We are working on a fosmid which contains only one exon for a gene with 15 isoforms. The isoforms have this exon at a different position on the gene in melanogaster according to the gene record finder but same position on the genome browser for ananassae when aligned using blastX. Although the co-ordinates for the exon are the same for all the isoforms the dot plots generated for each look different from each other. In such a case do we list these isoforms as unique or identical? We did generate separate files and screen shots for each but are not sure whether to report them individually or as a group of identical isoforms.
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If the isoforms in D. melanogaster use different unique sets of coding exons, please list each isoform as unique in the Annotation Report irrespective of whether the exons that are present in your project are shared across all the isoforms.