Find the ABCC11 gene on the cow genome. (a) Go to the Location tab for this gene. View the Alignments (image) for the 46 eutherian mammals EPO. Do all the mammals have an alignment in this region? Can you spot a difference in the alignment between Pecora (including cattle, goats, sheep and deers) and the remaining mammals?
(b) Let’s now see this alignment as text. Go to Alignments (text) for the 46 eutherian mammals EPO. Sort the aligned blocks by genomic coordinates and view the 3’ portion of the ABCC11 gene (smallest coordinates). Does it support your previous conclusions? Export the alignment without ancestral sequences as ClustalW.
(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 90 eutherian mammals EPO-Extended by configuring the page. What is the difference between the 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?
(a) Search for cow ABCC11 from the home page. Click on ABCC11 genomic coordinates 16:48165773-48247568:-1 in the search results to open the Location tab. Click on Alignments (image) at the left, and select the 46 eutherian mammals EPO multiple alignment by clicking on Select an alignment blue button. Scroll down to see the hidden and missing species.
All but 13 of the 46 mammals have an alignment at this region. ABCC11 gene model for the closely related Pecora species (cows, yak, goat, sheep and Yarkand deer) is longer when compared to the other species, with many additional exons at its 3’ end (left side of the image), which are absent in other taxa.
(b) Click on Alignments (text) in the left hand menu. The 46 eutherian mammals EPO alignment should be pre-selected. Scroll down to the table of alignment blocks. Sort the table by clicking on small arrows in the Location on Cow column header. The alignment blocks are now sorted by the genomic coordinates, with smalles coordiantes corresponding to the 3’ most end of ABCC11 (located on the reverse strand). Click on Block 3 to view the alignment.
Only 5 species have an alignment in this region, including cows, yak, goat, sheep and Yarkand deer, which is in agreement with our previous observation. Scroll up and click on Select another alignment blue button. Deselect Ancestral sequences by clicking on the x in the panel on the right, then Apply. Click on the blue Download alignment button, change File format to CLUSTALW, then Download.
(c) Click on Region in detail in the left hand menu. Turn on the Multiple alignments, Constrained elements and Conservation score for 90 eutherian mammals EPO-Extended tracks, all under the Comparative genomics in the Configure this page menu.
The 90 eutherian mammals EPO-Extended multiple alignment track is shown as pink block indicating that the whole region can be aligned at this locus. The GERP elements and GERP scores tracks show where the conserved sequence is located in the alignment. Conserved elements shown as pink boxes match up with exonic regions of the 5’-half of this cow gene (right side of the image). In general, exons tend to be highly conserved across taxa. Click on the track name and the i icon (information button) to read more about constrained elements (or any other data track).