Finding best matched transcript

[Morten]

Hi all,

I have a list of gene fragments in bed format that I would like to find the best matching mRNAs for. This has to adhered to the exon-exon structure of the mRNAs.
So I am trying to find a tool that will allow me to find mRNAs that have exon start and exon end coordinates that match with the gene fragment start and end coordinates.

Seems like this tool should be out there.
Does anyone know what I could use?

Thank you!