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Gene tree of the turbot clocka gene

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Gene tree of the turbot clocka gene

Let’s look at the gene tree of clocka in Scophthalmus maximus (turbot). This gene codes for a circadian clock regulator. Use Ensembl to find the following information:

  1. What is the gene tree ID for the the clocka gene in turbot? How many genes are in this tree? How many genes are in the super-tree?

  2. According to the gene tree, which species matches the European seabass sequence the most? What is the gene ID for this homologue?

  3. Export the gene tree as an image and in Newick format.

  1. Search for clocka in turbot. Open the Gene tab and click on Comparative Genomics: Gene tree in the left-hand panel.

    The gene tree ID is ENSGT00940000157580. There are 264 genes in this tree. There are a total of 1,447 genes in the super-tree.

  2. Find the turbot clocka node in the gene tree (this is highlighted in red font). Look for the most closely-related gene by following the phylogeny.

    From the phylogeny, we can see that Lates calcarifer (Barramundi perch) has the most similar sequence to the European seabass as it is the most closely-related sequence in the phylogeny.

  3. You can find download options at the top of the phylogeny. Click on Export image to download the image. You select which format you want to download the image as.

Click on Export to download the gene tree in different tree formats. Select Newick from the drop-down menu or the file format previews. You can also export alignments from this menu.