Exploring a genomic region in they honeybee
(a) Go to the region from 15,481,750 to 15,634,850 bp on Apis mellifera chromosome CM009931.2.
(b) How many genes are found in this region? Zoom in on the first exon of XM_016912519. Turn on the track Start/Stop codons. Can you see the start codon of XM_016912519?
(c) Highlight the start codon of XM_016912519. Zoom out to view the whole gene. Can you see where you highlighted?
(a) Go to the Ensembl metazoa homepage.
Select Search: Apis mellifera, type CM009931.2:15481750-15634850 and click Go.
(b) There are six genes within this region.
Drag out a box around the first exon of the gene, the partially filled red box on the right-hand side of the gene (5’ upstream on reverse strand) and click on Jump to region in the pop-up window to zoom in. If you have not zoomed in far enough, drag out another box and click on Jump to region.
The nucleotide sequence will appear either side of the blue contig as pale blue (C), yellow (G), green (A) and pink (T) boxes. As you zoom in further, you will see the letters on the bases.
Click on Configure this page and click on Sequence and assembly. Turn on the track for Start/stop codons.
Alternatively, you can find the tracks by typing the name into the yellow Find a track box at the top right. Close the menu.
Start codons are shown in green and stop codons in red. You should see a green start codon that coincides with the start of the filled in red box.
(c) Drag out a box around the green start codon and select Mark region. The highlighted region should be visible as a grey dotted line. Scroll up to the overview to drag out a box around the gene and select Jump to region, you will still see the highlight in this view.