Difference between revisions of "Part:BBa K5047006"
 
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This DNA sequence encodes a short hairpin RNA shRNA designed to target a specific region within the chitin synthase gene of the Asian hornet Vespa velutina. The target region is located on an exon common to all isoforms of the chitin synthase gene GeneID 124951980 Genbank XM_047501172.1 within the genomic coordinates NC_062188.1 19915311-19930067 iVesVel2.1 genome GCF_912470025.1. The specific target sequence spans from positions 19925853 to 19925878. This shRNA has been designed to keep GC content intermediate approx. 30 - 50% with 48% in this variant to avoid strong secondary structure. Additionally, this shRNA is the variant with the lowest number of potential off-target interactions compared to TS2 BBa_XXXXX TS3 BBa_XXXXX and TS4 BBa_XXXXX. This sequence has off-targets in Vespa mandarinia and Vespa crabro with one mismatch only.
  
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This shRNA contains the standard UUCAAGAGA 9 nt loop Brummelkamp Thijn R et al. A system for stable expression of short interfering RNAs in mammalian cells Science New York N.Y. vol. 2965567 2002 550-3 doi10.1126science1068999.
  
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Through secondary structure analysis performed by ViennaRNA the free energy of the thermodynamic ensemble is -48.96 kcalmol. The frequency of the minimum free energy structure in the ensemble is 40.08%. The ensemble diversity is 1.71.
  
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<!-- This DNA sequence encodes a short hairpin RNA (shRNA) designed to target a specific region within the chitin synthase gene of the Asian hornet (Vespa velutina). The target region is located on an exon common to all isoforms of the chitin synthase gene (GeneID: 124951980, Genbank: XM_047501172.1), within the genomic coordinates NC_062188.1:19,915,311-19,930,067 (iVesVel2.1 genome, GCF_912470025.1). The specific target sequence spans from positions 19’925’853 to 19’925’878. This shRNA has been designed to keep GC content intermediate (approx. 30 - 50%, with 48% in this variant) to avoid strong secondary structure. Additionally, this shRNA is the variant with the lowest number of potential off-target interactions compared to TS2 (BBa_XXXXX), TS3 (BBa_XXXXX) and TS4 (BBa_XXXXX). This sequence has off-targets in Vespa mandarinia and Vespa crabro with one mismatch only.
 
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​​This shRNA contains the optimized UGAUAUGUGCA loop (Schopman, Nick C T et al. “Optimization of shRNA inhibitors by variation of the terminal loop sequence.” Antiviral research vol. 86,2 (2010): 204-11. doi:10.1016/j.antiviral.2010.02.320).
 
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Through secondary structure analysis performed by ViennaRNA, the free energy of the thermodynamic ensemble is -50.39 kcal/mol. The frequency of the minimum free energy structure in the ensemble is 52.98%. The ensemble diversity is 0.70.
 
  
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===Usage and Biology===
 
===Usage and Biology===
  
 
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
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<partinfo>BBa_K5047004 SequenceAndFeatures</partinfo>
  
  
 
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===Functional Parameters===
 
===Functional Parameters===
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<partinfo>BBa_K5047004 parameters</partinfo>
 
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Latest revision as of 11:53, 30 September 2024

Constitutive promoter in Lactococcus lactis

This DNA sequence encodes a short hairpin RNA shRNA designed to target a specific region within the chitin synthase gene of the Asian hornet Vespa velutina. The target region is located on an exon common to all isoforms of the chitin synthase gene GeneID 124951980 Genbank XM_047501172.1 within the genomic coordinates NC_062188.1 19915311-19930067 iVesVel2.1 genome GCF_912470025.1. The specific target sequence spans from positions 19925853 to 19925878. This shRNA has been designed to keep GC content intermediate approx. 30 - 50% with 48% in this variant to avoid strong secondary structure. Additionally, this shRNA is the variant with the lowest number of potential off-target interactions compared to TS2 BBa_XXXXX TS3 BBa_XXXXX and TS4 BBa_XXXXX. This sequence has off-targets in Vespa mandarinia and Vespa crabro with one mismatch only.

This shRNA contains the standard UUCAAGAGA 9 nt loop Brummelkamp Thijn R et al. A system for stable expression of short interfering RNAs in mammalian cells Science New York N.Y. vol. 2965567 2002 550-3 doi10.1126science1068999.

Through secondary structure analysis performed by ViennaRNA the free energy of the thermodynamic ensemble is -48.96 kcalmol. The frequency of the minimum free energy structure in the ensemble is 40.08%. The ensemble diversity is 1.71.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]