RegulonDB RegulonDB 10.8: Gene Form
   

xisR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

intR xisR rcbA ralA ralR terminator ralAp ralAp intRp4 intRp4 TSS_1774 TSS_1774 TSS_1773 (cluster) TSS_1773 (cluster) TSS_1772 TSS_1772 TSS_1771 TSS_1771

Gene      
Name: xisR    Texpresso search in the literature
Synonym(s): ECK1343, G6677, b1346, ydaQ
Genome position(nucleotides): 1413237 <-- 1413452 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
44.91
External database links:  
ASAP:
ABE-0004519
ECHOBASE:
EB3142
OU-MICROARRAY:
b1346
PortEco:
ydaQ
STRING:
511145.b1346
COLOMBOS: xisR


Product      
Name: Rac prophage; excisionase
Synonym(s): XisR, YdaQ
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 8.456
Isoelectric point: 9.56
Motif(s):
 
Type Positions Sequence
5 -> 69 IFNEEWMVEYGLMLRTGLGARQIEAYRQNCWVEGFHFKRVSPLGKPDSKRGIIWYNYPKINQFIK

 

Classification:
Multifun Terms (GenProtEC)  
  8 - extrachromosomal --> 8.1 - prophage genes and phage related functions
Gene Ontology Terms (GO)  
molecular_function GO:1990837 - sequence-specific double-stranded DNA binding
biological_process GO:0032359 - provirus excision
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Liu X., et al., 2015
External database links:  
ECOCYC:
G6677-MONOMER
ECOLIWIKI:
b1346
INTERPRO:
IPR009634
INTERPRO:
IPR038146
PFAM:
PF06806
PRIDE:
P76057
REFSEQ:
NP_415862
SMR:
P76057
UNIPROT:
P76057


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


RNA cis-regulatory element    
Attenuation: Translational


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_1771 1412059 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_1772 1412113 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_1773 (cluster) 1412117 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_1774 1412124 reverse nd [RS-EPT-CBR] [2]
  promoter intRp4 1413260 reverse Similarity to the consensus
Read more >
[ICWHO] [3]


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] Liu X., Li Y., Guo Y., Zeng Z., Li B., Wood TK., Cai X., Wang X., 2015, Physiological Function of Rac Prophage During Biofilm Formation and Regulation of Rac Excision in Escherichia coli K-12., Sci Rep 5:16074

 [2] 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.

 [3] 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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