I'm performing blast searches with only exon regions for certain genes against various genomes(for different organisms). For example, I will blast regions 1..367, 368..444, 445..828 of the gene ACAN(https://www.ncbi.nlm.nih.gov/nuccore/NM_013227.3) against an organisms genome such as
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/315/GCF_000002315.4_Gallus_gallus-5.0/GCF_000002315.4_Gallus_gallus-5.0_genomic.fna.gz
For a lot of my blast searches, I'm only receiving hits that have a max query cover of about 30-40. If i perform the same blast searches on the transcript file
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/002/315/GCF_000002315.4_Gallus_gallus-5.0/GCF_000002315.4_Gallus_gallus-5.0_rna.fna.gz
On almost all my blast searches I am receiving hits that have a query cover around 80-100
What could be the reason for this. Exons should be completely connected within the genome shouldn't they? Why would blasting against the rna transcript files return hits with higher query covers than blasting against the genome?
