I want to study some gene expression of an animal, which genome sequence is not completely available. There are very limited data about the animal. But, there are some partial gene sequence. Can I design primers for PCR using the partial sequence ?
It depends on your objective, if it is a specific gene you can design your own set of primers, but if it is a common DNA marker (eg. COI) you can save time by using universal primers described in mammals, birds, reptiles, nematodes, etc.:
https://dnabarcoding101.org/lab/planning-prep.html#prseq
Complete coding sequence (CDS) is preferable for both qPCR and RT-PCR because CDs do not contain intron they only contain exons but mRNA sequences contain both coding and non-coding sequences.
Yes. you can use the partial sequences. Do set the primer designing parameters (Tm, GC content etc.) properly and do check in the output of the primer designing software critically that where it is ligating to the template and how much template will be amplified with the same. Also if you have lesser number of sequences do check for all the outputs as we receive five or more outputs after primer designing. (Also do check for repetition for primer sequence as well)
- Badges
- Science method