RNA Sequences corresponding to genomic regions which are retained in processed RNA (i.e., not spliced out).

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What are the reasons which make intron detection uncertain?

Intron/exon sequence detection seems to involve statistical prediction which can at best deliver a guess (until experimentally confirmed) as to where the splice site is. What are the reasons why ...
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Is intron removal coordinated?

Are the introns present in a nascent rna molecule removed simultaneously or are they removed in some sort of sequential fashion or is removal completely random?
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Why low variant frequency in exomeseq data (ANNOVAR)?

I've got an annotated ANNOVAR file with 300.000 nucleotide variants of 4 genomes. There's one thing I don't understand when looking at the data: Why are the variant frequencies so low in comparison to ...