Recently, my lab had a private vendor has assembled transcriptome contigs of several genes from a mammal. I do not have access to the raw files - only assembled contigs for genes.
I discovered on contig has a 100bp insert, right in the middle of the gene. I did a BLAST search of this 100bp insert (the rest of the gene aligns to pre-existing homologs in other species), but it returned nothing. I suspect it is a sequencing artifact.
Is there a way I can be sure that this insert is an artifact? Could it be the product of retrotransposition? What is the usual procedure for this kind of problem?