One compound heterozygous SNP found in upstream ( g.IVS 06-68 C>T) and downstream ( g.IVS 06+13 A>G) intronic region of DNA.
it may cause mutation/affect or not.
That's a tough one.
The most simple approach i can think of is to run qPCR on RNA of both genotypes, as to check whether one genotype may retain the intron 06 due to alteration of a splice site. Here I would recommend Sanger sequencing of the resulting amplicons, to confirm your genotypes.
If in both genotypes the introns are spliced out nonetheless, you can at least conclude that those mutations don't result in alternative splicing.
Kind regards
Hi there,
mutations in introns may actually alter the splice sites and may cause the intron to be retained with possible deleterious effects on the final transcript. In this regard qPCR may help you as Marc suggested. Also be aware that introns may have also effects on the expression level of those genes they are included in, a phenomenon that is called Intron Mediated Enhancement. So even if the splicing process is not altered, you may still have some effect on the expression of the genes were the mutated introns are.
I find intron mediated enhancement (IME) an absolutely stunning phenomenon, as if regulation of transcription wasn't complex enough.
However, in this case i'd say one could neglect the possibility of IME. Apparently introns with certain characteristics facilitate initiation of transcription upstream of themselves. This increases expression of a full pre-mRNA only if the intron with IME characteristics is within ~1000bp of the transcriptional start site. Hence IME characteristics may only be effective in the first or second intron of a gene.
My favorite study about IME (www.plantcell.org/cgi/doi/10.1105/tpc.17.00020)
Cheers
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