APARENT Variant Prediction

Predict the change in cut distribution and isoform score due to the input pA sequence variant.

Isoform end
Isoform start
APA Variant Prediction

Explanation of values, fields and graphics presented in the tool.

  • Reference Cleavage %
    The wildtype 3' cleavage distribution is shown as a black curve. 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.
  • Variant Cleavage %
    The variant 3' cleavage distribution is shown as either a red or green curve (depending on the effect of the variant).
  • Isoform Window
    The window frame shown on top of the cleavage distribution defines what cleavage positions define the isoform of interest. All isoform metrics (e.g. the variant isoform fold change) is calculated by aggregating the cleavage within this window.
  • Fold Change
    The APA isoform fold change of the selected SNV is shown in log scale.
  • Wildtype score
    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.

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.
  • Specify variant sequence
    Specify the variant sequence in the text area. You can specify multiply nucleotide subsitutions (or indels) as long as the sequence is 205 nucleotides (pad as required).
  • 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.