Question: What is Canonical/Non-canonical splicing?
gravatar for gprashant17
21 months ago by
gprashant1770 wrote:

I am using STAR aligner to align an RNA-seq data with a human reference genome and I was analysing the file. I am not sure what the following results mean:

Number of splices: GT/AG

Number of splices: GC/AG

Number of splices: AT/AC

Number of splices: Non-canonical :

I understand that the number of splices (total) gives the total number of splices in all the reads and number of splices (annotated) gives the those which are present in the annotation file.

What does canonical/non-canonical splicing mean?

splicing rna-seq star alignment ngs • 3.7k views
ADD COMMENTlink modified 21 months ago by Jean-Karim Heriche24k • written 21 months ago by gprashant1770
gravatar for Jean-Karim Heriche
21 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche24k wrote:

The canonical splice sites are those originally described and most commonly found (like in ~99% of introns) and have GT at the donor site (just after the 5' end of the cut) and AG at the acceptor site (just before the 3' end of the cut). The rarer variants GC/AG and AT/AC are also considered canonical and all other dinucleotide combinations are non-canonical.

ADD COMMENTlink written 21 months ago by Jean-Karim Heriche24k
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