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Glossary

APPRIS

APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods. It provides value to the annotations of the human, mouse, zebrafish, rat, and pig genomes. (http://nar.oxfordjournals.org/content/41/D1/D110.long).

APPRIS has selected a single CDS variant for each gene as the 'PRINCIPAL' isoform. Principal isoforms are tagged with the numbers 1 to 5, with 1 being the most reliable.

PRINCIPAL:1
Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS.
PRINCIPAL:2
Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant.
PRINCIPAL:3
Where the APPRIS core modules are unable to choose a clear principal variant and there more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated.
PRINCIPAL:4
Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with a distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant.
PRINCIPAL:5
Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant.

For genes in which the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the "candidate" variants not chosen as principal are labeled in the following way:

ALTERNATIVE:1
Candidate transcript(s) models that are conserved in at least three tested species.
ALTERNATIVE:2
Candidate transcript(s) models that appear to be conserved in fewer than three tested species.

Non-candidate transcripts are not tagged and are considered as "Minor" transcripts.

Further information and additional web services can be found at the APPRIS website.