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Exploring a SNP in Aedes aegypti

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Exploring a SNP in Aedes aegypti

The Aedes aegypti AAEL004743 gene is part of ABC transporter superfamily associated with mosquito development and arboviral infections. Go to Ensembl Metazoa and answer the following questions:

  1. How many variants have been identified in the gene that can cause a change in the protein sequence (i.e. missense variant)?

  2. What is the ID of the variant that changes the amino acid residue 45 from Leucine to histidine (hint: refer to an amino acid codon table)? What is the location of this SNP in the Aedes aegypti (Yellow fever mosquito, LVP_AGWG) genome? What are its possible alleles?

  3. Download the flanking sequence of this SNP in RTF (Rich Text Format). Can you change how much flanking sequence is displayed on the browser?

  4. Does this SNP cause a change at the amino acid level for other genes or transcripts?

  1. Click on Aedes aegypti (Yellow fever mosquito, LVP_AGWG) on the Ensembl Metazoa homepage. Search for AAEL004743 on the species page. In the left-hand side menu of the Gene tab, click on Variant table. Click on Consequences: All then, Turn All off and select only missense variant.

    The missense variant button indicates that there are 167 of these. Alternatively, you can count the number of variants in your filtered list.

  2. An amino acid codon table can be found on Wikipedia. Sort the AA coord column by clicking on the header and scroll down to find a variant at residue 45. The ID of this variant is supercont1.129:999463.

    The variant is located at position 2:289218453. The two possible alleles at this locus are T (reference) and A (alternative).

  3. Click on the link supercont1.129:999463, then click on Flanking sequence in the left-hand side menu. Now click on Download sequence and select File format > Rich Text Format (RTF).

    If you want to change how much flanking sequence is displayed on the browser, go back to the Flanking sequence page, click on the Configuration button and change the length of the sequence. The default settings is 400 bp.

  4. Click on Genes and regulation in the left-hand side menu.

    This SNP is an upstream gene variant in AAEL004763 (A sequence variant located 5’ of a gene).