When DNA is transcribed into an RNA molecule, there are often portions of the DNA sequence that are removed from the final molecule. This process of removing portions of sequence while transcribing RNA is called RNA splicing.
Interestingly, the DNA sequence for a single gene can give rise to multiple, different RNAs by including and excluding different parts of the gene sequence. These differences in RNA splicing can affect the function of the RNA or the proteins made from the RNA.
By sequencing the RNA, you can determine which splicing pattern(s) a gene is using.