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Zebrafish alignments

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 fish EPO-extended. 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 fish EPO-extended 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?

(a) Start in the Location tab (region in detail) for sardh. Click on Alignments (Image) at the left, and select the Multiple -> fish EPO-extended alignment in the menu in the view.

Zebrafish, Reedfish and Mexican Tetra are shown with an alignment in this region. Most species cannot be aligned at this region. This can also be seen in the Alignments (text) page (the exons are highlighted in red).

(b) You can export the alignments from either the Alignments (text) or Alignments (image) pages in the Location tab. Click on the blue Download alignments button at the top of the text page, or the icon at the top of the image, and choose ClustalW from the list.

(c) Click on Region in detail in the left hand menu. Turn on the multiple alignment, constrained elements and conservation score for fish EPO-extended tracks, all under the Comparative genomics menu by configuring the page.

The fish EPO-extended track shows very little alignment across this region. The Constrained elements and Conservation score tracks show the conserved sequence is located where in the alignment.

Higher conservation regions match up with exonic regions (exons tend to be highly conserved) of the gene.

Hover over the the Track name and the (i) information button to read more about constrained elements (or any other data track).