Zebrafish Genome Literacy Workshop 2023

Exercise 2 - exploring genes

Find the gene vegfaa and go to its Gene page. On which chromosome and which strand is the gene?

Chromosome 16. Reverse strand.

How many splice variants are there and what are their biotypes?

1. Protein coding.

Click on Phenotypes on the left-hand menu. Are there any human diseases or traits associated with vegfaa?

Susceptibility to microvascular complications of disabetes.

In the transcript table, go to the Transcript view for ENSDART00000167719. How many exons does the transcript have?

7.

Are any of the exons completely or partially untranslated? Use the Exons link to confirm.

The first and last exons are partially untranslated, as shown by the red UTRs bases in the Exons view.

Look at the General Identifiers for the transcript. Remembering that Ensembl annotation is seeded from UniProt protein alignments, does this transcript have an associated sequence in UniProtKB/Swiss-Prot? How well do they match?

Yes, O73682. Query and target have 100% identity.

You've identified a fish with a spotted anal fin and you want to see if any genes have been associated with this phenotype before. Search for "spotted anal fin" on Ensembl. You may have to filter for zebrafish results. Click on the phenotype. How many genes have been associated with it?

2

Look at the Gene Ontology annotation for each of the genes. Are there any commonalities in their GO terms?

Not really, except that both appear to be associated with plasma membrane.

Find the zebrafish braf gene. How many orthologues are predicted for braf? How many are one-to-one orthologues and how many are one-to-many? How many fish have no braf orthologue and what are they?

192. 169 are 1:1. 23 are 1:many. 2 fish - Chinook salmon and Chinese medaka.

How much sequence identity does the guppy braf protein have to the zebrafish one?

88.6% target identity and 84.7% query identity.

Click on Gene Tree. Which species have the most closely related genes to zebrafish braf? To see which species are in the collapsed Cyprininae node, you'll need to expand it by clicking on the funnel and choosing "expand this sub-tree".

3 species - goldfish, golden-line barbel and common carp

How many goldfish braf genes are there and how many duplication events produced them?

4 genes. 3 duplication events.

Click on the Location tab for braf to view the region around the gene on chromosome 4. Then click on Synteny. Are there any syntenic regions in medaka? Which chromosome are they on?

Yes, chromosome 23.

Looking at the 15 genes upstream of the zebrafish braf gene, how many of them have orthologues in medaka?

12.

Find your favourite gene in Ensembl and go to its Gene view. Does it have any orthologues and/or paralogues? Does it have any phenotypes? Do its homologues have any phenotypes? Try exploring some of the options in the left-hand menu of the Gene page.