RegulonDB RegulonDB 10.10: 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
ECOLIHUB:
 intR
OU-MICROARRAY:
 b1345
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:
 IPR013762
INTERPRO:
 IPR022000
INTERPRO:
 IPR011010
INTERPRO:
 IPR010998
INTERPRO:
 IPR002104
MODBASE:
 P76056
PFAM:
 PF00589
PFAM:
 PF12167
PRIDE:
 P76056
PROSITE:
 PS51900
PROSITE:
 PS51898
REFSEQ:
 NP_415861
UNIPROT:
 P76056


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


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 nd [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 nd [RS-EPT-CBR] [1]
  promoter TSS_1774 1412124 reverse nd [RS-EPT-CBR] [1]
  promoter intRp4 1413260 reverse nd [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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