
b4595 18 28 FnrS 45 55 -10.1 0.0241612 0.9422174 yciY uncharacterized protein
b2799 -72 -54 FnrS 58 78 -10.07 0.0246323 0.9422174 fucO L-12-propanediol oxidoreductase
b0031 -30 -8 FnrS 55 78 -10.05 0.024951 0.9422174 dapB dihydrodipicolinate reductase
b1656 13 20 FnrS 1 8 -10.04 0.0251117 0.9422174 sodB superoxide dismutase Fe
b4650 -27 -10 FnrS 36 59 -10.03 0.0252733 0.9422174 yibS pseudogene Rhs family protein
b3755 -17 -3 FnrS 47 60 -10.02 0.0254359 0.9422174 yieP putative transcriptional regulator
b2562 24 42 FnrS 71 89 -10.02 0.0254359 0.9422174 yfhL putative 4Fe-4S cluster-containing protein
b1305 -72 -60 FnrS 42 54 -9.99 0.0259293 0.9422174 pspB psp operon transcription co-activator
b0147 -41 -17 FnrS 61 83 -9.99 0.0259293 0.9422174 ligT 2'-5' RNA ligase
b0566 -7 20 FnrS 65 91 -9.97 0.026263 0.9422174 envY porin thermoregulatory transcriptional activator
b1444 -4 5 FnrS 69 77 -9.96 0.0264313 0.9422174 patD gamma-aminobutyraldehyde dehydrogenase
b4551 56 75 FnrS 38 56 -9.88 0.027813 0.9422174 yheV DUF2387 family putative metal-binding protein

Details of Selected Interaction Download Interaction Details 

Target

Query


		

		

		

		

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

			

			

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
				

					
					
				

				
			

		
 
		
		

		
		

		
		

			

		

		
		

	

	
	
	
	
	
	
	




			 
	





	
Job resubmission

	

		

			Use the following button if you want to resubmit the job with
			altered input or parameterization:
		

		

			
			Feeds the job parameters to the input page to resubmit the job.
			
		

	


	





	
de.NBI 
		usability assessment

	

		

			
				
				
			 
		

		

			Please 
			support us 
			by filling this 
			short quality survey 
			for evaluating this
			de.NBI
			service.
		

	





	





	
	
		 
		
When using IntaRNA please cite :







		 
	
	
	
		 
		



Results are computed with IntaRNA version 3.1.3 linking Vienna RNA package 2.4.14



		 
	

			





	About this web server
	  | 
	version 5.0.9
	  | 
	Copyright © 2012 - 2024 Bioinformatics Group Freiburg
	  | 
	de.NBI
	  | 
	Imprint and Disclaimer