RegulonDB RegulonDB 10.8: 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 Genome Browser
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: SdhX
Synonym(s): ECK4621, G0-17009, RybD, b4764, rybD, small regulatory RNA 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:0048027 - mRNA 5'-UTR binding
biological_process GO:0040033 - negative regulation of translation, ncRNA-mediated
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


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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