Search gene/transcript:
A system for annotating alternative splice isoforms
Search gene/transcript: e.g. TRMT2A-005 or ENSG00000099904 or RNF215

APPRIS [1] is a system that deploys a range of computational methods to provide value to the annotations of the human genome. APPRIS also selects one of the CDS for each gene as the principal isoform.

APPRIS defines the principal variant by combining protein structural and functional information and information from the conservation of related species.

The server has been used in the context of the scale up of the ENCODE project to annotate the Human genome but APPRIS is being used for other species:

20,738 protein-coding genes and 95,309 distinct alternative transcripts,
Gencode19/ Ensembl74
22,645 protein-coding genes and 51,610 gene transcripts,
GencodeM2/ Ensembl74
22,878 protein-coding genes and 25,659 gene transcripts,
25,344 genes with translations, and 41,282 transcripts,

All of our data is available free. Here you can also download the list of main isoforms selected by APPRIS.

The GENCODE annotation: an Encyclopædia of genes and gene variants

The National Human Genome Research Institute (NHGRI) launched ENCODE, the Encyclopedia Of DNA Elements, in September 2003, to carry out a project to identify all functional elements in the human genome sequence.

The aim of GENCODE as a sub-project of the ENCODE is the high accuracy annotation of all evidence-based gene features. The consortium is genarating a set of annotations including protein-coding loci, alternatively transcribed variants, transcribed non-coding loci, and pseudogenes. The annotation process involves manual curation, computational analysis and targeted experimental approaches.

APPRIS is a joint project between Centro Nacional de Investigaciones Oncologicas, CNIO and Instituto Nacional de Bioinformatica, INB.

[1] Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, Valencia A, Tress ML.
APPRIS: annotation of principal and alternative splice isoforms.
Nucleic Acids Res. 2013 Jan;41(Database issue):D110-7.