RegulonDB RegulonDB 10.8: Gene Form
   

ryfD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

clpB rrsG pgeF ryfD rluD Fis Fis Fis RyfD DksA DksA-ppGpp DksA-ppGpp ppGpp ryfDp ryfDp TSS_2908 (cluster) TSS_2908 (cluster) TSS_2907 TSS_2907 clpBp clpBp TSS_2905 TSS_2905 TSS_2904 (cluster) TSS_2904 (cluster) TSS_2903 (cluster) TSS_2903 (cluster) rrsGp1 rrsGp1 rrsGp2 rrsGp2 TSS_2902 TSS_2902

Gene      
Name: ryfD    Texpresso search in the literature
Synonym(s): ECK4418, G0-10600, b4609
Genome position(nucleotides): 2734153 <-- 2734295 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
40.56
External database links:  
PortEco:
ryfD
COLOMBOS: ryfD


Product      
Name: RyfD
Synonym(s): ig: 1603, small regulatory RNA RyfD
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related
Gene Ontology Terms (GO)  
biological_process GO:1900191 - negative regulation of single-species biofilm formation
GO:1902201 - negative regulation of bacterial-type flagellum-dependent cell motility
Note(s): Note(s): ...[more].
Evidence: [IDA] Inferred from direct assay
[IMP] Inferred from mutant phenotype
Reference(s): [1] Bak G., et al., 2015
[2] Kawano M., et al., 2005
External database links:  
ECOCYC:
RNA0-331
ECOLIWIKI:
b4609


Operon      
Name: ryfD         
Operon arrangement:
Transcription unit        Promoter
ryfD


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_2902 2731272 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_2903 (cluster) 2733127 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [3]
  promoter TSS_2904 (cluster) 2734197 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [3]
  promoter TSS_2905 2734202 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_2907 2734207 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_2908 (cluster) 2734293 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [3]


Evidence    

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



Reference(s)    

 [1] Bak G., Lee J., Suk S., Kim D., Young Lee J., Kim KS., Choi BS., Lee Y., 2015, Identification of novel sRNAs involved in biofilm formation, motility, and fimbriae formation in Escherichia coli., Sci Rep 5:15287

 [2] Kawano M., Reynolds AA., Miranda-Rios J., Storz G., 2005, Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli., Nucleic Acids Res 33(3):1040-50

 [3] 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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