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 1972078

Input and runtime details for job 1972078 (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 1972078 (server version trunk)

?Job Submitted & Queued@ Mon Jan 27 14:13:56 CET 2020
?IntaRNA Started@ Mon Jan 27 14:16:07 CET 2020
?IntaRNA Finished & Post-Processing@ Mon Jan 27 14:17:05 CET 2020
?Post-Processing Finished@ Mon Jan 27 14:18:21 CET 2020
?Job Completed@ Mon Jan 27 14:18:31 CET 2020
 DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=1972078&toolName=IntaRNA ( 30 days expiry )

Description of the job

MicC - 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
b2215 -67 -15 MicC 1 70 -21.53 5.2e-06 0.0190476 ompC outer membrane porin protein C
b0393 -71 -57 MicC 40 55 -16.11 0.0004508 0.7974595 rdgC nucleoid-associated ssDNA and dsDNA binding protein competitive inhibitor of RecA function
b1835 -15 11 MicC 35 58 -15.19 0.0008759 0.7974595 rsmF 16S rRNA m(5)C1407 methyltransferase SAM-dependent
b2239 56 74 MicC 41 66 -14.71 0.0012277 0.7974595 glpQ periplasmic glycerophosphodiester phosphodiesterase
b1346 -13 5 MicC 41 58 -14.56 0.0013626 0.7974595 ydaQ Rac prophage conserved protein
b4032 -14 21 MicC 31 65 -14.02 0.0019743 0.7974595 malG maltose transporter subunit
b4403 -8 11 MicC 1 21 -13.87 0.0021857 0.7974595 yjtD putative methyltransferase
b2314 -9 11 MicC 45 65 -13.85 0.0022155 0.7974595 dedD membrane-anchored periplasmic protein involved in septation
b3751 56 74 MicC 41 59 -13.8 0.0022915 0.7974595 rbsB D-ribose ABC transporter periplasmic binding protein ribose chemotaxis receptor
b2920 2 18 MicC 51 66 -13.62 0.0025864 0.7974595 scpC propionyl-CoA:succinate CoA transferase
b2550 -75 -62 MicC 43 56 -13.61 0.0026038 0.7974595 yphH putative DNA-binding transcriptional regulator
b4393 -12 11 MicC 35 55 -13.36 0.0030764 0.7974595 trpR transcriptional repressor tryptophan-binding
b1200 -75 -53 MicC 40 65 -13.35 0.0030969 0.7974595 dhaK dihydroxyacetone kinase PTS-dependent dihydroxyacetone-binding subunit
b4535 31 66 MicC 17 66 -13.33 0.0031383 0.7974595 yniD uncharacterized protein
b1218 -28 -2 MicC 45 65 -13.27 0.0032656 0.7974595 chaC cation transport regulator
b3617 -16 4 MicC 47 69 -12.98 0.003953 0.8150379 kbl glycine C-acetyltransferase
b4478 -9 3 MicC 43 54 -12.96 0.0040051 0.8150379 dgoD D-galactonate dehydratase
b2203 42 55 MicC 39 54 -12.96 0.0040051 0.8150379 napB nitrate reductase small cytochrome C550 subunit periplasmic
b0002 27 37 MicC 50 60 -12.71 0.0047142 0.8384433 thrA Bifunctional aspartokinase/homoserine dehydrogenase 1
b1383 33 62 MicC 41 69 -12.7 0.0047449 0.8384433 ydbL DUF1318 family protein
b4496 8 31 MicC 39 64 -12.68 0.0048068 0.8384433 yedS pseudogene outer membrane protein homology putative outer membrane protein
b3128 -16 6 MicC 40 66 -12.58 0.0051283 0.853862 garD D-galactarate dehydrogenase
b4255 -59 -46 MicC 42 54 -12.39 0.0057958 0.9230441 rraB protein inhibitor of RNase E
b1667 45 59 MicC 41 55 -12.31 0.0061007 0.9311193 ydhR putative monooxygenase
b4328 60 71 MicC 53 65 -11.97 0.007574 0.9679271 iadA isoaspartyl dipeptidase
b0170 -75 -65 MicC 39 48 -11.94 0.007719 0.9679271 tsf translation elongation factor EF-Ts
b0763 57 71 MicC 41 55 -11.91 0.0078666 0.9679271 modA molybdate ABC transporter periplasmic binding protein chlorate resistance protein
b4473 52 67 MicC 39 54 -11.89 0.0079665 0.9679271 smf DNA recombination-mediator A family protein
b1119 57 75 MicC 42 58 -11.87 0.0080676 0.9679271 nagK N-acetyl-D-glucosamine kinase
b1535 -13 20 MicC 33 63 -11.71 0.0089209 0.9679271 dgcZ diguanylate cyclase zinc-sensing
