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Orthologues and gene trees for the human BRAF gene

(a) How many orthologues are predicted for the human BRAF in primates? How much sequence identity does the tarsier (Carlito syrichta) protein have to the human one? Can you tell which end of the BRAF protein is more conserved between these two species by looking at the orthologue alignment?

(b) Go to the Gene tree for this gene. View the Wasabi alignment of all the proteins in primates. Can you see a large gap in the alignment around position 450? Which species match the human sequence?

(a) Go to Ensembl homepage, choose human from the drop-down list 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 21 primates reported in the summary table.

Search for tarsier in the table below.

The percentage of identical amino acids in the tarsier protein (the orthologue) compared with the gene of interest. i.e. human BRAF (the target species/gene) is 93.95%. This is known as the Target %id. The identity of the gene of interest (human BRAF) when compared with the orthologue (tarsier BRAF, the query species/gene) is 88.48% (the Query %id). Note the difference in the values of the Target and Query %id reflects the different protein lengths for the human and tarsier BRAF genes.

Click on the View Sequence Alignments link in the Orthologue column to View Protein Alignment in Clustal W format.

Conserved amino acids are indicated by asteriks. The alignment around the N-terminus looks poorer, when compared to the C-terminus end.

(b) Click on Gene tree in the left hand menu. All of the primates are enclosed in a lilac box. Click on the furthest left node in the box to get a pop-up labelled Primates. Alternatively, scroll to the bottom of the page, and select Order from Collapse all the nodes at the taxonomic rank. Primates will appear as a red triangle. Click on Wasabi viewer in the pop-up menu to see the alignment. Scroll to position 450.

Greater bamboo lemur, mouse lemur, crab-eating macaque, Bolivian squirrel monkey, marmoset and Ma’s night monkey all match the human sequence.