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How To Know Which Reads Is In Intron Or Exon

Hi everyone,

I mapped the short read sequence of miRNA with an species different from human and mouse. The genome is completed in this species. How I can know if these reads are in intron or exon?

Cheers,

sara

mirna read
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updated by Larry_Parnell Larry_Parnell • written by Sara • Sara

2 answers

Every microRNA (miR) gene that I have seen mapped to the genome - in mouse or human (or other species) - maps either within an intron of a protein-coding gene or as a distinct transcription unit outside of any other gene. Thus, I would not expect to find any miRs mapping to exons.

The question is a bit unclear to me, so I am guessing here. If you have sequence reads and need to map these as within exons, then they should map to the RefSeq mRNAs. Also, see Jeremy's response.

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written by Larry_Parnell Larry_Parnell

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