RegulonDB RegulonDB 11.1: Gene Form
   

ssrS gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

fau zapA ssrS TSS_3191 (cluster) TSS_3191 (cluster) ssrSp1 ssrSp1 TSS_3189 TSS_3189 TSS_3188 TSS_3188 ssrSp2 ssrSp2 ssrSp ssrSp TSS_3186 TSS_3186 TSS_3185 TSS_3185

Gene      
Name: ssrS    Texpresso search in the literature
Synonym(s): ECK2906, EG30099, b2911, ssr
Genome position(nucleotides): 3055983 --> 3056165
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 55.19
External database links:  
ASAP:
 ABE-0009556
ECHOBASE:
 EB4262
ECOLIHUB:
 ssrS
OU-MICROARRAY:
 b2911
COLOMBOS: ssrS


Product      
Name: 6S RNA
Synonym(s): Ssr, SsrS
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level
Gene Ontology Terms (GO)  
Note(s): Note(s): ...[more].
Evidence: [EXP-IDA] Inferred from direct assay
Reference(s): [1] Brownlee GG. 1971
[2] Lal A., et al., 2018
[3] Sklar J., et al., 1975
[4] Somasekhar G., et al., 1983
[5] Trown PW., et al., 1973
[6] Wassarman KM., et al., 2000
External database links:  
ECOCYC:
 6S-RNA
ECOLIWIKI:
 b2911


Operon      
Name: ssrS-fau         
Operon arrangement:
Transcription unit        Promoter
ssrS
ssrS-ygfA
ssrS
ssrS-ygfA
ssrS
ssrS-ygfA


Transcriptional Regulation      
Display Regulation             
Activated by: Fis
Repressed by: H-NS, Lrp, Fis, StpA


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_3185 3055639 forward nd [RS-EPT-CBR] [7]
  promoter TSS_3186 3055757 forward nd [RS-EPT-CBR] [7]
  promoter TSS_3188 3055764 forward nd [RS-EPT-CBR] [7]
  promoter TSS_3189 3055899 forward nd [RS-EPT-CBR] [7]
  promoter TSS_3191 (cluster) 3055983 forward nd [RS-EPT-CBR] [7]


Evidence    

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


Reference(s)    

 [1] Brownlee GG., 1971, Sequence of 6S RNA of E. coli., Nat New Biol 229(5):147-9

 [2] Lal A., Krishna S., Seshasayee ASN., 2018, Regulation of Global Transcription in Escherichia coli by Rsd and 6S RNA., G3 (Bethesda) 8(6):2079-2089

 [3] Sklar J., Yot P., Weissman SM., 1975, Determination of genes, restriction sites, and DNA sequences surrounding the 6S RNA template of bacteriophage lambda., Proc Natl Acad Sci U S A 72(5):1817-21

 [4] Somasekhar G., Szybalski W., 1983, Mapping of the Q-utilization site (qut) required for antitermination of late transcription in bacteriophage lambda., Gene 26(2-3):291-4

 [5] Trown PW., Meyer PL., 1973, Recognition of template RNA by Q polymerase: sequence at the 3'-terminus of Q 6S RNA., Arch Biochem Biophys 154(1):250-62

 [6] Wassarman KM., Storz G., 2000, 6S RNA regulates E. coli RNA polymerase activity., Cell 101(6):613-23

 [7] 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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