View intron feature evidence in the Genome Data Viewer and Sequence Viewer

Are you a researcher who works on gene biology and are interested in alternative splice patterns in your gene or genes of interest?  If so, be sure to explore the intron feature evidence available in graphics views of genome assemblies annotated by NCBI. You can view the NCBI evidence used for calling splice variant for genes, add other intron feature evidence tracks, and use new display and filter options that make it easier to interpret the data .

Figure 1. Graphical view of the monoamine oxidase gene (MAOA, MOAB) region on the human X  chromosome showing intron features tracks (‘RNA-seq intron features, aggregate’ and ‘Intropolis RNA-Seq intron features’). Mousing-over an intron feature activates a tooltip that shows details such as the number of reads with the splice site, the location on the chromosome, the length of the intron and the donor and acceptor bases at the splice site. The Intropolis track was added through the search feature of the Configure Tracks menu and configured (bottom menu) so that the features were sorted by strand and filtered so that only features with greater than 500 reads appear.

When you view a chromosome or scaffold for an NCBI RefSeq genome in the Genome Data Viewer (GDV) or using the Sequence Viewer, you’ll see a track labeled ‘RNA-seq intron features, aggregate’ that shows splice junctions inferred from analysis of RNA-seq data from the NCBI’s Sequence Read Archive (SRA). The ends of the splicing features correspond to splice donor and acceptor junctions, while the line in between denotes the intron span and contains an arrowhead that indicates the direction of splicing. The number on top of each feature indicates the number of spliced RNA-seq reads supporting that splice pattern.  You can also hover over each intron feature in the track to show a tooltip containing more information, including the nucleotides at the splice site (e.g. GT-AG) and the precise location on the assembly molecule. You can find more intron feature tracks to add to your view by searching in the Configure Tracks menu.

Due to the growth and increased read depth of high throughput RNA-seq data, RNA-seq analysis tracks have also grown in size with many more splice features, and it can be difficult to interpret all the possible data in the tracks. We’ve added new display options that let you sort and filter the data, making it easier to interpret.  Simply click on the track title (or on the configure icon on the right of the track) to access the track display settings. You can sort the features by number of spliced reads, or by the strand, and filter by the data in view by the number of spliced reads. You can use this option  to simplify the data in the track to exclude reads that may be outliers. Hidden features won’t be exported to PDF or SVF images created from you view.

Figure 1 shows a graphics view of the intron features for the two monoamine oxidase genes on the human X chromosome that demonstrates many of the display options described above.

You can use the intron feature tracks to evaluate the evidence for splicing in the annotated transcript variants your gene of interest. You can also find evidence for new splice junctions at your favorite gene, or even evidence for not-yet annotated genes!

For more information about track rendering and track settings, see our Sequence Viewer legends documentation.  Please contact us if you have any questions or suggestions about the intron features displays.



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