RegulonDB RegulonDB 10.7: Gene Form
   

ssrA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

intA smpB ssrA terminator anti-terminator anti-anti-terminator TSS_2971 TSS_2971 ssrAp ssrAp ssrAp2 ssrAp2

Gene      
Name: ssrA    Texpresso search in the literature
Synonym(s): ECK2617, EG30100, b2621, sipB
Genome position(nucleotides): 2755593 --> 2755955 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
52.89
External database links:  
ASAP:
ABE-0008624
CGSC:
35783
ECHOBASE:
EB4263
OU-MICROARRAY:
b2621
PORTECO:
ssrA
REGULONDB:
b2621
M3D: ssrA
COLOMBOS: ssrA
PortEco: b2621


Product      
Name: TmRNA
Synonym(s): "ssrA, 10Sa RNA, 10Sa", SipB, SsrA, tmRNA, transfer-messenger RNA
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.4 - RNA degradation
  2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
  2 - information transfer --> 2.3 - protein related --> 2.3.6 - turnover, degradation
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional
  5 - cell processes --> 5.6 - protection --> 5.6.4 - drug resistance/sensitivity
  6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)  
molecular_function GO:0005515 - protein binding
GO:0043022 - ribosome binding
biological_process GO:0070929 - trans-translation
GO:0070930 - trans-translation-dependent protein tagging
GO:0072344 - rescue of stalled ribosome
Note(s): Note(s): ...[more].
Evidence: [IDA] Inferred from direct assay
Reference(s): [1] Kirby JE., et al., 1994
[2] Muto A., et al., 1996
[3] Nakano H., et al., 2001
[4] Oh BK., et al., 1990
[5] Ray BK, et al., 1979
[6] Roche ED., et al., 1999
[7] Williams KP. 2003
External database links:  
ECOCYC:
SSRA-RNA
ECOLIWIKI:
b2621


Operon      
Name: ssrA         
Operon arrangement:
Transcription unit        Promoter
ssrA


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 ssrAp2 2755507 forward Similarity to the consensus
Read more >
[ICWHO] [8]
  promoter TSS_2971 2756133 forward nd [RS-EPT-CBR] [9]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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



Reference(s)    

 [1] Kirby JE., Trempy JE., Gottesman S., 1994, Excision of a P4-like cryptic prophage leads to Alp protease expression in Escherichia coli., J Bacteriol 176(7):2068-81

 [2] Muto A., Sato M., Tadaki T., Fukushima M., Ushida C., Himeno H., 1996, Structure and function of 10Sa RNA: trans-translation system., Biochimie 78(11-12):985-91

 [3] Nakano H., Goto S., Nakayashiki T., Inokuchi H., 2001, Temperature-sensitive mutations in various genes of Escherichia coli K12 can be suppressed by the ssrA gene for 10Sa RNA (tmRNA)., Mol Genet Genomics 265(4):615-21

 [4] Oh BK., Chauhan AK., Isono K., Apirion D., 1990, Location of a gene (ssrA) for a small, stable RNA (10Sa RNA) in the Escherichia coli chromosome., J Bacteriol 172(8):4708-9

 [5] Ray BK, Apirion D., 1979, Characterization of 10S RNA: a new stable rna molecule from Escherichia coli., Mol Gen Genet. Jul 2;174(1):25-32.

 [6] Roche ED., Sauer RT., 1999, SsrA-mediated peptide tagging caused by rare codons and tRNA scarcity., EMBO J 18(16):4579-89

 [7] Williams KP., 2003, Traffic at the tmRNA gene., J Bacteriol 185(3):1059-70

 [8] 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

 [9] 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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