Variation data in Phaseolus vulgaris
-
Go to Ensembl Plants and find the PHAVU_001G219900g gene in Phaseolus vulgaris and go to its Location tab. Can you see the variation track?
-
Zoom in around the first exon of this gene. Are any missense variants mapped in the translated region of this exon?
- Select Phaseolus vulgaris from the Species search drop-down menu and search for
PHAVU_001G219900g. In the results page, you can click on the coordinates 1:48,238,848-48,245,168 to go straight to the Location tab. Scroll down to the Region in detail view. The variation track (phaseolus_vulgaris_eva_PRJEB18671) is shown at the bottom of the view.If you don’t see the Variation - All sources track, click Configure this page on the left-hand panel, search for the track in the pop-up menu and enable the track by clicking on the square next to the track name. Close the pop-up window and wait for the track to load.
- Zoom in around the first exon of this gene by drawing a box in the respective region (you can change your mouse action by clicking the Drag/Select icons at the top right-hand corner of the view). Note the gene is on the reverse strand (this is signified by the < sign next to the transcript name, and it is located below the Contigs track), so the first exon will be on the right hand side of that image. The variation legend is shown at the bottom of the page, telling you what the colours mean.
There are four missense variants within the region; 1:48244305:C_T:PRJEB18671, 1:48244362:T_G:PRJEB18671, 1:48244426:G_A:PRJEB18671, 1:48244435:T_A:PRJEB18671.
Missense variants are shown in yellow. Click on the variants to get additional information on that variant including location. You can zoom into the region if the variant block is too small to click.
The variants are found at 1:48244305, 1:48244362, 1:48244426, 1:48244435.mSNPs are tagged with ambiguity codes (zoom into the region if you cannot see this). You can find a useful IUPAC ambiguity code guid on the bioinformatics.org website.
