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Exploring a genomic region in turkey

(a) Go to the region from 2,533,290 to 2,562,211 on turkey chromosome 2. How many contigs make up this portion of the assembly (contigs are contiguous stretches of DNA sequence that have been assembled solely based on direct sequencing information)? How many assembly gaps are in this region?

(b) Zoom in on the 5’ end of RTN4 gene. Has a 5’-UTR been annotated?

(c) Zoom out back to the entirety of RTN4 and turn on the All repeats track. Are there any repeats in this region? Can you remove this track again?

(d) Save this image in PDF format.

(e) Export the genomic sequence of the region you started with in (a) in FASTA format. View the output as text.

(a) Go to the Ensembl homepage.

Select Search: Turkey and type 2:2533290-2562211 in the text box (or alternatively leave the Search drop-down list like it is and type turkey 2:2533290-2562211 in the text box). Click Go.

This genomic region is made up of three contigs (ADDD01035359.1, ADDD01101758.1 and ADDD01081608.1) indicated by the alternating light and dark blue coloured bars in the Contigs track.

Zoom into the dark blue contig ADDD01101758.1 by dragging a box around it with your mouse, then click on Jump to region in the pop-up menu.

There are two gaps, one upstream and one downstream of contig ADDD01101758.1. The previous view gave the wrong impression that there was only a single gap.

To go back to the region you started with, type 2:2533290-2562211 into the Location: search box in the middle of the page and click Go.

(b) Drag a box around the 5’ end of the transcript RTN4-201 and click on Jump to region.

A 5’-UTR has not been annotated.

(c) Once you are back in the original region, click on Configure this page on the left. Type all repeats in the Find a track box. Turn the All repeats track on and close the menu.

There are several repeats across the region, shown as grey boxes.

To remove the track, click on the track name, then the ‘X’ in the pop-up window.

(d) Click on the Export this image icon above the image and then on the Download button to download the image in PDF format.

(e) Click on the Export data button in the side menu. Then click on Next> and Text.

Note that the sequence has a header line that provides information about the genome assembly, the chromosome, the start and end coordinates and the strand.