Each major genome version has several subreleases, which you can see here: http://www.ensembl.org/info/website/archives/assembly.html. For instance, the mouse has the following for the mm10 genome: GRCm38.p4 GRCm38.p3 GRCm38.p2 GRCm38.p1
My problem: I have a some data which is annotated with the Ensemble version 84, which was done on GRCm38.p4. Now I need to extract the sequences for each gene, and I am using the following R package, which was generated in 2011, with the first subrelease of the genome (GRCm38.p1 I guess): http://bioconductor.org/packages/release/data/annotation/html/BSgenome.Mmusculus.UCSC.mm10.html
Can I simply do that, or I need to extract the sequence specifically for GRCm38.p4?
So more precisely, my questions are: (Q) What is the difference between the genome subreleases? Can they be used interchangeably without major concerns? Do the genomic coordinates differ between subreleases?