How to make a custom annotation set?

[dudududu12138]

Hello, I saw the built-in annotation file (https://github.com/Illumina/SpliceAI/blob/master/spliceai/annotations/grch38.txt). But I want to make a custom annotation set. And I want to know how did you define exons? I mean, there are more than one transcripts in some genes. And the exons may overlap. How do you deal with the situation? I list an example below : This gene has two transcripts. Exon30976-31097 and exon 30976-31109 have the same start position but different end position.

Thank you very much for helping me!