1. Go to metazoa.ensembl.org. Open the drop-down list or click on View full list of all Ensembl Metazoa species. In a latin binomial species name, the first word represents the genus. Type Anopheles into the filter box in the top left to find all genomes with this word in the binomial.

   There are 22 Anopheles genomes (some species are represented by more than one genome).

2. Click on Anopheles gambiae (African malaria mosquito, PEST), and then on More information and statistics.

   The assembly hosted is AgamP4 (INSDC Assembly GCA_000005575.1) which was revised in Feb 2006.

(a) Go to the Ensembl metazoa homepage.

Select Search: Anopheles gambiae (African malaria mosquito, PEST), type 2L:7300000-7450000 and click Go.

The region is located on the cytogenetic band 21B.

(b) There are nine genes within this region and one that overlaps the end.

Drag out a box around the second exon of the gene, the second red box from the left and click on Jump to region in the pop-up window to zoom in. If you have not zoomed in far enough, drag out another box and click on Jump to region.

The nucleotide sequence will appear either side of the blue contig as pale blue (C), yellow (G), green (A) and pink (T) boxes. As you zoom in further, you will see the letters on the bases.

Click on Configure this page and click on Sequence and assembly. Turn on the track for Start/stop codons.

Alternatively, you can find the tracks by typing the name into the yellow Find a track box at the top right. Close the menu.

Start codons are shown in green and stop codons in red. You should see a green start codon that coincides with the start of the filled in red box.

(c) Drag out a box around the green start codon and select Mark region. The highlighted region should be visible as a grey dotted line. Scroll up to the overview to drag out a box around the gene and select Jump to region, you will still see the highlight in this view.

1. Go to the Ensembl Metazoa homepage. Select Atta cephalotes (Leaf-cutter ant) from the species list and type LOC105618535 in the search box. Click Go. Click on LOC10561855.

2. Click on Show transcript table.

The transcript is 3451 base pairs and the length of the encoded protein is 810 amino acids.

Click on the Ensembl Transcript ID XM_012200067.1 in the transcript table.

It has nine exons.

Click on Sequence - Exons in the side menu.

The last exon is partially untranslated (sequence shown in orange). This can also been seen from the fact that in the transcript diagram on the Gene summary and Transcript summary pages the boxes representing the last exon is partially unfilled.

1. Click on the blue Export data button. Under Options for FASTA sequence, select Genomic: Unmasked, cDNA and Peptide sequence. Click Next>. Click on Text.

This returns three sequences (one gene, one transcript and one protein sequence).

(a) Go to metazoa.ensembl.org/index.html. Click on Anopheles gambiae (African malaria mosquito, PEST) from the popular species list.

Search for para and click on the AGAP004707 link in the results.

Click on GO: biological process in the side menu.

There are nine GO terms listed. GO:0006811 ion transport, GO:0006814 sodium ion transport and GO:0019228 neuronal action potential are some of the terms listed.

(b) If the transcript table is hidden, click on Show transcript table to see it.

There are 13 protein coding transcripts.

Click on Transcript comparison in the left hand menu. Click on Select transcripts. Either select all the transcripts labelled protein coding one-by-one, or click on the drop down and select Protein coding. Close the menu.

(c) Click on the transcript named AGAP004707-RH. Click on Exons in the left hand menu.

There are 32 exons, of which exon 32 is longest with 1,017 bp.

1. Go to the Ensembl Protists homepage. Select Plasmodium falciparum from the species list and type PF3D7_1145400 in the search box. Click Go. Click on PF3D7_1145400 in the search results. You can find the strand orientation and coordinates in the gene Summary page.

   PF3D7_1145400 is located on the reverse strand of chromosome 11 between 1,800,544 and 1,803,550.

2. Click on Show transcript table.

   The transcript is 2,514 base pairs and the length of the encoded protein is 837 amino acids.

   Click on the transcript ID CZT99117 in the transcript table.

   It has four exons.

3. You can find this information in a number of places: the transcript table, External references on the Gene tab or General identifiers on the Transcript tab.

   The UniProt ID that maps to protein encoded by the PF3D7_1145400 transcript is Q8IHR4.

4. Click on GO: Biological process in the side menu of the Gene tab.

   The PF3D7_1145400 gene is involved in mitochondrial fission.

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).

Go to the Ensembl Metazoa homepage and click on the link Tools at the top of the page. Click on Variant Effect Predictor and enter the variants in the text box:

Note: Variation data input can be done in a variety of formats. See more details about the different data formats and their structure in this VEP documentation page. Click Run. When your job is listed as Done, click View Results.

You will get a table with the consequence terms from the Sequence Ontology project (http://www.sequenceontology.org/) (i.e. synonymous, missense, downstream, intronic, 5’ UTR, 3’ UTR, etc) provided by VEP for the listed SNPs. You can also upload the VEP results as a track and view them on Location pages in Ensembl. SIFT is available for missense SNPs only.

(a) Yes, there is one syntenic region in Aedes aegypti to Anopheles gambiae chromosome 3R, which is in the centre of this view. Aedes aegypti chromosomes 2 has a syntenic region to A. gambiae chromosome 3R.

(b) Scroll down to the bottom of the page.

There is a homologue AAEL000599 in Aedes aegypti of Anopheles gambiae AGAP009734.

Go to Ensembl Metazoa. Click on BioMart on the navigation bar at the top of the page. Click the New button on the toolbar on the top left-hand corner, choose the Ensembl Metazoa Genes database and Bemisia tabaci Uganda 1 dataset. Now, filter for the genes with Gene type: Protein coding and Limit to genes: With AlphaFold DB import only.

Make sure the box next to the filter is ticked, otherwise the filter won’t work. Click the Count button on the toolbar.
> This will give you 20 / 13802 Genes.

Go to Attributes on the left-hand panel. Select Gene stable ID, Protein stable ID, AlphaFold DB import Click on Results on the toolbar and the table will display the options you have selected as attributes.

Go to Attributes on the left-hand panel. Expand the SEQUENCES section by clicking on the + box and select Peptide. Select the appropriate header information from the HEADER INFORMATION.

Click on Results on the toolbar and the sequence will be shown as FASTA format. You can export the sequence by downloading it directly to your local machine or sending it to your email.