RegulonDB RegulonDB 10.8: Gene Form
   

mcaS gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

abgR smrA mcaS CRP TSS_1762 TSS_1762 smrAp1 smrAp1 TSS_1761 TSS_1761 mcaSp mcaSp

Gene      
Name: mcaS    Texpresso search in the literature
Synonym(s): ECK1336, G0-8899, IS061, b4426, isrA
Genome position(nucleotides): 1405659 <-- 1405751 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.61
Reference(s): [1] Jorgensen MG., et al., 2012
External database links:  
ASAP:
ABE-0047247
ECHOBASE:
EB4510
PortEco:
isrA
COLOMBOS: mcaS


Product      
Name: IsrA
Synonym(s): IS061, McaS, mcaS, mcsA, small regulatory RNA McaS
Type: small RNA
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.7 - antisense RNA
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.1 - translation attenuation and efficiency
  3 - regulation --> 3.1 - type of regulation --> 3.1.3 - posttranscriptional --> 3.1.3.3 - inhibition / activation of enzymes
  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
GO:0001000 - bacterial-type RNA polymerase core enzyme binding
biological_process GO:0045947 - negative regulation of translational initiation
GO:0051100 - negative regulation of binding
GO:0045948 - positive regulation of translational initiation
GO:0070928 - regulation of mRNA stability, ncRNA-mediated
GO:1900191 - negative regulation of single-species biofilm formation
GO:1902021 - regulation of bacterial-type flagellum-dependent cell motility
Note(s): Note(s): ...[more].
Evidence: [IDA] Inferred from direct assay
[IMP] Inferred from mutant phenotype
Reference(s): [2] Boehm A., et al., 2012
[3] Chen S., et al., 2002
[1] Jorgensen MG., et al., 2012
[4] Mihailovic MK., et al., 2018
[5] Thomason MK., et al., 2012
External database links:  
ECOCYC:
IS061-RNA
ECOLIWIKI:
b4426


Operon      
Name: mcaS         
Operon arrangement:
Transcription unit        Promoter
mcaS


Transcriptional Regulation      
Display Regulation             
Activated by: CRP


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_1761 1405810 reverse nd [RS-EPT-CBR] [6]
  promoter smrAp1 1405936 forward Similarity to the consensus
Read more >
[ICWHO] [7]
  promoter TSS_1762 1405955 forward nd [RS-EPT-CBR] [6]


Evidence    

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

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Jorgensen MG., Nielsen JS., Boysen A., Franch T., Moller-Jensen J., Valentin-Hansen P., 2012, Small regulatory RNAs control the multi-cellular adhesive lifestyle of Escherichia coli., Mol Microbiol 84(1):36-50

 [2] Boehm A., Vogel J., 2012, The csgD mRNA as a hub for signal integration via multiple small RNAs., Mol Microbiol 84(1):1-5

 [3] Chen S., Lesnik EA., Hall TA., Sampath R., Griffey RH., Ecker DJ., Blyn LB., 2002, A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome., Biosystems 65(2-3):157-77

 [4] 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

 [5] Thomason MK., Fontaine F., De Lay N., Storz G., 2012, A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli., Mol Microbiol 84(1):17-35

 [6] 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.

 [7] 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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