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 6571257

Input and runtime details for job 6571257 (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 6571257 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:18:03 CET 2020
?IntaRNA Started@ Mon Jan 27 14:20:22 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:21:19 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:22:25 CET 2020
?Job Completed@ Mon Jan 27 14:22:35 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=6571257&toolName=IntaRNA ( 30 days expiry )

Description of the job

Spot42 - 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
b0367 -75 -66 Spot42 52 61 -10.23 0.0132937 0.9238006 tauC taurine ABC transporter permease
b1004 -75 -56 Spot42 10 32 -9.83 0.0166769 0.9238006 wrbA NAD(P)H:quinone oxidoreductase
b4174 -75 -61 Spot42 42 57 -9.36 0.0217476 0.9238006 hflK modulator for HflB protease specific for phage lambda cII repressor
b3503 -75 -69 Spot42 1 7 -9.14 0.0246155 0.9238006 arsC arsenate reductase
b2294 -75 -67 Spot42 48 56 -8.74 0.0308106 0.9238006 yfbU UPF0304 family protein
b0646 -74 -67 Spot42 1 8 -10.27 0.0129952 0.9238006 djlB putative HscC co-chaperone uncharacterized J domain-containing protein
b3921 -74 -67 Spot42 50 57 -9.55 0.0195371 0.9238006 yiiR DUF805 family putative inner membrane protein
b0882 -74 -44 Spot42 3 32 -9.02 0.0263331 0.9238006 clpA ATPase and specificity subunit of ClpA-ClpP ATP-dependent serine protease chaperone activity
b2602 -71 -60 Spot42 7 18 -10.62 0.0106505 0.9238006 yfiL lipoprotein
b3816 -71 -41 Spot42 4 37 -10.38 0.012208 0.9238006 corA magnesium/nickel/cobalt transporter
b2797 -68 -54 Spot42 55 69 -15.99 0.0004824 0.8439588 sdaB L-serine dehydratase 2
b1792 -68 -32 Spot42 40 73 -9.23 0.0234 0.9238006 yeaO DUF488 family protein
b4553 -64 -42 Spot42 53 74 -11.45 0.006633 0.9238006 ysaB uncharacterized protein
b3224 -61 -50 Spot42 1 12 -16.33 0.0003958 0.8439588 nanT sialic acid transporter
b1106 -58 -52 Spot42 1 7 -10.06 0.0146397 0.9238006 thiK thiamine kinase
b1623 -58 -51 Spot42 1 8 -9.03 0.0261856 0.9238006 add adenosine deaminase
b2216 -57 -49 Spot42 3 11 -10.78 0.009723 0.9238006 rcsD phosphotransfer intermediate protein in two-component regulatory system with RcsBC
b3934 -56 -44 Spot42 41 56 -10.45 0.0117318 0.9238006 cytR Anti-activator for CytR-CRP nucleoside utilization regulon
b0721 -55 -44 Spot42 4 15 -10.51 0.0113383 0.9238006 sdhC succinate dehydrogenase membrane subunit binds cytochrome b556
b3709 -53 -42 Spot42 1 13 -9.62 0.0187797 0.9238006 tnaB tryptophan transporter of low affinity
b0369 -53 -46 Spot42 1 8 -8.81 0.0296259 0.9238006 hemB 5-aminolevulinate dehydratase (porphobilinogen synthase)
b0835 -52 -36 Spot42 1 13 -10 0.0151462 0.9238006 rimO ribosomal protein S12 methylthiotransferase
b2506 -51 -37 Spot42 55 68 -11.81 0.0053979 0.9238006 yfgI nalidixic acid resistance protein putative periplasmic protein
b3685 -51 -36 Spot42 54 68 -11.08 0.0081942 0.9238006 yidE putative transporter
b0523 -51 -41 Spot42 3 13 -8.91 0.0280104 0.9238006 purE N5-carboxyaminoimidazole ribonucleotide mutase
b1927 -50 -39 Spot42 48 59 -13.13 0.0025285 0.9238006 amyA cytoplasmic alpha-amylase
b4621 -48 -41 Spot42 1 8 -11.15 0.0078733 0.9238006 yjbS uncharacterized protein
b2150 -48 -22 Spot42 1 24 -9.49 0.0202101 0.9238006 mglB methyl-galactoside transporter subunit
b1347 -46 -34 Spot42 20 32 -10.44 0.0117987 0.9238006 ydaC DUF1187 family protein Rac prophage putative double-strand break reduction protein
b2659 -45 -24 Spot42 1 24 -10.83 0.0094499 0.9238006 csiD carbon starvation protein
b2801 -39 -29 Spot42 46 56 -12.84 0.002988 0.9238006 fucP L-fucose transporter
