Whole genome alignments
(a) Find the zebrafish BRCA2 gene and go to the Region in detail page. Turn on the BLASTz/LASTz alignment tracks for human, Japanese medaka, Mexican tetra and stickleback. Does the degree of conservation between zebrafish 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?
(b) Have a look at the Conservation score and Constrained elements tracks for the set of fish EPO. Do these tracks confirm what you already saw in the pairwise alignment tracks?
(c) Retrieve the genomic alignment for a constrained element. Highlight the bases that match in >50% of the species in the alignment.
(a) Select Zebrafish from the species selector drop-down list and type brca2 in the search box. Click Go. Click on 15:31911989-31928519:1 below BRCA2 (Zebrafish Gene) to go to the Region in detail page.
Click Configure this page in the side menu, then BLASTz/LASTz alignments under the Comparative genomics menu. Select human, Japanese medaka, Mexican tetra and stickleback in Normal style.
Yes, the degree of conservation does reflect the evolutionary relationship between zebrafish and the other species; the highest degree of conservation is found in Mexican tetra, followed by the other fish, and finally human. Especially the exonic sequences of BRCA2 seem to be highly conserved between the various species, which is what is to be expected because these are supposed to be under higher selection pressure than intronic and intergenic sequences.
(b) Click Configure this page in the side menu, then Conservation regions under the Comparative genomics menu.
Select Conservation score and Constrained elements for the fish EPO-Extended.
Both the Conservation score and Constrained elements tracks largely correspond with the data seen in the pairwise alignment tracks; all exons of the BRCA2 gene show a high degree of conservation (note the UTRs which are not conserved).
(c) Click on a constrained element (brown block). Click on View alignments (text) in the pop-up menu. Click Configure this page in the side menu. Select Show conservation regions. SAVE and close.
The conserved regions will be shown in light blue.