Exploring a genomic region (mouse and human)
You find a deletion in the mouse genome that severely affects development, and you want to investigate it. Go to this region (base pair coordinates 136197000-136283000 on mouse chromosome 4).
(a) How many protein coding transcripts does the gene in this region have?
(b) You want to see if any of these transcripts might be expressed in brain tissue. Turn on the RNASeq gene model for brain.
(c) Find this same view (Region in Detail) for the human orthologue of the mouse gene.
(d) To understand crucial variants, you want to investigate if there are any missense variants in the most diverse population available. Turn on the 1000 Genomes AFR (African population) track.
(a) Go to the Ensembl homepage.
Select Search: Mouse and type 4:136197000-136283000 in the text box (or alternatively leave the Search drop-down list like it is and type mouse 4:136462271-136562270 in the text box). Click Go.
This region encodes the Luzp1 gene, which has six protein-coding transcripts (splice variants).
(b) Click Configure this page in the side menu (or on the cog wheel icon in the top left hand side of the bottom image).
Click RNASeq models in the left hand menu. Click on the box in the matrix for Brain: Gene model. Turn it on, using expanded with labels. Close the menu.
There is a gene model based on RNASeq evidence that matches to Luzp1-004.
(c) There are several ways to do this. One way is to click on a Luzp1 transcript, and in the pop-up menu, click on the Gene ID (ENSMUSG00000001089). This should bring you to the Gene Tab for mouse Luzp1.
In the left hand menu, click Orthologues. Find the human orthologue in the list, and click on its location: 1:23410516-23504301:-1.
You should be in Region in Detail for human, showing Luzp1 transcripts.
(d) Click Configure this page in the side menu (or on the cog wheel icon in the top left hand side of the bottom image).
Type 1000 in the Find a track text box. Select 1000 Genomes -AFR
Save and close the new configuration by clicking on ✓ (or anywhere outside the pop-up window).
There are many missense variants (coloured yellow) in these transcripts.