How To Know Which Reads Is In Intron Or Exon
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Entering edit mode
12.8 years ago
Sara ▴ 130

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 • 4.1k views
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Entering edit mode
12.6 years ago

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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