RegulonDB RegulonDB 10.8: Gene Form
   

sokC gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

nhaA mokC hokC sokC NhaR NhaR NhaR NhaR terminator TSS_43 TSS_43 TSS_42 TSS_42 nhaAp1 nhaAp1 nhaAp2 nhaAp2 TSS_41 TSS_41 hokCp4 hokCp4

Gene      
Name: sokC    Texpresso search in the literature
Synonym(s): ECK0019, G0-9581, b4413, sof
Genome position(nucleotides): 16952 --> 17006 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
47.27
External database links:  
ASAP:
ABE-0047238
ECHOBASE:
EB4290
PortEco:
sokC
COLOMBOS: sokC


Product      
Name: SokC
Synonym(s): SokC, sof
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] Kawano M., et al., 2005
[2] Pedersen K., et al., 1999
External database links:  
ECOCYC:
RNA0-141
ECOLIWIKI:
b4413


Operon      
Name: sokC         
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 hokCp4 16951 reverse Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter TSS_41 16961 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_42 18023 forward nd [RS-EPT-CBR] [4]
  promoter TSS_43 18025 forward nd [RS-EPT-CBR] [4]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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



Reference(s)    

 [1] 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

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

 [3] 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

 [4] 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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