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Synteny

Start at Ensembl homepage. (a) Find the rhodopsin (RHO) gene in human. Go to the Location tab and click Synteny at the left. Are there any syntenic regions in dog? If so, which chromosomes are shown in this view?

(b) Stay in the Synteny view. Is there a homologue in dog for human RHO? Are there more genes in this syntenic block with homologues? Which dog chromosome is this human genomic region syntenic to?

(a) Search for human RHO from the home page. Click on RHO genomic coordinates 3:129528639-129535344:1 in the search results to open the Location tab. Click Synteny at the left and change the species to Dog next to the image.

Yes, there are multiple syntenic regions in dog to human chromosome 3, which is in the centre of this view. Dog chromosomes 6, 20, 23, 31, 33, and 34 have syntenic regions to human chromosome 3.

(b) Scroll down to the bottom of the page to see a list of homologous genes on both genomes.

There is no homologue of human RHO in dog. Click 15 upstream genes or 15 downstream genes to view neighbouring genes in this syntenic block. There are many neighbouring genes with homologues in dog. Human genes in this region are homologous to dog genes on chromosome 20, which is also indicated by the red boxes in the image above as this genomic block on human chromosome 3 is syntenic to dog chromosome 20.