Whole genome alignments
(a) Find the human BRCA2 gene and go to the Region in detail page. Turn on the BLASTz/LASTz alignment tracks for chicken, chimp, mouse 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?
(b) Have a look at the Conservation score and Constrained elements tracks for the set of 90 eutherian mammals and 63 amniota vertebrates. Do these tracks confirm what you already saw in the pairwise alignment tracks?
(C) Retrieve the genomic alignment (text) across 63 amniotes for a constrained element matching up with exon 15 of the golden transcript. Highlight the bases that match in >50% of the species in the alignment. Is this sequence exonic in all species?
(a) Select Human from the species selector drop-down list and type brca2 in the search box. Click Go. Click on 13:32315086-32400266:1 below BRCA2 (Human 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 Chicken, Chimpanzee, Mouse and Platypus in Normal style.
Yes, the degree of conservation does reflect the evolutionary relationship between human and the other species; the highest degree of conservation is found in chimp, followed by mouse, platypus and chicken, respectively. 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 90 eutherian mammals EPO-Extended and 65 amniota vertebrates Mercator-Pecan.
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 exons of the golden transcript (ENST00000380152.8) to reveal their rank in transcript. Exon 15 can be found in the middle. Click on a constrained element in 63 way GERP elements track matching up with this exon. Click on View alignments (text) in the pop-up menu, then Configure this page in the side menu. Select Show conservation regions to highlight bases matching in majority of the species in this alignment.
Exons are indicated by red lettering. All but Indian cobra and eastern brown snake have exonic sequence in this region.