RegulonDB RegulonDB 10.8: Gene Form
   

ryfA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pepB sseA sseB ryfA IS128 C0614 ryfAp11 ryfAp11

Gene      
Name: ryfA    Texpresso search in the literature
Synonym(s): ECK2518, G0-8879, PAIR3b, b4440, tp1
Genome position(nucleotides): 2653855 --> 2654158 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.63
External database links:  
ASAP:
ABE-0047260
ECHOBASE:
EB4526
PortEco:
ryfA
COLOMBOS: ryfA


Product      
Name: RyfA
Synonym(s): PAIR3, PAIR3b, Tp1, small regulatory RNA RyfA, tp1
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] Rivas E., et al., 2001
[3] Rudd KE. 1999
External database links:  
ECOCYC:
RYFA-RNA
ECOLIWIKI:
b4440


Operon      
Name: ryfA         
Operon arrangement:
Transcription unit        Promoter
 


Regulation by small RNA    
  Display Regulation
small RNA IS129


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 ryfAp11 2653699 forward Similarity to the consensus
Read more >
[ICWHO] [4]


Evidence    

 [ICWHO] Inferred computationally without human oversight



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] Rivas E., Klein RJ., Jones TA., Eddy SR., 2001, Computational identification of noncoding RNAs in E. coli by comparative genomics., Curr Biol 11(17):1369-73

 [3] Rudd KE., 1999, Novel intergenic repeats of Escherichia coli K-12., Res Microbiol 150(9-10):653-64

 [4] 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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