Orthologues and gene trees for the zebrafish braf gene.
(a) How many orthologues are predicted for this gene in fish?
(b) How much sequence identity does the guppy protein have to the zebrafish one? Click on the Alignment link next to the Ensembl identifier column to view a protein alignment in Clustal format.
(c) Go to the gene tree for this gene. What are the closest genes to zebrafish braf in this gene tree?
(a) Go to www.ensembl.org, choose Zebrafish and search for braf. Click through to the Gene tab view.
On the gene tab, click on Orthologues at the left side of the page to see all the orthologous genes. There are 1:1 orthologues in 52 fish, 1:many orthologues in 10 fish and 2 fish with no orthologues.
(b) The percentage of identical amino acids in the guppy protein (the orthologue) compared with the gene of interest. i.e. zebrafish braf (the target species/gene) is 88.6%. This is known as the Target %ID. The identity of the gene of interest (zebrafish braf) when compared with the orthologue (guppy braf, the query species/gene) is 84.7% (the query %ID).
Note the difference in the values of the Target and Query % ID reflects the different protein lengths for the zebrafish and guppy braf genes.
(c) Click on Gene tree in the left hand menu. The closest genes in the tree to zebrafish braf are found in a collapsed node labelled Characiphysae. Click on the node to get a pop-up, then expand this subtree to see the genes. The five genes closest to zebrafish braf are Mexican tetra, red-bellied piranha, electric eel and channel catfish.
