RegulonDB RegulonDB 10.9: Gene Form
   

yzfA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

tamB ytfP yzfA chpS chpB tamA anti-anti-terminator anti-terminator terminator terminator anti-terminator anti-anti-terminator TSS_5078 TSS_5078 chpSp2 chpSp2 chpSp1 chpSp1 yzfAp2 yzfAp2 TSS_5077 TSS_5077 TSS_5076 TSS_5076

Gene      
Name: yzfA    Texpresso search in the literature
Synonym(s): ECK4219, EG11213, b4223, ileR, yjfA
Type: Phantom Gene
Genome position(nucleotides): 4447976 <-- 4448245 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.22
Note(s): yzfA was originally described as the ileR locus Weiss DL,1986. However, in a personal communication to Kenn Rudd (see the EcoGene database entry), Ron Somerville stated that yzfA is not the IleR structural gene.
yfzA was deaccessioned in ASAP in 2007. Comment in ASAP: yzfA (b4223) is no longer thought to be an actual gene and has been deaccessioned; this reading frame is on the opposite strand of ytfP
Eric Neeno-Eckwall, personal communication 11/7/2018: YtfP is highly conserved among the enterobacteria, with conservation of genome context as far out as Vibrio. I looked at a couple of examples, and the coding sequence of yzfA is not conserved. It would be a pseudogene in Dickeya, and would have a long C-terminal extension in Salmonella (and is not predicted by GeneMark). A version in Escherichia albertii (87% nucleotide identity for ytfP) would require a different start codon and is also not predicted by GeneMark.
Previous UniProt ID: P08339
External database links:  
ASAP:
ABE-0013816
ECHOBASE:
EB4373
ECOLIHUB:
yzfA
ECOLIWIKI:
b4223
OU-MICROARRAY:
b4223
STRING:
316407.85676974
COLOMBOS: yzfA


Operon      
Name: yzfA         
Operon arrangement:
Transcription unit        Promoter
yzfA


RNA cis-regulatory element    
Attenuation: Transcriptional


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_5076 4445404 forward nd [RS-EPT-CBR] [1]
  promoter TSS_5077 4447908 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_5078 4448430 forward nd [RS-EPT-CBR] [1]


Evidence    

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



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.


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