Introduction exercises

 

Homepage, assemblies and species

Exercise 1 – Panda

(a) Go to the species homepage for Panda. What is the name of the genome assembly for Panda?

(b) Click on More information and statistics. How long is the Panda genome (in bp)? How many coding genes have been annotated?

Exercise 2 – Zebrafish

What previous assemblies are available for zebrafish?

Exercise 3 – Mosquitoes

(a) Go to Ensembl Metazoa. How many species of the genus Anopheles are represented in Ensembl Metazoa?

(b) When was the current Anopheles gambiae genome assembly last revised?

Exercise 4 – Bacteria

Go to Ensembl Bacteria and find the species Belliella baltica. How many coding and non-coding genes does it have?

Region in detail

Exercise 5 – Exploring a genomic region in human

(a) Go to the region from 31,937,000 to 32,633,000 bp on human chromosome 13. On which cytogenetic band is this region located? 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)?

(b) Zoom in on the BRCA2 gene.

(c) Configure this page to turn on the Tilepath track in this view. What is this track? Are there any Tilepath clones that contain the complete BRCA2 gene?

(d) Create a link for this display. Email it to your neighbour. Open the link they sent you and compare your display. If there are differences, can you work out why?

(e) Export the genomic sequence of the region you are looking at in FASTA format.

(f) Turn off all tracks you added to the Region in detail page.

Exercise 6 – Exploring assembly exceptions in human

(a) Go to the region 21:32630000-32870000 in human. What is the red highlighted region? What is its name?

(b) Can you see the assembly exceptions in the Chromosome overview at the top? How many regions with assembly exceptions are on chromosome 21?

(c) Can you compare this assembly exception with the reference? What is different between this assembly exception and the version on the primary assembly?

Exercise 7 – Exploring a genomic region in Anopheles gambiae

(a) Go to the region from 7,300,000 to 7,450,000 bp on Anopheles gambiae chromosome 2L. On which cytogenetic band is this region located?

(b) How many genes are found in this region? Zoom in on the second exon of AGAP004970-RA. Turn on the track Start/Stop codons. Can you see the start codon of AGAP004970-RA?

(c) Highlight the start codon of AGAP004970-RA. Zoom out to view the whole gene. Can you see where you highlighted?

Extra Exercise 8 – Exploring CRISPR sites

You want to do some CRISPR manipulation of the human SMC3 gene. You are looking for a CRISPR site within the locus 10:110578600-110578700.

(a) Go to the locus above and turn on the CRISPR track. How many CRISPR sites can you see in this locus?

(b) Do any of the CRISPR sites overlap any phenotype causing variants? What are the identifiers of these sites and variants?

(c) Mark the region of the negative strand CRISPR sites that overlap these variants, then zoom out to see the whole SMC3 gene. In which exon of the SMC3-201 transcript are the CRISPR sites found?