I would like to design primers that are complimentary or begin in the UTRs (5' and the 3') of a gene? Where exactly and how do I find the coding sequence that includes the UTRS ?
Hi,
Have you checked NCBI transcriptome database or assembled genomes? If your organism is not on those lists, you can try phylogenetically the most closely related organism to yours.
Cheers
Use the ENSEMBL database website and search for the gene of interest of yours. It will give you transcript details, including the UTR regions. Pick your base pair and then design your primer through the primer 3 tool. Hope this will help you.
Hi Sophia Hyman
There are lots of software and tools depending on what type of sequence you have. You can have an overview of different gene-finding software here: (http://www.geneprediction.org/software.html). However, ORF finder (https://www.ncbi.nlm.nih.gov/orffinder/) might be a good option to try.
After finding the ORF and UTR regions, you can use different primer designing tools and software (Primer3, SnapGene, etc.) to obtain primers corresponding to the UTRs.
Good luck
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