I was wondering about the structure of transcripts for the side-II gene. We had expressed the protein several years ago for the extracellular interactome study using a cDNA clone called RT02374. When I recently subcloned and sequenced a fragment from this, I noticed that RT02374 has a 9 nucleotide insertion in the coding region, adding the residues DIK.  However, this insertion is not present in any of the predicted side-II transcripts.  It does seem to be present in the genome, however, when I run a segment of the cDNA against the genome assembly. There is no Gold clone standard for side-II.  Why is this version with the insertion not one of the annotated transcripts, since it is in the cDNA?
From FlyBase (LC): This is clearly an error in the side-II gene model annotation. In addition to the two RT cDNAS, there is RNA-Seq junction support.  We will make this correction.