RegulonDB RegulonDB 10.7: Gene Form
   

sokB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

trg mokB hokB sokB yncP CRP Fis Fis terminator trgp1 trgp1 mokBp3 mokBp3 sokBp sokBp sokBp3 sokBp3

Gene      
Name: sokB    Texpresso search in the literature
Synonym(s): ECK1414, G0-9611, b4429
Genome position(nucleotides): 1492119 --> 1492174 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.79
External database links:  
ASAP:
ABE-0047249
ECHOBASE:
EB4289
PORTECO:
sokB
REGULONDB:
b4429
M3D: sokB
COLOMBOS: sokB
PortEco: sokB


Product      
Name: SokB
Synonym(s): antisense RNA blocking mokB and hokB translation, putative small regulatory RNA SokB
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.6 - antisense RNA
Gene Ontology Terms (GO)  
Note(s): Note(s): ...[more].
Evidence: [HIFS] Human inference of function from sequence
[IDA] Inferred from direct assay
Reference(s): [1] Faridani OR., et al., 2006
[2] Kawano M., et al., 2005
[3] Pedersen K., et al., 1999
[4] Schneider D., et al., 2000
[5] Woods R., et al., 2006
External database links:  
ECOCYC:
RNA0-165
ECOLIWIKI:
b4429


Operon      
Name: sokB         
Operon arrangement:
Transcription unit        Promoter
 


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 sokBp3 1492116 forward Similarity to the consensus
Read more >
[ICWHO] [6]
  promoter mokBp3 1492305 reverse Similarity to the consensus
Read more >
[ICWHO] [6]


Evidence    

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Faridani OR., Nikravesh A., Pandey DP., Gerdes K., Good L., 2006, Competitive inhibition of natural antisense Sok-RNA interactions activates Hok-mediated cell killing in Escherichia coli., Nucleic Acids Res 34(20):5915-22

 [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] Pedersen K., Gerdes K., 1999, Multiple hok genes on the chromosome of Escherichia coli., Mol Microbiol 32(5):1090-102

 [4] Schneider D., Duperchy E., Coursange E., Lenski RE., Blot M., 2000, Long-term experimental evolution in Escherichia coli. IX. Characterization of insertion sequence-mediated mutations and rearrangements., Genetics 156(2):477-88

 [5] Woods R., Schneider D., Winkworth CL., Riley MA., Lenski RE., 2006, Tests of parallel molecular evolution in a long-term experiment with Escherichia coli., Proc Natl Acad Sci U S A 103(24):9107-12

 [6] 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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