Exploring a genomic region in texel sheep
(a) Go to a region in the texel sheep genome: 18:7146000-7409000. What genes are found in this region? What strand are they on?
(b) Zoom into the start of the first exon of the gene on the left. Zoom in until you can see the genome sequence as coloured bases.
(c) Turn on the tracks for Translated sequence and Start/Stop codons. Can you find the start codon? What does this tell you about the gene?
(a) Go to the Ensembl homepage.
Choose Sheep breeds from the list of genomes then click through to the Sheep (texel) genome.
From there, search for 18:7146000-7409000 and click Go.
There are three genes in this region, ENSOARG00000010005 and ENSOARG0000001010 on the forward strand, and ENSOARG00000010101 on the reverse strand.
(b) Drag a box around the start of the first exon, at the left of the view, with your mouse. 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.
(c) Click on Configure this page and click on Sequence and assembly. Turn on the tracks for Translated sequence and Start/stop codons.
Alternatively, you can find the tracks by typing their names into the yellow Find a track box at the top right. Close the menu.
You can now see the amino acid sequence in all three frames on both strands above and below the nucleotide sequence. Start and stop codons are highlighted either side of these. Start codons are shown in green and stop codons in red.
There is no start codon or methionine residue at the 5’ end of this gene. This suggests that this gene model is incomplete.