Splice junction coordinates for Ensembl transcripts

Question

[AJ_S]

Hello kind folks,

I have mapped some long-read mouse sequencing to the mouse cDNA sequences.

I now have a list of Ensembl transcripts (e.g. ENSMUST00000232790.2) along with my alignments. How can I use ensembl tools / biomart to determine the "structure" of each transcript, and in particular, the position of the splice junctions relative to the transcript?

I believe this should be possible to do using ensembl tools. I just don't know where to begin.

Best wishes, AJ

Answer 1

[Emily]

Yes, you can get this from BioMart. In the attributes, select "Structures" from the panel at the top, then expand "EXON" and select the type of coordinates you are interested in, for example.