Select Oryza sativa Japonica from the homepage to go to its species information page. Click on More information and statistics.

Oryza sativa Japonica has 37,960 coding and 1,011 non-coding genes.

1. Go to Ensembl Plants and click on Triticum aestivum on the front page of Ensembl Plants to go to the species information page. Under the Genome assembly section of the species page, you will find the number of cultivars in wheat.

   There are 14 cultivars.

2. Click on More information and statistics in the Genome assembly section and scroll down to the paragraph on Assembly.

   The assembly and annotations were generated by the International Wheat Genome Sequencing Consortium (IWGSC).

3. Stay on the More information and statistics page. You can find some summary statistics on the right-hand side.

   The T. aestivum (IWGSC) assembly has 107,891 coding and 12,853 non-coding genes.

4. Go to the Ensembl Plants homepage. Click on View full list of all species in the All genomes panel. Filter the table by entering Triticum in the text box on the top right-hand corner of the table.

   Besides T. aestivum are 4 other Triticum species available in Ensembl: Triticum dicoccoides (wild emmer wheat), Triticum spelta (spelt), Triticum turgidum (domesticated emmer wheat) and Triticum urartu (red wild einkorn wheat).

1. On the homepage, click on View full list of all Ensembl Plants species underneath the coloured search block. Type Solanum into the filter box in the top left-hand corner of the table.

   There are three Solanum genomes: Solanum lycopersicum (tomato), and Solanum tuberosum RH89-039-16 and Solanum tuberosum (both potato).

2. Click on S. lycopersicum, then on More information and statistics.

   The genome was revised in April 2018.

Select Coffea canephora from the drop down species list, or click on View full list of all species, then choose Coffea canephora from the list to go to the species homepage.

1. The coffee variety represented in Ensembl Plants is Coffea canephora (Robusta coffee). The Arabica coffee variety is not currently represented in Ensembl Plants.

Click on on More information and statistics.

1. The AUK_PRJEB4211v1 _Coffea canephora assembly was submitted by Genoscope CEA.

2. The genome is 568,611,505bp in length. There are 25,574 coding genes annotated across the genome.

In the Ensesmbl Bacteria homepage, start to type H37Ra into the Search for a genome search box (you can find this in the coloured block at the top of the homepage). It will auto-complete, allowing you to select M. tuberculosis H37Ra str. ATCC25177 from the drop-down list. Click on More information and statistics.

M. tuberculosis H37Ra str. ATCC25177 has 4,080 coding and 47 non-coding genes.

Go to Ensembl Fungi [https://fungi.ensembl.org/index.html]. Select Botrytis cinerea from the drop down species list, or click on View full list of all species, then choose Botrytis cinerea from the list to go to the species homepage.

Click on on More information and statistics.

1. The ASM83294v1 Botrytis cinerea assembly was submitted by Wageningen University and Syngenta.

2. The genome is 42,630,066 bp in length. There are 11,707 coding genes annotated across the genome.

Select Chicken from the drop down species list, or click on View full list of all Ensembl species, then choose Chicken from the list to go to the species homepage. Click on on More information and statistics.

The bGalGal1.mat.broiler.GRCg7b assembly was submitted by Vertebrate Genomes Project on January 2021.

1.Select Pig from the drop down species list, or click on View full list of all Ensembl species, then choose Pig from the list to go to the species homepage. Click on More information and statistics.

Pig has 22,063 coding genes and 13,154 non-coding genes.

1. The Sscrofa11.1 assembly of the pig genome was produced in January 2017 by the Swine Genome Sequencing Consortium (SGSC).

(a) Select Sheep from the drop down species list, or click on View full list of all Ensembl species, then choose Sheep from the list.

The assembly is Oar_rambouillet_v1.0 or GCA_002742125.1.

(b) Click on More information and statistics. Statistics are shown in the tables on the left.

The length of the genome is 2,869,914,396 bp. There are 20,506 coding genes.

Select Atlantic cod from the drop down species list, or click on View full list of all Ensembl species, then choose Atlantic cod from the list to go to the species homepage. Click on on More information and statistics.

The length of the genome is 669,949,713 bp. There are 23,515 coding and 5,339 non-coding genes annotated.

1. Go to the Ensembl Plants homepage. Select Oryza sativa Japonica from the Species drop-down list and type 1:405000-453000. Click Go.

2. Click on Configure this page to open the menu. You can find the AGILENT:G2519F-015241 track under Oligo probes in the left-hand menu, or by using the Find a track box at the top right. Turn on the track as Normal then save and close the menu. As the AGILENT:G2519F-015241 track is stranded, it appears at the top and bottom of the view.

   There are 5 probes mapped to this region on the positive strand and one probe on the reverse strand.

3. Drag a box around the reverse strand probe then click on Mark region to highlight.

   The highlighted region maps to two transcripts: Os01t0107900-02 and Os01t0107900-01

1. Go to the Ensembl Plants homepage. Select Search: Triticum aestivum and type 2D:378720500-378780600 in the text box. Click Go.

2. There are two genes displayed in the Genes track. They are both located on the reverse strand. The IDs are

3. There are two tracks which have mapping to this gene: Genes and Alternative gene models. Click the track names for more information on their source.

