How To Putatively Identify Intronic Regions/Splice Sites Based On Sequence In Lincrna?

Question

[Eric]

Hello,

I have a list of unannotated lincRNA (cf. Human Body Map, Broad Institute) and in order to make primers for these, I need to identify intronic regions. Any ideas how to putatively identify intronic regions/splice sites based on sequence in lincRNA?

Thanks.

[Sean Davis]

When you say you have "unannotated lincRNA", what do you have? Do you have FASTA sequence, some identifiers, or something else?

[Eric]

FASTA sequence.

Answer 1

[JC]

If you have the fasta sequence for each lincRNA, I will map them using blat to the reference genome, that will give you the genomic coordinates for exons/introns.

[Eric]

Broad Institute's put their lincRNA catalog onto the UCSC browser now, so this is certainly the easiest route. Thanks.