CD45R isoforms in RNA-seq

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Hello!

I am classifying cells using human scRNA-seq data processed through cellranger, and I realize that my cleaned data only has expression information to the level of CD45R/PTPRC and does not have information on CD45R isoforms CD45RA and CD45RO which are useful for differentiating immune cell types. I do not believe that these isoforms are differentiated in the reference genome I used since they don't have different gene symbols.

Does anyone have experience with differentiating the two in RNA-seq? Would this require creating a custom reference genome?

Thanks!


RNAseq

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