Whole genome alignments
Go to www.ensembl.org to find the DBH gene on the zebra finch genome.
( a) Go to the Location page for this gene. View the Alignments (image) and Alignments (text) for the sauropsids EPO. Do all the birds 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 and conservation score for the sauropsids EPO-extended by configuring the page.
Turn on the Constrained elements for the sauropsids EPO-extended and compare the two tracks: are there any differences?
What is the difference between the multiple alignment track and the Constrained elements already turned on by default? Which regions of the gene, do most of the constrained element blocks match up to? How can you find more information on how the constrained elements track was generated?
(a) Start in the Location tab for DBH (ENSTGUG00000005640). Click on Alignments (Image) at the left.
Click on Select alignment -> Multiple alignments -> sauropsids EPO then close the menu.
Canary, great tit, japanese quail, chicken and turkey have an alignment at this region. This can also be seen in the Alignments (text) page, where the exons are highlighted in red.
(b) You can export the alignments from either Alignments (images) or Alignments (text) pages. Click on the blue Download alignments button at the left, and choose Clustal from the list.
(c) Click on Region in detail in the left hand menu. Turn on the following tracks by configuring the page: Multiple alignments and Conservation score for sauropsids EPO-extended. Both tracks are under the Comparative genomics menu.
The sauropsids EPO-extended just shows that the whole region for the dbh gene can be aligned among these species of birds and reptiles. The Constrained elements and Conservation score tracks show where the conserved sequence is located in the alignment.
Higher conservation regions match up with exonic regions (exons tend to be highly conserved) of the gene. Note that there are intronic regions that seem to be fairly conserved across the species available.
Click on the track name and the (i) information button to read more about constrained elements (or any other data track).
