RegulonDB RegulonDB 10.10: Gene Form
   

rydB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

sufA ydiH rydB OxyR OxyR IHF IscR IscR NsrR IscR Fur NsrR rydBp1 rydBp1 rydBp2 rydBp2 sufAp sufAp

Gene      
Name: rydB    Texpresso search in the literature
Synonym(s): ECK1681, G0-8876, IS082, b4430, tpe7
Genome position(nucleotides): 1764713 <-- 1764780 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.94
External database links:  
ASAP:
 ABE-0047250
ECHOBASE:
 EB4514
ECOLIHUB:
 rydB
COLOMBOS: rydB


Product      
Name: small regulatory RNA RydB
Synonym(s): IS082, RydB, RydB small RNA regulator of RpoS, Tpe7
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related
Gene Ontology Terms (GO)  
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] Chen S., et al., 2002
[2] Komasa M., et al., 2011
[3] Wassarman KM., et al., 2001
External database links:  
ECOCYC:
 RYDB-RNA
ECOLIWIKI:
 b4430


Operon      
Name: rydB         
Operon arrangement:
Transcription unit        Promoter
rydB


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 rydBp2 1764924 reverse nd [ICWHO] [4]
  promoter rydBp1 1764930 reverse nd [ICWHO] [4]


Evidence    

 [ICWHO] Inferred computationally without human oversight


Reference(s)    

 [1] Chen S., Lesnik EA., Hall TA., Sampath R., Griffey RH., Ecker DJ., Blyn LB., 2002, A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome., Biosystems 65(2-3):157-77

 [2] Komasa M., Fujishima K., Hiraoka K., Shinhara A., Lee BS., Tomita M., Kanai A., 2011, A screening system for artificial small RNAs that inhibit the growth of Escherichia coli., J Biochem 150(3):289-94

 [3] Wassarman KM., Repoila F., Rosenow C., Storz G., Gottesman S., 2001, Identification of novel small RNAs using comparative genomics and microarrays., Genes Dev 15(13):1637-51

 [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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