Overview of Help-Pages

Alternative Transcripts

[Introduction] [Table Output]
[Graphical Overview in Genome Browser] [Graphical Overview in Locus / Alignment view]


The Alternative Transcripts section in ElDorado gives an overview of the alternative transcripts known for a single gene. The superpositioning of the transcripts helps to understand how transcripts differ in their exon/intron structure and which transcripts are regulated by distinct promoters. For those species where chips are available, probes from the selected microarrays are displayed in the graphical view to show which of the alternative transcripts are covered by the probes on the chip.


The result page contains several sections:

Graphical overview of the aligned transcripts (Locus Viewer)

The figure is a graphical representation of the transcripts listed in the table above and their genomic context. The transcripts are arranged by their genomic location.

In this example we observe four transcripts on the human CAPN12 gene (antisense strand!). They are transcribed from three independent tissue specific promoters (yellow boxes). Two of the transcripts (AK127390 and NM_144691) start from the same promoter but exhibit different 3'UTRs (dark green boxes to the left).

alternative transcripts

The graphic consists of four parts:

The main sequence panel

The main sequence panel contains all transcripts as listed in the table view of the output. For each transcript, a separate sequence is depicted as a line with all annotated elements. Thus, the transcripts appear below each other with differently annotated exons, introns or UTRs.

The colored field to the right of the transcript labels indicates the quality of the transcript (gold, silver, bronze).

The navigation panel

The view on the sequence can be changed by using the zoom- and scroll element in the lower right part of the graphics. The navigation panel contains a scaled down version of the sequence and a red box which marks the currently selected part of the sequence that is visible in the main sequence panel above. By default, the whole sequence is displayed.

slider To zoom in or out, click on the red box in the navigation panel and adjust the box by reducing the size via its handles (the small white boxes top left and bottom right of the red box). The sequence in the main panel will adjust to the selected window.

If you want to scroll along the sequence, move the red box within the navigation panel by sliding it with the mouse to the desired position. Alternatively you can click anywhere inside the scrollbar to jump to the desired destination.

The selection panel

The selection panel contains a tree with all elements that can be toggled on or off for display. Tree hierarchies can be shown or hidden by clicking on the label or the ^ - symbol. Checkboxes provide the possibility to toggle the visibility of

Individual transcripts can be removed from the main sequence panel by clicking on the checkboxes.

The toolbar

zoom/navigation exporting the complete result page to HTML (including all graphics in JPG format)
zoom/navigation exporting the graphics or a selected region to a certain format (JPG, PNG, TIFF, PNM), based on the current settings of zoom and element selection
zoom/navigation selection of a region which can then be exported
zoom/navigation recalculation of the layout, i.e. the graphics is displayed as it was set up by default