RegulonDB RegulonDB 11.0: Gene Form
   

exoD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

intD insEF3 insF3 unknown peaD insE3 exoD xisD intDp6 intDp6 TSS_682 TSS_682

Gene      
Name: exoD    Texpresso search in the literature
Synonym(s): ECK0531, G6295, b0539, ybcC
Type: Pseudo Gene
Genome position(nucleotides): 566098 <-- 566361
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.62
Note(s): ybcC had increased transcriptional levels upon osmotic upshift in experiments using DNA macroarrays 12218039.
External database links:  
ASAP:
 ABE-0001850
ECHOBASE:
 EB2253
ECOLIHUB:
 ybcC
ECOLIWIKI:
 b0539
ECOO157CYC:
 EXOW
ECOO157CYC:
 Z0951
ECOO157CYC:
 Z3367
OU-MICROARRAY:
 b0539
STRING:
 316407.85674674
UNIPROT:
 P75717
COLOMBOS: exoD


Product      
Name: DLP12 prophage; putative exonuclease ExoD
Sequence: Get amino acid sequence Fasta Format
Isoelectric point: 5.156
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
External database links:  
ALPHAFOLD:
 P75717
ECOCYC:
 G6295-MONOMER
UNIPROT:
 P75717


Operon      
Name: exoD         
Operon arrangement:
Transcription unit        Promoter
exoD


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_682 566013 reverse nd [RS-EPT-CBR] [1]
  promoter intDp6 566101 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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