b1901 -37 -30 Spot42 1 8 -11.04 0.0083834 0.9238006 araF L-arabinose ABC transporter periplasmic binding protein
b2221 -36 -27 Spot42 1 11 -10.63 0.01059 0.9238006 atoD acetyl-CoA:acetoacetyl-CoA transferase alpha subunit
b1302 -35 6 Spot42 21 57 -11.97 0.004925 0.9238006 puuE 4-aminobutyrate aminotransferase PLP-dependent
b4361 -33 -23 Spot42 55 65 -9.75 0.0174491 0.9238006 dnaC DNA biosynthesis protein
b0333 -32 -26 Spot42 1 7 -10 0.0151462 0.9238006 prpC 2-methylcitrate synthase
b1300 -28 -13 Spot42 44 58 -9.81 0.0168668 0.9238006 puuC gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase succinate semialdehyde dehydrogenase
b0511 -28 10 Spot42 18 58 -9.6 0.0189931 0.9238006 ybbW putative allantoin transporter
b2715 -28 -21 Spot42 1 8 -9.51 0.0199833 0.9238006 ascF cellobiose/arbutin/salicin-specific PTS enzymes IIB and IC components
b0885 -27 -10 Spot42 42 58 -13.52 0.0020193 0.9238006 aat leucyl/phenylalanyl-tRNA-protein transferase
b4311 -27 -16 Spot42 1 12 -11.59 0.0061225 0.9238006 nanC N-acetylnuraminic acid outer membrane channel protein
b3078 -27 -20 Spot42 1 8 -10.33 0.0125598 0.9238006 ygjI putative transporter
b2357 -27 -17 Spot42 55 65 -10.32 0.0126314 0.9238006 yfdN CPS-53 (KpLE1) prophage uncharacterized protein
b0969 -24 -15 Spot42 50 59 -9.29 0.0226226 0.9238006 tusE mnm(5)-s(2)U34-tRNA 2-thiolation sulfurtransferase
b2407 -22 -16 Spot42 1 7 -8.77 0.0302973 0.9238006 xapA purine nucleoside phosphorylase 2 nicotinamide 1-beta-D-riboside synthase
b3238 -21 -5 Spot42 39 54 -9.61 0.0188861 0.9238006 yhcN cadmium and peroxide resistance protein stress-induced
b0347 -21 -6 Spot42 41 57 -8.74 0.0308106 0.9238006 mhpA 3-(3-hydroxyphenyl)propionate hydroxylase
b0728 -20 -9 Spot42 23 34 -9.01 0.0264814 0.9238006 sucC succinyl-CoA synthetase beta subunit
b4465 -18 -2 Spot42 39 56 -8.82 0.0294603 0.9238006 yggP putative Zn-binding dehydrogenase
b0757 -17 39 Spot42 1 59 -14.73 0.001003 0.9238006 galK galactokinase
b2548 -17 -11 Spot42 1 7 -9.25 0.023138 0.9238006 yphF putative sugar ABC transporter periplasmic binding protein
b1553 -15 -1 Spot42 20 34 -9.05 0.025893 0.9238006 rzpQ Rz-like protein Qin prophage
b1751 -14 -2 Spot42 21 33 -9.65 0.0184641 0.9238006 ydjY putative ferrodoxin-like lipoprotein
b3908 -12 16 Spot42 1 34 -9.96 0.0154934 0.9238006 sodA superoxide dismutase Mn
b1398 -10 -2 Spot42 1 9 -13.17 0.0024709 0.9238006 paaK phenylacetyl-CoA ligase
b2561 -7 16 Spot42 11 32 -10.17 0.0137542 0.9238006 yfhH putative DNA-binding transcriptional regulator
b3690 -4 11 Spot42 17 31 -9.42 0.0210242 0.9238006 cbrA colicin M resistance protein FAD-binding protein putative oxidoreductase
b1586 -1 24 Spot42 5 28 -9.23 0.0234 0.9238006 ynfD DUF1161 family periplasmic protein
b2980 2 16 Spot42 18 33 -10.39 0.0121389 0.9238006 glcC glycolate-inducible glc operon transcriptional repressor autorepressor
b2319 3 19 Spot42 20 36 -9.12 0.0248939 0.9238006 usg putative semialdehyde dehydrogenase
b3683 5 16 Spot42 55 66 -9.25 0.023138 0.9238006 glvC pseudogene arbutin specific enzyme IIC component of PTSenzyme Transport of small molecules: Carbohydrates organic acids alcohols PTS system arbutin-like IIB component PTS system arbutin-like IIC component
b3092 6 69 Spot42 1 57 -10.14 0.0139903 0.9238006 uxaC uronate isomerase
b2582 6 19 Spot42 4 16 -9.03 0.0261856 0.9238006 trxC thioredoxin 2
b0246 8 14 Spot42 1 7 -8.71 0.0313324 0.9238006 yafW CP4-6 prophage antitoxin of the YkfI-YafW toxin-antitoxin system
b0774 9 28 Spot42 4 24 -9.09 0.0253174 0.9238006 bioA 78-diaminopelargonic acid synthase PLP-dependent
