Transcripts in REFSEQ and ENSEMBL canonical transcripts file

In UCSC curated canonical transcripts set, there are some discrepancies when multiple transcripts are used for a given gene. The shorter transcripts have been removed and the transcript with the appris_principal_1 tag is retained in the Ion Reporter™ Software REFSEQ canonical transcript set. This tag is used by gencode to mark the primary transcript of a specific gene. If the appris_principal_1 tag is missing, the longest transcript is used so that there is just one canonical transcript for a given gene. If two transcripts are the same length, Ion Reporter™ Software includes both genes and lists them in alphabetical order.

The UCSC transcripts for the following genes are replaced with the transcripts in the New transcript column in Ion Reporter™ Software: