RegulonDB RegulonDB 11.1: 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 sokCp sokCp hokCp4 hokCp4

Gene      
Name: sokC    Texpresso search in the literature
Synonym(s): ECK0019, G0-9581, b4413, sof
Genome position(nucleotides): 16952 --> 17010
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 45.76
External database links:  
ASAP:
 ABE-0047238
ECHOBASE:
 EB4290
ECOLIHUB:
 sokC
COLOMBOS: sokC


Product      
Name: small regulatory RNA antitoxin SokC
Synonym(s): SokC, antisense RNA blocking mokC and hokC translation, 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)  
biological_process GO:0035194 - post-transcriptional gene silencing by RNA
Note(s): Note(s): ...[more].
Evidence: [COMP-HINF-FN-FROM-SEQ] Human inference of function from sequence
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Pedersen K., et al., 1999
[2] Poulsen LK., et al., 1991
External database links:  
ECOCYC:
 RNA0-141
ECOLIWIKI:
 b4413


Operon      
Name: sokC         
Operon arrangement:
Transcription unit        Promoter
sokC


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 nd [COMP-AINF] [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    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

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

 [2] Poulsen LK., Refn A., Molin S., Andersson P., 1991, The gef gene from Escherichia coli is regulated at the level of translation., Mol Microbiol 5(7):1639-48

 [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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