Really basic question about SL1 transplicing:
When an exon is “SL1-spliced” does it always remove the upstream exon? I’m working with a large multi-exon gene that has many of these SL1 sites throughout. I’m wondering if the SL1 sites on internal exons result in the removal of upstream exons because they are effectively splice to a new leader. Or, do these exons get joined and just use the SL1 as an intermediate. I find the SL1 splicing thing very confusing.