A heterozygous SNP is located in the 3'-UTR of a gene. Also the gene has atleast 4 isoforms. I want to sequence the genotype of the SNP present in the 3-'UTR of the RNA of all isoforms. How can I separate the isoforms and get the genotype of the SNP?
Hi Guru,
I think you will have to design degenerate primers to amplify all possible isoforms, clone them and then sequence them. Your will have to do this until you get all the sequences (or the ones you are interested in). This paper might be useful.
http://link.springer.com/article/10.1007%2Fs00360-012-0719-y#page-1
Good luck!
wich gene and what species? I want to look on genbank first to answer. I don't know if you really want to use degenerate primers for SNPs. Maybe just some nice alignments and primer design on area of interest.
Actually I want to seperate the isoforms of SH3GL2 where a SNP rs104930 is located in the 3'-UTR of the gene in human being.
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