Annotation of genome with non-cannonical splice site

Question

[praasu]

Hi,

I have genomic sequence and RNA-seq of a given eukaryotic organism (protista). This organism is believed to present a significant number of non-canonical introns. Therefore, I would like annotate gene with non-canonical splice site i.e not 5GT-AG'3. For this, I have assembled genome and RNA-seq fasta file. I have tried to annotate with exonerate and snap in maker pipeline. It doesn't seems to work, because I am only getting transcript with cannonical intron. I would really appreciate if someone can help me with this.