Explanation of values, fields and graphics presented in the tool.
The 3' cleavage distribution of each PAS is shown as a blue bar chart. The values (Cleavage %) are non-normalized (they do not sum to 100%). Rather, Cleavage % is scaled with respect to the strength of the PAS relative to the average affinity of a distal, well-separated PAS.
The window frame shown on top of the cleavage distribution defines what cleavage positions define the isoform of interest. All isoform metrics are calculated by aggregating the cleavage within this window.
The aggregate APA isoform log odds ('strength') of the wildtype sequence, with respect to the average affinity of a well-separated, distal PAS. The histogram to the right shows the distribution of native human pA sites and their isoform scores. This metric is an unbiased estimate of the overall affinity (strength) of the PAS sequence, in relation to all other possible PAS configurations.
Instructions on how to use the tool.
Choose gene and pA site
Select the gene of interest in the dropdown list above the cleavage curve. Choosing a gene populates the dropdown to the right with the annotated pA sites of that gene. We currently provide integration with APADB (V2) and PolyADB (V3).
(Optional) Specify custom pA sequence
Instead of choosing from a list of native human pA sites, you can paste your own custom pA sequence in the text area. Note: The sequence must be 205 nucleotides.
Define isoform window
Drag the tabs of the isoform window over the region of the cleavage distribution according to what pA positions you wish to include in the isoform of interest.
Zoom and pan the sequence
Zoom and pan into specific regions of the sequence by pressing the zoom buttons above the cleavage curve, or simply by scrolling and dragging with the mouse over the cleavage curve.