Ensembl Protists: the Plasmodium vivax genome
Go to the Ensembl protists homepage and choose P. vivax.
(a) What is the assembly of the P. vivax genome available in Ensembl Protists? How many protein-coding genes have been annotated on that genome? How long is chromosome 14 in base pairs? Is there a karyotype available for this species?
(b) Search for this genomic region on chromosome 11: 956236-966235. How many intron-containing genes have been annotated in this region?
(c) Go to the Gene tab of this gene. Can you find some of the molecular functions assigned to its product based on GO (Gene Ontology)?
(d) Go to the transcript tab and find out if there are cross reference entries attached to this transcript, for example from UniProt. If so, can you find the alignment between the two entries?
Start at http://protists.ensembl.org. Click on View full list of all species, then select Plasmodium vivax.
(a) There are two assemblies for Plasmodium vivax: ASM241v2/GCA_000002415.2 and PvP01/GCA_900093555.1.
Click on the genome to go to the homepage, then select More information and statistics.
There are 5,389 coding genes in ASM241v2/GCA_000002415.2.
Go back to the species homepage and select View karyotype. Click on the chromosome to go to the chromosome summary page.
Chromosome 14 is 3,120,417 bp long.
(b) Go back to the species homepage and paste 11:956236-966235 into the search box to go to the region view. There are three genes in this region, but only one has introns.
(c) Click on the gene, to get a pop-up, then on the gene ID. Click on GO: Molecular function in the left-hand menu.
Magnesium ion binding and catalytic activity are some of the GO terms associated with this gene.
(d) Click on the transcript tab at the top. Go to General identifiers in the left-hand menu.
There is a matching UniProt protein A5K2A0 linked to this transcript.
Click on align to see the alignment.