full lenght gene amplification from RNA seq data

Question

[maryum]

Hello, I need your help. I have sequences of my desired gene (WRKY TF) from RNA seq data (it was a denovo assembly performed on agave sisalana). Now i need to amplify full length of that gene for which I designed degenerate primers (from 1st nt of gene to the end) . However, I am unable to get the desired band. My gene size is 1000 bp but the bands I am having after PCR amplification is near to 1000 bp (around 800-700 bp) but not exactly 1000 bp. Please help me to sort this issues..

Note: Please find the gel pic in the attachment. ladder used is 1 kb

[GenoMax]

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