Hi everyone,
A gene is present in an "organism A" and its sequence can be found online on NCBI. An orthologue of the same gene is present in "organism B" but can't be found on the NCBI. Can I use the gene sequence of that "organism A" to design my primers and amplify the orthologue of the gene present in "organism B"? Both organisms belong to fungi but are from different classes.
Dear Jawad,
If the gene from organism A and B has the same conserved region flanking the gene of interest, sure.
Hello
Apparently this is the only approach for you. Consider my experience: Do a multiple alignment on the sequence originated from multiple organisms closely related to your desired organism. Then find conserved region/s, then you may design primers for those conserved region. It would increase the chance of amplification.
Hi, Muhammad Jawad , sometimes you can find undescripted sequences for your target organism, I mean "ncbi nucleotide" without gene or mRNA description. Once I found very similar sequence to known from closely related species. It was very useful for me because I marked the borders of gene and design primers in the sequence.
To do this you need to define the clade to which A and B belong. If you can find sequences other than A which are more distant than B, then any sequence that is conserved between them (and A) should also be conserved in B.
Andrew Jenkins Andrei S. Babenka Ali Javadmanesh Andrew Ting Thank you very much for your replies and valuable suggestions. A lot of things are cleared now.
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