Hello everyone, I have coordinates for a set of retained introns and I would like to obtain the Ensembl transcript Ids that contain these retained introns. Also, I would like to extract the information about the "type" of transcript (like known protein coding or known nonsense mediated decay).
I can do this manually by going to the UCSC browser and checking which Ensembl transcripts contain these retained introns and then from the Ensembl IDs, I can check the "type" of these transcripts from Ensembl website. But, I am wondering if there is a quick way to do this. This would be very useful if I have a long list of retained introns.
I would appreciate any help. Thanks so much.