Exon falls within a gap in the assembly

Question

[PoGibas]

Downloaded published gene annotation and after extracting fasta sequences noticed that one exon is only Ns. Intersected annotation with gaps in the assembly and it appears that one exon (short, around 20bp ) falls within a gap.

How to be sure that this exons really falls within a gap before I contact authors?

Edited

Exon starts 10bp from the end of the gap.

Answer 1

[Istvan Albert]

To make sure that annotations match the genome I would extract actual sequences that correspond to these annotations with say bedtools getfasta and look at not just the Ns but also start/stop codons and also that the annotated genes actually get transcribed to proteins that you expect to see.