Part:BBa_K5047022
DNA encodes a shRNA binds to chitin synthase gene of V. velutina.
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_0475011721 within the genomic coordinates NC_0621881 19915311-19930067 iVesVel21 genome GCF_9124700251. The specific target sequence spans from positions 19925844 to 19925869. This shRNA has been designed to keep GC content intermediate approx 30 - 50% with 44% in this variant to avoid strong secondary structure. This sequence has off-targets in Vespa mandarinia one mismatch Vespa crabro one INDEL and Rhorus exstirpatorius one mismatch. 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 862 2010 204-11 doi101016jantiviral201002320. Through secondary structure analysis performed by ViennaRNA the free energy of the thermodynamic ensemble is -47.39 kcalmol. The frequency of the minimum free energy structure in the ensemble is 53.22%. The ensemble diversity is 068.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
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