RegulonDB RegulonDB 11.1: Gene Form
   

ffs gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybaZ ybaA ffs terminator terminator TSS_610 TSS_610 ffsp7 ffsp7 ffsp5 ffsp5 ffsp6 ffsp6

Gene      
Name: ffs    Texpresso search in the literature
Synonym(s): ECK0449, EG30027, b0455
Genome position(nucleotides): 476448 --> 476561
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 64.04
External database links:  
ASAP:
 ABE-0001579
CGSC:
 18373
ECHOBASE:
 EB4190
ECOLIHUB:
 ffs
OU-MICROARRAY:
 b0455
COLOMBOS: ffs


Product      
Name: signal recognition particle 4.5S RNA
Synonym(s): Ffs
Type: small RNA
Cellular location: cytosol
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.6 - rRNA, stable RNA
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
  2 - information transfer --> 2.3 - protein related --> 2.3.5 - export, signal peptide cleavage
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
cellular_component GO:0048501 - signal recognition particle, plasma membrane targeting
molecular_function GO:0043022 - ribosome binding
biological_process GO:0006614 - SRP-dependent cotranslational protein targeting to membrane
Note(s): Note(s): ...[more].
Reference(s): [1] Avdeeva ON., et al., 2002
[2] Bailey SC., et al., 1979
[3] Gu SQ., et al., 2003
[4] Huang Y., et al., 1994
[5] Jensen CG., et al., 1994
[6] Malygin A., et al., 1996
[7] Phillips GJ., et al., 1992
[8] Zwieb C., et al., 2005
External database links:  
ECOCYC:
 FFS-RNA
ECOLIWIKI:
 b0455


Operon      
Name: ffs         
Operon arrangement:
Transcription unit        Promoter
ffs


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 ffsp6 476288 forward nd [COMP-AINF] [9]
  promoter ffsp5 476399 forward nd [COMP-AINF] [9]
  promoter ffsp7 476422 forward nd [COMP-AINF] [9]
  promoter TSS_610 476448 forward nd [RS-EPT-CBR] [10]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Avdeeva ON., Myasnikov AG., Sergiev PV., Bogdanov AA., Brimacombe R., Dontsova OA., 2002, Construction of the 'minimal' SRP that interacts with the translating ribosome but not with specific membrane receptors in Escherichia coli., FEBS Lett 514(1):70-3

 [2] Bailey SC., Apirion D., 1979, Repetitive DNA in Escherichia coli: multiple sequences complementary to small stable RNAs., Mol Gen Genet 172(3):339-43

 [3] Gu SQ., Peske F., Wieden HJ., Rodnina MV., Wintermeyer W., 2003, The signal recognition particle binds to protein L23 at the peptide exit of the Escherichia coli ribosome., RNA 9(5):566-73

 [4] Huang Y., Gong L., Zhang L., Li S., Zhu S., 1994, [Comparative study of single strand conformation polymorphism of 4.5S RNA gene in enterobacteria], Wei Sheng Wu Xue Bao 34(2):100-5

 [5] Jensen CG., Pedersen S., 1994, Concentrations of 4.5S RNA and Ffh protein in Escherichia coli: the stability of Ffh protein is dependent on the concentration of 4.5S RNA., J Bacteriol 176(23):7148-54

 [6] Malygin A., Karpova G., Westermann P., 1996, Hybridization of two oligodeoxynucleotides to both strands of an RNA hairpin structure increases the efficiency of RNA-DNA duplex formation., FEBS Lett 392(2):114-6

 [7] Phillips GJ., Silhavy TJ., 1992, The E. coli ffh gene is necessary for viability and efficient protein export., Nature 359(6397):744-6

 [8] Zwieb C., van Nues RW., Rosenblad MA., Brown JD., Samuelsson T., 2005, A nomenclature for all signal recognition particle RNAs., RNA 11(1):7-13

 [9] 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

 [10] 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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