Compara exercises

Exercise 1 – Orthologues, paralogues and gene trees for the human BRAF gene

 (a) How many orthologues are predicted for this gene in primates?

How much sequence identity does the Tarsius syrichta protein have to the human 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 marmoset. Is there a genomic alignment between marmoset and human? Is there a gene for both species in this region?

 

Exercise 2 – Zebrafish orthologues

Go to www.ensembl.org to find the sardh gene on the zebrafish genome.

(a) Go to the Location page for this gene. View the Alignments (image) and Alignments (text) for the 11 fish. Which fish genomes are represented in the alignment? Do all the fish show a gene in these alignments?

(b) Export the alignments (as Clustal).

(c) Click on the Region in detail link at the left and turn on the tracks for multiple alignments, constrained elements and conservation score for the 11 fish EPO by configuring the page.

What is the difference between the 11 fish EPO multiple alignment track and the Constrained elements track? Which regions of the gene do most of the constrained element blocks match up to?

Can you find more information on how the constrained elements track was generated?

 

Exercise 3 – Synteny

Go to www.ensembl.org

Find the Rhodopsin (RHO) gene for Human. Go to the Location tab.

(a) Click Synteny at the left. Are there any syntenic regions in dog? If so, which chromosomes are shown in this view?

(b) Stay in the Synteny view. Is there a homologue in dog for human RHO? Are there more genes in this syntenic block with homologues?

 

Exercise 4 – Whole genome alignments

(a) Find the Ensembl BRCA2 (Breast cancer type 2 susceptibility protein) gene for human and go to the Region in detail page.

(b) Turn on the LASTZ-net alignment tracks for chickenchimpmouse and platypus. Does the degree of conservation between human and the various other species reflect their evolutionary relationship? Which parts of the BRCA2 gene seem to be the most conserved? Did you expect this?

(c) Have a look at the Conservation score and Constrained elements tracks for the set of 53 mammals and the set of 27 amniota vertebrates. Do these tracks confirm what you already saw in the tracks with pairwise alignment data?

(d) Retrieve the genomic alignment for a constrained element. Highlight the bases that match in >50% of the species in the alignment.

 

Bonus Exercise 5 – Exporting paralogues with BioMart

Export a list of all human genes on chromosome 14 which have a paralogue, including the gene names, the last common ancestor and the identity between the genes.