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Exploring the mouse Dpp6 gene

Genetic variation in the dipeptidylpeptidase 6 Gene (DPP6) in humans has previously been strongly associated with amyotrophic lateral sclerosis (ALS), a lethal disorder caused by progressive degeneration of motor neurons in the brain.

(a) Search for the Dpp6 gene in mouse and click on the ENSMUST00000071500 transcript to open the transcript tab. How many exons make up this transcript?

(b) Click on Exons to display the exon sequences of the transcript. Which exon contains the translation start? What is the exon ID of the largest exon? What is the start and end phase of exon 2?

(c) Click on Protein summary. How many protein domains or features fall within the second exon? What is the PFAM protein domain at the C-terminus of the protein and how many exons does it fall into? Which amino acid positions does the domain above cover?

(d) Click on Domains and features. Which domains are associated with Pfam? How many genes in the mouse genome have the IPR002469 domain? What chromosomes are these genes found on?

(a) Go to the Ensembl homepage.

Select Search: Mouse and type Dpp6. Click Go.

Click on either the Ensembl ID ENSMUSG00000061576 or the MGI official gene name Dpp6. From the transcript table, click on the link for transcript ENSMUST00000071500 to open the transcript tab.

ENSMUST00000071500 consists of 26 exons.

(b) Click on Exons, which can be found on the left of the page. The translation start is found in the first exon (ENSMUSE00000725552), shown in dark blue text.

The largest exon is the final exon (856 bp), which has the exon ID ENSMUSE00000773588.

Exon 2 has a start and end phase of 0 and 1 respectively, which means that the codon at the start of the exon starts at the first nucleotide and the codon at the end of the exon ends at nucleotide 2. Notice that the end phase of each exon is the same as the start phase of the next exon.

(c) Click on Protein Summary in the menu on the left hand side of the page. Alternating exons are shown on the protein as different shades of purple.

There are two predicted protein domains that fall within the second exon: low complexity (seg) and a transmembrane helix.

Click on a domain or feature to view further information.

The C-terminal PFAM domain is Peptidase_S9B (PF00326), which spans or partially spans seven exons, covering amino acid positions 582-787.

(d) Click on Domains & features.

Looking at the Domains table you should notice that there are two domains associated with Pfam: PF00326 and PF00930.

Click on Display all genes with this domain next to IPR002469. This should now display the genes that have the IPR002469 domain located on the karyotype and as a table.

Six genes have this domain and they are found on chromosomes 1, 2, 5, 9 and 17.