Investigate data in Ensembl Rapid Release
You’re interested in finding the gene UQCRQ in Wild Bactrian camel, which is only available in Ensembl Rapid Release.
(a) Search for UQCRQ in human on ensembl.org and export the protein sequence of the canonical transcript.
(b) Use BLAST on rapid.ensembl.org to search for the human UQCRQ sequence in the Wild Bactrian camel protein database. How many hits do you get? Based on these results, what can you say about the copy number of this gene in Wild Bactrian camel?
(c) Go to the location of the top BLAST hit and turn on tracks for RNA-seq gene models. In what cell types is there evidence of expression of this gene?
(a) Start at ensembl.org and search for UQCRQ. Go to the top search result, ENSG00000164405.
Expand the transcript table by clicking on Show transcript table, then select the canonical transcript ENST00000378670.8 and go to Protein to select the protein sequence.
(b) Open rapid.ensembl.org and go to BLAST. Paste the protein sequence into the box.
In the Search against box, click on the cross to remove whatever species is there, then select Add/remove species. Type Wild Bactrian camel into the search box then select Camelus ferus (Wild Bactrian camel) - GCA_009834535.1 reference when it appears, then hit Apply.
Select Protein database, then hit Run. When your job has completed, click on View results.
You should have two hits, to ENSCFEP00005028030 and ENSCFEP00005005840. Both hits are full length and highly scoring with low e-values. This suggests that there was a gene duplication in Wild Bactrian camel.
(c) Click on 3:92177026-92177937 to go to the location of the top hit. You will see the BLAST hit in the region, mapping to the two coding exons of the gene.
Click on Configure this page, then go into the RNASeq models section. Hover over Gene models then select All. Close the menu.
You will see gene models in all the cell types listed, indicating expression.
