Hello,could you please suggest to me how I can design C. elegans's...

Myriam Gorospe
An example to design divergent primers to detect circular RNAs
1. Determine the mature circRNA sequence
The following is the potential mature sequence of hsa_circ_0113501 circRNA CCTCTTGGGATAGTTTGAAGGAAGTTGAGTGAGACAACAATGATGAGGGCAATATAGCTTTAAAAGAATGAATTCACTCTTACTTTTGCATTGATTCTGAAGAGGAGAGATAAGCGAGGTTTATGGTGAGAGCAAAGTGGTGATGAACAGGCAAGGGAAGCAGATTTGGCTATAGAAAGCAG
2. Determine about 90 nucleotides from each end (5’ and 3’) as indicated below.
CCTCTTGGGATAGTTTGAAGGAAGTTGAGTGAGACAACAATGATGAGGGCAATATAGCTTTAAAAGAATGAATTCACTCTTACTTTTGCATTGATTCTGAAGAGGAGAGATAAGCGAGGTTTATGGTGAGAGCAAAGTGGTGATGAACAGGCAAGGGAAGCAGATTTGGCTATAGAAAGCAG
3. The same can be done if the sequence is longer than this example.
4. Insert the (90 nt) from the 5’ start at the end of the 3’ as shown below. This will create the junction.

TGATTCTGAA GAGGAGAGAT AAGCGAGGTT TATGGTGAGA GCAAAGTGGT GATGAACAGG CAAGGGAAGC AGATTTGGCT ATAGAAAGCA GCCTCTTGGGA TAGTTTGAAG GAAGTTGAGT GAGACAACAA TGATGAGGGC AATATAGCTT TAAAAGAATG AATTCACTCT TACTTTTGCA T
5. Insert the sequence in primer 3 to design primers spanning the junction.
Forward primer: TGGTGAGAGCAAAGTGGTGA
Reverse primer: GCCCTCATCATTGTTGTCTCA

Dear Divya,
Thanks for following our protocol. Unfortunately, I don’t know if there is any web tool available for designing divergent primer for C. Elegan. As described in the the above Procedure (A), You can design divergent primer by preparing the backsplice junction amplicon and use Primer 3 to design primers.

Best,
Amaresh