APARENT APA Isoform Prediction

Predict the cut distribution and isoform proportion of two competing pA signals. The cut profiles are predicted by a siamese neural network and weighted according to a linear fit against human APA isoform proportions from APADB.

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Site Distance
APA Isoform Prediction

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

  • Cleavage %
    The 3' cleavage distribution of each PAS is shown as a blue bar chart. The values (Cleavage %) are by default normalized (they sum to 100%).
  • Isoform Window
    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.
  • Isoform %
    The Proximal or Distal APA Isoform Abundance (as percentage).

Instructions on how to use the tool.

  • Choose gene and APA sites
    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 adjacent APA sites of that gene. We currently provide integration with APADB (V2) and PolyADB (V3).
  • (Optional) Specify custom pA sequences
    Instead of choosing from a list of native human pA sites, you can paste your own custom pA sequences in the text areas. Note: The sequences 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 curves.