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 particular 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.

For both GRCh38 and hg19 references, the default canonical transcript for the BRCA1 gene has changed in Ion Reporter™ Software 5.12 for both REFSEQ and ENSEMBL canonical transcripts.

• In Ion Reporter™ Software 5.10 and earlier, BRCA1 default REFSEQ canonical transcript is: NM_007300.3. In Ion Reporter™ Software 5.12 and later, the default BRCA1 REFSEQ canonical transcript is: NM_007294.3.

• In Ion Reporter™ Software 5.10 and earlier, BRCA1 default ENSEMBL canonical transcript is: ENST00000471181.7. In Ion Reporter™ Software 5.12 and later, the default BRCA1 ENSEMBL canonical transcript is: ENST00000357654.8.

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