Use PacBio's iso-seq data to look for variant

Question

[yanweng]

I am trying to identify A to I RNA modification in human genome. I have a list of potential modification sites identified by Illumina RNA-seq. I hope to find, for a certain gene with x modification sites identified by Illumina, how many modification sites can be found in the transcripts mapped to the gene (by PacBio). Like below, there are 3 modifications identified by Illumina data, how can I find the modification in each transcript in PacBio data?

ref: ATTGAATCGTAG

Illumina: GTTGGGTCGTAG

PacBio: transcript1. GTTGAATCGTAG transcript2. ATTGGATCGTAG transcript3. ATTGGGTCGTAG