RegulonDB RegulonDB 10.8: Gene Form
   

intR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

intR ttcA xisR intRp4 intRp4 TSS_1774 TSS_1774 TSS_1773 (cluster) TSS_1773 (cluster) TSS_1772 TSS_1772 TSS_1771 TSS_1771 ttcAp5 ttcAp5 TSS_1770 TSS_1770

Gene      
Name: intR    Texpresso search in the literature
Synonym(s): ECK1342, G6676, b1345, ydaP
Genome position(nucleotides): 1412000 <-- 1413235 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 42.96
External database links:  
ASAP:
 ABE-0004517
ECHOBASE:
 EB3141
OU-MICROARRAY:
 b1345
PortEco:
 intR
STRING:
 511145.b1345
COLOMBOS: intR


Product      
Name: Rac prophage; putative integrase
Synonym(s): IntR, YdaP
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 47.539
Isoelectric point: 10.438
Motif(s):
 
Type Positions Sequence
203 -> 391 SKTEFNALMESEKGQSQNLWKFAVYSGLRHGELAALAWEDVDLEKGIVNVRRNLTILDMFGPPKTNAGIRTVTLLQPALEALKEQYKLTGHHRKSEITFYHREYGRTEKQKLHFVFMPRVCNGKQKPYYSVSSLGARWNAAVKRAGIRRRNPYHTRHTFACWLLTAGANPAFIASQMGHETAQMVYEIY
197 -> 404 IKPDPLSKTEFNALMESEKGQSQNLWKFAVYSGLRHGELAALAWEDVDLEKGIVNVRRNLTILDMFGPPKTNAGIRTVTLLQPALEALKEQYKLTGHHRKSEITFYHREYGRTEKQKLHFVFMPRVCNGKQKPYYSVSSLGARWNAAVKRAGIRRRNPYHTRHTFACWLLTAGANPAFIASQMGHETAQMVYEIYGMWIDDMNDEQIA
81 -> 176 KTFGELCDIWTKIKETELTTNTMKKTKSQLKTLRIIICESTPISHIRYSDILNYRNELLHGETLYLDNPRSNKKGRTVRTVDNYIALLCSLLRFAY
5 -> 69 PTGVEIRGRYIRIWFMFRGKRCRETLKGWEITNSNIKKAGNLRALIVHEINSGEFEYLRRFPQSS

 
Classification:
Multifun Terms (GenProtEC)  
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
biological_process GO:0044826 - viral genome integration into host DNA
GO:0006310 - DNA recombination
GO:0015074 - DNA integration
GO:0046718 - viral entry into host cell
GO:0075713 - establishment of integrated proviral latency
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
 G6676-MONOMER
ECOLIWIKI:
 b1345
INTERPRO:
 IPR011010
INTERPRO:
 IPR022000
INTERPRO:
 IPR013762
INTERPRO:
 IPR010998
INTERPRO:
 IPR002104
MODBASE:
 P76056
PFAM:
 PF12167
PFAM:
 PF00589
PRIDE:
 P76056
PROSITE:
 PS51900
PROSITE:
 PS51898
REFSEQ:
 NP_415861
SMR:
 P76056
UNIPROT:
 P76056


Operon      
Name: recET-ralR-rcbA-xisR-intR         
Operon arrangement:
Transcription unit        Promoter
 


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_1770 1411438 reverse nd [RS-EPT-CBR] [1]
  promoter ttcAp5 1411985 reverse Similarity to the consensus
Read more > 		[ICWHO] [2]
  promoter TSS_1771 1412059 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1772 1412113 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1773 (cluster) 1412117 reverse For this promoter, there
Read more > 		[RS-EPT-CBR] [1]
  promoter TSS_1774 1412124 reverse nd [RS-EPT-CBR] [1]
  promoter intRp4 1413260 reverse Similarity to the consensus
Read more > 		[ICWHO] [2]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [2] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

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