b3139 13 19 Spot42 1 7 -9.42 0.0210242 0.9238006 agaC N-acetylgalactosamine-specific enzyme IIC component of PTS
b1862 13 20 Spot42 1 8 -9.04 0.0260389 0.9238006 yebB DUF830 family protein
b1212 15 28 Spot42 43 56 -13.07 0.0026174 0.9238006 prmC RF-1 and RF-2 N5-glutamine methyltransferase
b3664 17 32 Spot42 40 56 -10.58 0.0108957 0.9238006 adeQ adenine permease high affinity adenine:H+ symporter
b3311 17 25 Spot42 1 9 -9.59 0.0191007 0.9238006 rpsQ 30S ribosomal subunit protein S17
b3051 19 28 Spot42 3 12 -10.36 0.0123476 0.9238006 yqiK PHB family membrane protein function unknown
b0718 20 33 Spot42 1 14 -10.35 0.0124179 0.9238006 ybgQ putative outer membrane protein
b1385 21 37 Spot42 55 71 -11.57 0.006193 0.9238006 feaB phenylacetaldehyde dehydrogenase
b1343 21 34 Spot42 11 24 -8.89 0.0283265 0.9238006 dbpA ATP-dependent RNA helicase specific for 23S rRNA
b4659 25 32 Spot42 49 56 -8.71 0.0313324 0.9238006 yabP pseudogene pentapeptide repeats-containing
b2962 26 68 Spot42 4 57 -10.78 0.009723 0.9238006 yggX oxidative damage protective factor for iron-sulfur proteins
b3465 27 38 Spot42 54 65 -8.75 0.0306386 0.9238006 rsmD 16S rRNA m(2)G966 methyltransferase SAM-dependent
b0954 28 49 Spot42 9 31 -9.87 0.0163036 0.9238006 fabA beta-hydroxydecanoyl thioester dehydrase
b0559 38 49 Spot42 46 58 -9.04 0.0260389 0.9238006 ybcW DLP12 prophage uncharacterized protein
b0705 41 48 Spot42 49 56 -9.4 0.0212627 0.9238006 ybfL pseudogene DDE domain transposase familyputative factor Not classified putative receptor protein
b1695 43 63 Spot42 48 71 -8.85 0.028969 0.9238006 ydiO putative acyl-CoA dehydrogenase
b1867 51 72 Spot42 5 25 -9.93 0.0157589 0.9238006 yecD isochorismatase family protein
b2467 55 61 Spot42 1 7 -9.96 0.0154934 0.9238006 nudK GDP-mannose pyrophosphatase
b1391 56 67 Spot42 55 66 -10.65 0.0104701 0.9238006 paaD ring 12-phenylacetyl-CoA epoxidase subunit
b0307 57 71 Spot42 48 60 -10.37 0.0122776 0.9238006 ykgF ferridoxin-like LutB family protein putative electron transport chain YkgEFG component
b3354 58 73 Spot42 43 57 -8.76 0.0304675 0.9238006 yheU UPF0270 family protein
b3878 60 67 Spot42 1 8 -10.22 0.0133694 0.9238006 yihQ putative sulpholipid alpha-glucosidase alpha-glucosyl fluoride glucosidase
b1921 60 75 Spot42 49 65 -9.65 0.0184641 0.9238006 fliZ RpoS antagonist putative regulator of FliA activity
b3827 60 68 Spot42 1 9 -9.16 0.0243401 0.9238006 yigM putative inner membrane EamA-like transporter
b1182 60 69 Spot42 20 29 -8.85 0.028969 0.9238006 hlyE hemolysin E
b1487 61 69 Spot42 48 56 -9.48 0.0203245 0.9238006 ddpA DD-dipeptide ABC transporter periplasmic binding protein
b1563 62 72 Spot42 44 55 -9.07 0.0256036 0.9238006 relE Qin prophage toxin of the RelE-RelB toxin-antitoxin system
b2622 62 69 Spot42 49 56 -9.01 0.0264814 0.9238006 intA CP4-57 prophage integrase
b2935 63 75 Spot42 52 64 -12.34 0.003983 0.9238006 tktA transketolase 1 thiamine triphosphate-binding
b1596 63 73 Spot42 56 66 -10.86 0.0092897 0.9238006 ynfM putative arabinose efflux transporter
b0878 64 73 Spot42 47 56 -9.01 0.0264814 0.9238006 macA macrolide transporter membrane fusion protein (MFP) component
b0973 67 75 Spot42 48 56 -11.79 0.0054601 0.9238006 hyaB hydrogenase 1 large subunit
b2619 67 75 Spot42 1 9 -8.94 0.0275429 0.9238006 ratA toxic UPF0083 family protein inhibitor of 70S ribosome formation
b0062 67 73 Spot42 1 7 -8.79 0.0299597 0.9238006 araA L-arabinose isomerase
b1056 68 75 Spot42 49 56 -9.26 0.023008 0.9238006 yceI periplasmic high pH-inducible lipid-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 5.0.10
	  | 
	Copyright © 2012 - 2024 Bioinformatics Group Freiburg
	  | 
	de.NBI
	  | 
	Imprint and Disclaimer