Validating splice site using protein sequence

Question

[praasu]

Dear All,

I have assembled genome and RNA-seq with some novel protista genome. I have aligned the raw RNA-seq reads to genome and assembled the transcript using stringtie. So, I have gtf file. Now I want to validate the splice site using protein sequence from closing related species. I want to take only transcripts for the downstream analysis, whose splice sites are supported by protein evidence. Let me know if you have any suggestion for the same. Thank you very much in advance 😊

[benformatics]

Why not just translate the regions and blast them?