Orthologues and gene trees for the Gallus gallus (Chicken) BRAF gene
- Let’s explore the orthologues of the chicken BRAF gene.
- How many orthologues are predicted for the chicken BRAF in sauropsida (birds and reptiles)?
- How much sequence identity does the Anolis carolinensis (Green anole) protein have to the chicken one?
- Export the protein alignment in Clustal format.
- Look at the orthologue in human. Is there a genomic alignment between human and chicken? Is there a gene for both species in this region?
- Go to the Ensembl homepage, select Chicken from the drop-down list in the blue search box, enter BRAF and click Go. Open the **Gene tab and click on Comparative Genomics: Orthologues at the left-hand panel to see all the orthologous genes.
There 25x 1:1 and 1x 1:many orthologues in sauropsida.
Find Green anole in the Selected orthologues (you can use the filter in the top right-hand corner).
The percentage of identical amino acids in the Green anole protein (the orthologue) compared with the gene of interest. i.e. chicken BRAF (the target species/gene) is 84.42%. This is known as the Target %id. The identity of the gene of interest (chicken BRAF) when compared with the orthologue (Green anole BRAF, the query species/gene) is 94.67% (this is the Query %id).
Click on the View Sequence Alignments link in the Orthologue column of the Selected orthologues table and select View Protein Alignment in the pop-up menu. To download the alignment, click on the Download homology button and select the CLUSTALW file format in the pop-up menu.
- Click on Comparative Genomics: Genomic alignments in the left-hand panel. Click on Select an alignment and add Human in the pop-up menu. In the table, select Block 1 to view the largest block of aligned sequence (this will lead you to the Location tab). Click on Display full alignment. In the alignment, sequences coloured in red are exons.
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 Codons: START/STOP codons in the options.
Note: You can visualise the alignment in the genomic context in the Comparative Genomics: Region Comparison page (blue lines connect homologous genes between species). Go to Select species or regions, add Human and close the pop-up menu. Click on Configure this page. In the pop-up menu under Comparative features category, enable the Join genes option. You may need to zoom out on the Region in detail view to see blue lines connecting all the homologous genes between chicken and human genes in that region.
