Which source of annotation files to use, Ensembl or UCSC?
Ensembl annotates more genes than RefGene and UCSC ，but it should be pointed out that many of the transcripts in particular have very weak evidence, and can interfere in some cases with proper assignment of specific base pairs to the canonical gene. That said I still prefer it, because it is more comprehensive.
Difference between UCSC and Ensembl genomes
Both resources use the same assembly but each annotates it using their own pipeline with different gene definitions so you shouldn"t expect the annotations to be identical. Whatever you"re doing, you should pick one reference on stick to it, a mix and match approach will most of the time give you inconsistent results.
Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference? - Bioinformatics Stack Exchange
The GENCODE annotation is made by merging the Havana manual gene annotation and the Ensembl automated gene annotation. The GENCODE annotation is the default gene annotation displayed in the Ensembl browser.
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