b0333 51 74 MicC 6 28 -11.71 0.0089209 0.9679271 prpC 2-methylcitrate synthase
b2746 36 51 MicC 38 55 -11.7 0.008977 0.9679271 ispF 2C-methyl-D-erythritol 24-cyclodiphosphate synthase
b1065 -67 -40 MicC 46 69 -11.69 0.0090334 0.9679271 mdtH multidrug resistance efflux transporter conferring overexpression resistance to norfloxacin and enoxacin
b0686 -75 -45 MicC 40 74 -11.49 0.0102341 0.9679271 ybfF acyl-CoA esterase
b2771 -18 -8 MicC 9 19 -11.47 0.0103621 0.9679271 ygcS putative MFS sugar transporter membrane protein
b3943 29 43 MicC 40 55 -11.46 0.0104267 0.9679271 yijE EamA-like transporter family protein
b1891 33 54 MicC 45 65 -11.45 0.0104916 0.9679271 flhC flagellar class II regulon transcriptional activator with FlhD
b1466 54 67 MicC 42 56 -11.27 0.011728 0.9679271 narW nitrate reductase 2 (NRZ) delta subunit (assembly subunit)
b0301 -74 -54 MicC 45 66 -11.24 0.011947 0.9679271 rclC reactive chlorine species (RCS) stress resistance inner membrane protein
b1384 14 37 MicC 41 66 -11.12 0.0128619 0.9679271 feaR transcriptional activator for tynA and feaB
b0982 -12 18 MicC 22 56 -11.1 0.0130207 0.9679271 etp O-antigen capsule forming protein-tyrosine-phosphatase Etk-P dephosphorylase
b3655 46 64 MicC 40 59 -11.06 0.0133437 0.9679271 yicH putative inner membrane-anchored periplasmic AsmA family protein
b0556 -72 -57 MicC 42 55 -11.05 0.0134256 0.9679271 rzpD DLP12 prophage putative murein endopeptidase
b4230 -10 7 MicC 47 65 -11.03 0.0135909 0.9679271 ytfT putative sugar ABC transporter permease
b1771 -14 4 MicC 2 19 -11 0.0138425 0.9679271 ydjG methylglyoxal reductase NADH-dependent
b4297 57 71 MicC 39 53 -10.98 0.0140126 0.9679271 yjhG putative dehydratase
b2445 51 64 MicC 50 63 -10.98 0.0140126 0.9679271 yffN CPZ-55 prophage uncharacterized protein
b0585 33 53 MicC 39 56 -10.95 0.0142715 0.9679271 fes enterobactin/ferrienterobactin esterase
b1833 43 54 MicC 7 18 -10.92 0.0145348 0.9679271 yebS inner membrane PqiA domain protein
b4664 -70 -61 MicC 56 65 -10.92 0.0145348 0.9679271 ibsD toxic membrane protein
b3354 1 75 MicC 8 70 -10.9 0.0147129 0.9679271 yheU UPF0270 family protein
b2091 4 16 MicC 50 62 -10.87 0.0149839 0.9679271 gatD galactitol-1-phosphate dehydrogenase Zn-dependent and NAD(P)-binding
b0688 -10 5 MicC 41 54 -10.86 0.0150753 0.9679271 pgm phosphoglucomutase
b2918 -71 -56 MicC 38 54 -10.85 0.0151672 0.9679271 argK membrane ATPase/protein kinase
b0034 61 72 MicC 53 64 -10.82 0.0154461 0.9679271 caiF cai operon transcriptional activator
b2103 43 53 MicC 47 57 -10.8 0.0156347 0.9679271 thiD hydroxy-methylpyrimidine kinase and hydroxy-phosphomethylpyrimidine kinase
b1590 2 26 MicC 40 66 -10.74 0.0162135 0.9679271 ynfH oxidoreductase membrane subunit
b0354 -12 7 MicC 50 67 -10.71 0.0165104 0.9679271 yaiL DUF2058 family protein
b1385 -3 20 MicC 1 21 -10.7 0.0166105 0.9679271 feaB phenylacetaldehyde dehydrogenase
b4271 -9 24 MicC 23 54 -10.7 0.0166105 0.9679271 intB pseudogene integrase homologyIS phage Tn Phage-related functions and prophages KpLE2 phage-like element P4-like integrase
b0553 14 23 MicC 49 58 -10.68 0.0168124 0.9679271 nmpC DLP12 prophage truncated outer membrane porin (pseudogene)IS phage Tn Phage or Prophage Related outer membrane porin protein locus of qsr prophage
b2374 42 60 MicC 38 58 -10.67 0.0169142 0.9679271 frc formyl-CoA transferase NAD(P)-binding
b2573 48 57 MicC 56 65 -10.66 0.0170166 0.9679271 rpoE RNA polymerase sigma E factor
b1676 -60 -49 MicC 39 54 -10.62 0.017432 0.9679271 pykF pyruvate kinase I
