introns as a subset of mRNAs

[rathankar]

Hi all
can we have introns as a subset of mRNAs. pls let me know.
in yeast genome, if found that a few mRNAs has intronic regions too. how can this be

[pbluescript]

It could be DNA contamination, unspliced RNAs, retained introns, another transcript, etc. It's a common event with RNA-Seq data.

[rathankar]

is it that before we proceed for analysis, we need to remove all such regions

[Richard Finney]

Let's call them "intronic unspliced reads" : IURs. ... and ... yes ... they do happen to varying amounts depending (I think) on preparation.

Let's ask a couple of questions ...
What analysis are you going to do? Count coverage for exons? Find SNPS?
Are you going to define IURs as "only hits intron" or "partially hits intron"?

You don't know if a read that hits an exon only is also immature so you can't filter them (unless somehow you can associate the read with its pair which hits an IUR).

If the IURs happen evenly throughout the transcribing regions genome and occur in relative proportion to the occurance of mature transcript, you might not filter them.
Sadly, it's probably that maturation is taking place at differing rates depending on the gene [ just a guess, I don't know for sure].

....
hmmmm ... Why not try both methods (filtering and not filtering) and see of it affects the results.

[rathankar]

I am an application scientist working for apsara innovations currently working on pipeline pilot NGS collection
i have an yeast repository in which the complete genome is downloaded along with its features. I queried these features for mRNA query and then had a subquery to extract all the records which had intron as its feature in the mRNA sequence. The output is i got around 120 sequences that had introns in mRNA sequence. what do i understand by this

[Richard Finney]

User pbluescript summarized it well : It could be DNA contamination, unspliced RNAs, retained introns, another transcript, etc. It's a common event with RNA-Seq data..