Why are there differences between RefSeq and Ensembl transcripts and exons?

Ensembl and RefSeq transcripts differ in that Ensembl transcripts are mapped onto the reference genome, whereas RefSeq transcripts are mapped onto mRNA sequences. Due to differences between reference genomes and individual mRNAs, some RefSeq mRNA’s might not map perfectly to the reference genome, resulting in the possibility of small differences between Ensembl and RefSeq transcripts. AlamutTM Visual Plus uses Splign (a tool developed by RefSeq) to align all transcripts to the genome build.

For more information please see: https://www.ensembl.org/Help/Faq?id=294