b2118 34 64 MicC 7 42 -10.57 0.0179646 0.9679271 yehI DUF4132 domain-containing protein
b0642 3 35 MicC 23 53 -10.52 0.0185126 0.9679271 leuS leucyl-tRNA synthetase
b1456 57 69 MicC 8 20 -10.52 0.0185126 0.9679271 rhsE pseudogene Rhs family
b1776 -72 8 MicC 8 70 -10.51 0.018624 0.9679271 ydjL putative Zn-dependent NAD(P)-binding oxidoreductase
b1406 58 71 MicC 41 53 -10.5 0.0187361 0.9679271 ydbC putative NAD(P)-binding oxidoreductase
b1256 14 29 MicC 41 58 -10.38 0.0201313 0.9679271 ompW outer membrane protein W
b2986 36 51 MicC 38 55 -10.36 0.0203731 0.9679271 yghT putative ATP-binding protein
b4551 57 72 MicC 48 65 -10.34 0.0206176 0.9679271 yheV DUF2387 family putative metal-binding protein
b2331 -26 -17 MicC 56 65 -10.33 0.0207409 0.9679271 smrB putative DNA endonuclease
b2501 -15 7 MicC 40 65 -10.33 0.0207409 0.9679271 ppk polyphosphate kinase component of RNA degradosome
b2247 42 62 MicC 30 55 -10.24 0.021882 0.9679271 rhmD L-rhamnonate dehydratase
b1152 17 28 MicC 37 48 -10.21 0.0222753 0.9679271 jayE pseudogene e14 prophagePhage or Prophage Related
b1068 -66 -50 MicC 51 66 -10.2 0.0224078 0.9679271 yceM putative oxidoreductase
b2830 63 75 MicC 40 54 -10.17 0.0228099 0.9679271 rppH RNA pyrophosphohydrolase
b2848 -72 -62 MicC 44 55 -10.16 0.0229454 0.9679271 yqeJ uncharacterized protein
b0907 -13 8 MicC 38 56 -10.15 0.0230817 0.9679271 serC 3-phosphoserine/phosphohydroxythreonine aminotransferase
b2069 37 49 MicC 46 59 -10.11 0.0236344 0.9679271 yegD Hsp70 chaperone family protein
b3690 16 45 MicC 32 56 -10.08 0.0240571 0.9679271 cbrA colicin M resistance protein FAD-binding protein putative oxidoreductase
b1551 -38 -27 MicC 47 58 -10.03 0.0247772 0.9679271 ynfN Qin prophage cold shock-induced protein
b4153 -59 -48 MicC 47 58 -9.99 0.0253678 0.9679271 frdB fumarate reductase (anaerobic) Fe-S subunit
b0294 -9 12 MicC 45 66 -9.97 0.0256679 0.9679271 ecpR putative transcriptional regulator for the ecp operon
b3005 -12 11 MicC 46 65 -9.93 0.0262783 0.9679271 exbD membrane spanning protein in TonB-ExbB-ExbD complex
b3673 -10 11 MicC 7 25 -9.9 0.0267449 0.9679271 emrD multidrug efflux system protein
b1817 -20 -10 MicC 9 19 -9.88 0.0270603 0.9679271 manX fused mannose-specific PTS enzymes: IIA component/IIB component
b1507 -16 4 MicC 47 63 -9.86 0.0273792 0.9679271 hipA inactivating GltX kinase facilitating persister formation toxin of HipAB TA pair autokinase
b4327 3 12 MicC 89 98 -9.85 0.0275399 0.9679271 hypT hypochlorite-responsive transcription factor
b3334 -68 -23 MicC 4 55 -9.85 0.0275399 0.9679271 gspM general secretory pathway component cryptic
b2422 -39 -29 MicC 56 66 -9.83 0.027864 0.9679271 cysA sulfate/thiosulfate transporter subunit
b0633 2 18 MicC 39 55 -9.83 0.027864 0.9679271 rlpA septal ring protein suppressor of prc minor lipoprotein
b3619 59 71 MicC 6 18 -9.81 0.0281917 0.9679271 hldD ADP-L-glycero-D-mannoheptose-6-epimerase NAD(P)-binding
b1093 -8 1 MicC 57 65 -9.81 0.0281917 0.9679271 fabG 3-oxoacyl-[acyl-carrier-protein] reductase
b1140 -67 -42 MicC 44 68 -9.8 0.0283569 0.9679271 intE e14 prophage putative integrase
b0126 30 44 MicC 40 52 -9.79 0.028523 0.9679271 can carbonic anhydrase
b4187 -2 10 MicC 41 52 -9.78 0.02869 0.9679271 aidB DNA alkylation damage repair protein flavin-containing DNA binding protein weak isovaleryl CoA dehydrogenase
b0572 -60 -37 MicC 45 65 -9.78 0.02869 0.9679271 cusC copper/silver efflux system outer membrane component
b3996 -15 -6 MicC 45 54 -9.78 0.02869 0.9679271 nudC NADH pyrophosphatase

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