RegulonDB RegulonDB 11.0: Gene Form
   

sdhX gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

sucD mngR sdhX mngAp mngAp TSS_860 TSS_860 TSS_859 TSS_859 TSS_858 TSS_858

Gene      
Name: sdhX    Texpresso search in the literature
Synonym(s): ECK4621, G0-17009, b4764, rybD
Genome position(nucleotides): 765050 --> 765150
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
48.51
Reference(s): [1] De Mets F., et al., 2019
[2] Miyakoshi M., et al., 2019


Product      
Name: small regulatory RNA SdhX
Synonym(s): RybD, SdhX
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)  
molecular_function GO:0005515 - protein binding
GO:0003729 - mRNA binding
GO:0048027 - mRNA 5'-UTR binding
biological_process GO:0040033 - RNA-mediated gene silencing by inhibition of translation
Note(s): Note(s): ...[more].
Evidence: [IMP] Inferred from mutant phenotype
Reference(s): [1] De Mets F., et al., 2019
[2] Miyakoshi M., et al., 2019
[3] Sridhar J., et al., 2007
External database links:  
ECOCYC:
RNA0-403


Operon      
Name: sdhCDAB-sucABCD-sdhX         
Operon arrangement:
Transcription unit        Promoter
sdhCDAB-sucABCD-sdhX
sdhDAB
sucAB
sucABCD-sdhX


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_858 764187 forward nd [RS-EPT-CBR] [4]
  promoter TSS_859 764211 forward nd [RS-EPT-CBR] [4]
  promoter TSS_860 764423 forward nd [RS-EPT-CBR] [4]


Evidence    

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



Reference(s)    

 [1] De Mets F., Van Melderen L., Gottesman S., 2019, Regulation of acetate metabolism and coordination with the TCA cycle via a processed small RNA., Proc Natl Acad Sci U S A 116(3):1043-1052

 [2] Miyakoshi M., Matera G., Maki K., Sone Y., Vogel J., 2019, Functional expansion of a TCA cycle operon mRNA by a 3' end-derived small RNA., Nucleic Acids Res 47(4):2075-2088

 [3] Sridhar J., Rafi ZA., 2007, Identification of novel genomic islands associated with small RNAs., In Silico Biol 7(6):601-11

 [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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