Given that transcriptome sequences are obtained from mRNA, is it necessary to specify intron and exon positions when analizing genetic variation and divergence with this kind of data? Or is it not necessary because in theory, introns should not be present in transcriptome sequences?
I will appreciate very much any information about this topic.
Well introns have SNPs which I would class as genetic information.
Divergence can also be found in non-coding regions such as changes in repetitive elements.
But No, the transcriptome does not contain usually introns unless its lncRNA
I disagree - intron retention and read throughs can occur in tumour transcriptome sequences that contain splicing aberrations and mutations in stop codons, etc. So while in your case, looking at genetic divergence in presumably healthy individuals, you may not want to include introns, this is not the case for all tissues.
In single-nucleus RNA sequencing experiments of brain tissue there are instances of "intronic regions" being captured in the transcriptome. With the current lack of gene models for brain tissue it is most likely that these data represent splice variants that aren't present in other cell types.
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