Exploring a genomic region in Ovis aries Texel (Sheep)
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Go to the region 18:7146000-7409000 in the Texel Sheep genome. What genes are found in this region? What strand are they on?
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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.
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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?
- Go to the Ensembl homepage. Click on View full list of all species. Use the filter in the top right-hand corner of the table to search for Sheep. Click on Sheep (texel) from the list of genomes to open the species information page. From there, search for 18:7146000-7409000 and click Go.
There are three genes in this region, ENSOARG00000010005 and ENSOARG00000010107 on the forward strand, and ENSOARG00000010101 on the reverse strand.
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Make sure that your cursor action is set to Select a region. with your cursor, drag a box around the start of the first exon of the ENSOARG00000010005 gene, at the left of the view. 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 around the first exon 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 tracks for Translated sequence and Start/stop codons. Alternatively, you can find the tracks by typing their names into the search field in the top left-hand corner. 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.
