Orthologues, paralogues and gene trees for the human VEGFA gene
(a) Ovarian tumours in humans seem to be associated with the overexpression of VEGFA. Have orthologues of this gene been identified in birds in Ensembl?
(b) How much sequence identity does the chicken protein have to the human VEGFA protein?
(c) Go to the orthologue in chicken. Can you find the pairwise genomic alignment between the chicken and turkey VEGFA genes?
(a) Go to www.ensembl.org, choose human and search for VEGFA. Click on the Orthologues link in the result page to see all the orthologous genes to human VEGFA.
Tick the Sauropsida box to see which bird species have got VEGFA orthologues.
Many bird species in Ensembl have got an orthologous gene to VEGFA. Note that for all of them the orthologue relationship is 1-to-1: only one copy is found in each species.
(b) Click on the Alignment (protein) link in the table under Compare to see the alignment and some stats such as %coverage and % identity.
The chicken protein is 44% identical to the human one. But only 27% of the human protein is identical to its chicken counterpart. Note the differences in length between the two proteins.
(c) There is more than one way to get to the answer.
Option 1: click on the chicken orthologue to open the gene tab. Click Genomic alignments at the left. Then select Turkey and click Apply.
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.
Option 2: Go to the location tab of the chicken VEGFA gene and then click on Region Comparison view at the left. Click on Select species or regions at the left and click on the + to select Turkey. Save and close. You should see an alignment between the turkey VEGFA gene region and the VEGFA gene region in chicken.
(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 marmoset and human genes in that region).