Hi All,

I intend to amplify a full length lncRNA that I am currently working on. The lncRNA of my interest is not accurately annotated in the ENSEMBLE or UCSC databases- what I was able to see based on my RNAseq reads and cloning + sequencing of smaller fragments.

3' end mapping was less challenging as a sequence is more specific. Also it was possible to determine 3'-end cleavage and polyadenilation region.

5' end on the contrary is full of repeats and even if I want to move upstream with closely anchored primers it's simply impossible to design specific ones. How to map it?

Any advice is really welcome!