When I get the genes (GenomicFeatures function) from a TxDb generated from UCSC using the following command:

txdb.ucsc <- makeTxDbFromUCSC("**dm3**","ensGene")
genes(txdb.ucsc)

All the names look like normal ensembl IDs.

FBgn0000003, FBgn0000008, FBgn0000014, etc..

When I switch to the newer Drosophila genome:

txdb.ucsc <- makeTxDbFromUCSC("**dm6**","ensGene")
genes(txdb.ucsc)

All the ensembl.ids have a ".1" appended to the end

All the names don't look like normal ensembl IDs.

FBgn0000003.1, FBgn0000008.1, FBgn0000014.1, etc..

Is there something I am missing here to avoid this? Other than this simple fix --> gsub("[.]1$","",names(x))

Even when I fix it, the names are still unique so its not a matter of duplicate names. My question then is really why is it even there...