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Exploring the zebrafish vegfaa gene

(a) Find the zebrafish vegfaa (vascular endothelial growth factor Aa) gene, and go to the Gene tab.

  • On which chromosome and which strand of the genome is this gene located?
  • How many transcripts (splice variants) are there and how many are protein coding?
  • How long is the protein encoded by ENSDART00000167719.2?
  • What are some functions of vegfaa according to the Gene Ontology consortium?

(b) Click on Phenotype at the left side of the page. Are there any diseases or traits associated with this gene? Is the human orthologue of vegfaa associated with any diseases, according to MIM (Mendelian Inheritance in Man)?

(c) In the transcript table, click on the transcript ID for vegfaa-201, and go to the Transcript tab.

  • How many exons does it have?
  • Are any of the exons completely or partially untranslated?
  • Is there an associated sequence in UniProtKB/SwissProt? Have a look at the General identifiers for this transcript.

(d) Are there microarray (oligo) probes that can be used to monitor ENSDART00000167719 expression?

(a) Go to the Ensembl homepage.

Select Search: Zebrafish and type vegfaa. Click Go.

Click on the Ensembl ID ENSDARG00000103542.

  • Chromosome 16 on the reverse strand.
  • Ensembl has one transcript annotated for this gene, which is protein coding.
  • It codes for a protein of 188 amino acids

Click on GO:molecular function to see that growth factor activity and heparin binding are associated with vegfaa.

(b) Click on Phenotype at the left side of the page. Scroll down to see phenotypes associated with orthologues. You may find it easier to use the filter box at the top right to narrow down to MIM or human.

This gene is associated with MICROVASCULAR COMPLICATIONS OF DIABETES, SUSCEPTIBILITY TO, 1 in human.

(c) Click on ENSDART00000167719.

It has seven exons. This is shown in the Transcript summary or in the left hand side menu Exons.

Click on the Exons link in this side menu.

Exons 1 and 7 are partially untranslated (UTR sequence is shown in red). You can also see this in the cDNA view if you click on the cDNA link in the left side menu.

O73682 from UniProt/Swiss-Prot matches the translation of the Ensembl transcript. Click on O73682 to go to UniProtKB, or click align for the alignment.

(d) Click on Oligo probes in the side menu.

Probesets from AFFY Zebrafish, AGILENT G2518A and AGILENT G2519F match to this transcript sequence. Expression analysis with any of these probesets would reveal information about the transcript. Hint: this information can sometimes be found in ArrayExpress