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Orthologues and gene trees for the chicken BRAF gene

(a) How many orthologues are predicted for the chicken BRAF in sauropsida? How much sequence identity does the tarsier (Anolis carolinensis) protein have to the chicken one? Click on the Alignment link next to the Ensembl identifier column to view a protein alignment in Clustal format.

(b) Go to the orthologue in turkey. Is there a genomic alignment between turkey and chicken? Is there a gene for both species in this region?

(a) Go to Ensembl homepage, choose chicken 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 25 sauropsida and 1:many in one.

The percentage of identical amino acids in the Anole lizard protein (the orthologue) compared with the gene of interest. i.e. chicken BRAF (the target species/gene) is 90.71%. This is known as the Target %ID. The identity of the gene of interest (chicken BRAF) when compared with the orthologue (Anole lizard BRAF, the query species/gene) is 90.82% (the query %ID).

Note the difference in the values of the Target and Query % ID reflects the different protein lengths for the chicken and anole lizard BRAF genes.

(b) Go to the orthologues page and click on the Turkey orthologue to open the gene tab.

Click Genomic alignments at the left. Then select Alignment: Chicken (Gallus gallus) – lastz and click Go. Choose Block 1 to get the largest block of aligned sequence.

The red sequence is present in exons, so there is a gene in both species in this region. You can find where the start and stop codons are located if you configure this page and select START/STOP codons.

(Note: To see a blue line connecting homologous genes in the Region Comparison view page, click on configure this page and under Comparative features select join genes. Zoom out on the location view to see blue lines connecting all the homologous genes between turkey and chicken genes in that region).