I am trying to quantify the expression of splice variants of a gene I am interested in. I would typically do this using Kallisto ( via the Galaxy server) and to do this I use a reference transcriptome. There is a splice variant which I am particularly interested in - its existence is very abundant in the literature, being recorded since the early 90s! However the variant is very poorly annotated and is not identified as a splice variant on Ensembl. Is their a way I could modify an existing Ensembl transcriptome ( or make a completely new transcriptome) which would include this variant.