RegulonDB RegulonDB 11.1: Gene Form
   

chiX gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybaP ybaK ybaQ chiX ybaPp6 ybaPp6 ybaPp4 ybaPp4 ybaPp3 ybaPp3 ybaQp ybaQp ybaQp3 ybaQp3 TSS_649 TSS_649 TSS_648 TSS_648 TSS_647 TSS_647 TSS_646 TSS_646 chiXp chiXp

Gene      
Name: chiX    Texpresso search in the literature
Synonym(s): ECK4396, G0-9382, b4585, micM, rybC, sroB
Genome position(nucleotides): 507204 --> 507287
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 36.9
External database links:  
ASAP:
 ABE-0285117
ECOLIHUB:
 micM
COLOMBOS: chiX


Product      
Name: small regulatory RNA ChiX
Synonym(s): ChiX, MicM, RybC, SroB
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related
Gene Ontology Terms (GO)  
molecular_function GO:0005515 - protein binding
GO:0003729 - mRNA binding
GO:0048027 - mRNA 5'-UTR binding
biological_process GO:0035194 - post-transcriptional gene silencing by RNA
GO:1900191 - negative regulation of single-species biofilm formation
Note(s): Note(s): ...[more].
Evidence: [EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Kiselev S., et al., 2021
[2] Mandin P., et al., 2009
[3] Mihailovic MK., et al., 2018
[4] Rasmussen AA., et al., 2009
External database links:  
ECOCYC:
 RNA0-123
ECOLIWIKI:
 b4585


Operon      
Name: chiX         
Operon arrangement:
Transcription unit        Promoter
chiX


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 TSS_646 507216 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_647 507236 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_648 507241 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_649 508097 reverse nd [RS-EPT-CBR] [5]
  promoter ybaQp3 508174 forward nd [COMP-AINF] [6]
  promoter ybaPp3 508262 reverse nd [COMP-AINF] [6]
  promoter ybaPp4 508264 reverse nd [COMP-AINF] [6]
  promoter ybaPp6 508284 reverse nd [COMP-AINF] [6]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Kiselev S., Markelova N., Masulis I., 2021, Divergently Transcribed ncRNAs in Escherichia coli: Refinement of the Transcription Starts Assumes Functional Diversification., Front Mol Biosci 8:610453

 [2] Mandin P., Gottesman S., 2009, A genetic approach for finding small RNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system., Mol Microbiol 72(3):551-65

 [3] Mihailovic MK., Vazquez-Anderson J., Li Y., Fry V., Vimalathas P., Herrera D., Lease RA., Powell WB., Contreras LM., 2018, High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites., Nat Commun 9(1):4084

 [4] Rasmussen AA., Johansen J., Nielsen JS., Overgaard M., Kallipolitis B., Valentin-Hansen P., 2009, A conserved small RNA promotes silencing of the outer membrane protein YbfM., Mol Microbiol 72(3):566-77

 [5] 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.

 [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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