APPRIS was developed using version 3c of the GENCODE annotation (Ensembl 56), which was the initial Ensembl/GENCODE merge, and currently runs GENCODE version 7 (Ensembl 62). Between GENCODE 3c and 7, the annotation was cleaned of ∼2000 genes (mostly automatic annotations removed by Ensembl), while more 10 000 new annotated coding variants were added. GENCODE release 7 recognizes 20 687 protein-coding genes and 84 408 distinct-coding transcripts. APPRIS is updated with each new stable GENCODE release and is currently being updated to GENCODE version 12.