4. Click Export data in the left-hand menu. Leave the default parameters as they are. Click Next>. Click on Text. Note that the sequence has a header that provides information about the genome assembly, the chromosome, the start and end coordinates and the strand. For example:
   >2D dna:chromosome chromosome:IWGSC:2D:378720500:378780600:1

5. Click on Polyploid view in the left hand menu to view the homoeologous regions. Click on Export image. This will open a pop-up menu of the different image formats you can export, which are PNG and PDF.

1. Go to the Ensembl Plants homepage, select Coffea canephora from the Species drop-down list and type 1:23704000-23766000 in the text box. Click Go.

2. Draw with your mouse a box encompassing the GSCOC_T00030044001 transcript (with ID CDP09644). Click on Jump to region in the pop-up menu.

3. Click Configure this page in the side menu (or on the cog wheel icon in the top left hand side of the bottom image). Go into Repeat regions in the left-hand menu then select Repeats (Repbase). Click on the (i) button to find out more information.

   Repeats identified by RepeatMasker, using the Repbase library of repeat profiles.
   Save and close the new configuration by clicking on ✓ (or anywhere outside the pop-up window). There are no repeats from Repbase overlapping GSCOC_T00030044001.

4. Click Share this page in the side menu. Copy the URL. Get your neighbour’s email address and compose an email to them, paste the link in and send the message. When you receive the link from them, open the email and click on your link. You should be able to view the page with the new configuration and data tracks they have added to in the Location tab. You might see differences where they specified a slightly different region to you, or where they have added different tracks.

5. Click Export data in the side menu. Leave the default parameters as they are (FASTA sequence should already be selected). Click Next>. Click on Text. Note that the sequence has a header that provides information about the genome assembly, the chromosome, the start and end coordinates and the strand. For example:
   >1 dna:chromosome chromosome:AUK_PRJEB4211_v1:1:23755890:23764847:1

6. Click Configure this page in the side menu. Click Reset configuration. Click ✓.

1. Go to the Ensembl homepage. Select Chicken from the drop-down menu in the blue box and enter 5:38111022-38265293 into the text box. Click Go.

   This genomic region is made up of one contig indicated by the dark blue coloured bar in the Contigs track.

2. Make sure your cursor is set to the Select a region action (you can change your cursor action in the top right-hand corner of the Region in detail view). Drag a box around the ESRRB gene (note that you will need to highlight the feature itself, i.e. the block, rather than the label) and click on Jump to region.

3. Click on Configure this page in the left-hand panel to open the configuration menu. Enter RefSeq GFF3 annotation into the search box in the top left-hand corner. To enable the track, click on the square next to the track name RefSeq GFF3 annotation and select the Expanded with labels style. Save and close the pop-up menu.

4. Click on the Export this image icon above the image and then on the Download button to download the image in PDF format.

1. Go to the Ensembl homepage. Select Pig from the drop-down menu in the blue box and enter 11:8,805,953-8,858,418 in the text box. Click Go.

2. Click Configure this page in the left-hand menu (or on Add/remove tracks at the top left-hand corner of the Region in detail image). Type TRF into the search field in the top left-hand corner of the pop-up menu. Enable the Tandem repeats (TRF) track on the right. You can click on the i icon on the far left for a track description.

   The TRF track locates adjacent copies of a pattern of nucleotides. Save and close the new configuration by clicking on the check icon in the top right-hand corner of the pop-up menu or by clicking anywhere outside the pop-up menu. There are 19 TRF that overlap this region.

3. Click Share this page in the left hand-side panel. Copy the URL, get your neighbour’s email address and send them the URL you copied. When you receive the link from them, open the email and click on your link. You should be able to view the page with the new configuration and data tracks they have added.

4. Click on Export data in the left-hand menu. Leave the default parameters as they are. Click Next> and view the sequence in a new browser tab by clicking on Text. The sequence is in FASTA formatwhich comprises a header (beginning with >) that provides information about the genome assembly (primary_assembly:Sscrofa11.1), the chromosome, the start and end coordinates and the strand. For example:
   >primary_assembly:Sscrofa11.1:11:8805953-8858418:1

5. Click on Reset configuration at the top of the Region in detail image.

1. Go to the Ensembl homepage. Click on View full list of all species. Use the filter in the top right-hand corner of the table to search for Sheep. Click on Sheep (texel) from the list of genomes to open the species information page. From there, search for 18:7146000-7409000 and click Go.

   There are three genes in this region, ENSOARG00000010005 and ENSOARG00000010107 on the forward strand, and ENSOARG00000010101 on the reverse strand.

2. Make sure that your cursor action is set to Select a region. with your cursor, drag a box around the start of the first exon of the ENSOARG00000010005 gene, at the left of the view. 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 around the first exon 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.

3. Click on Configure this page and click on Sequence and assembly. Turn on the tracks for Translated sequence and Start/stop codons. Alternatively, you can find the tracks by typing their names into the search field in the top left-hand corner. Close the menu. You can now see the amino acid sequence in all three frames on both strands above and below the nucleotide sequence. Start and stop codons are highlighted either side of these. Start codons are shown in green and stop codons in red.

   There is no start codon or methionine residue at the 5’ end of this gene. This suggests that this gene model is incomplete.

1. Go to the Ensembl homepage. Select Rainbow trout from the Species drop-down list and type 3:49000000-49400000 in the text box. Click Go.

2. Draw with your mouse a box encompassing the myo3b transcripts. Click on Jump to region in the pop-up menu.

3. Click Configure this page in the side menu (or on the cog wheel icon in the top left hand side of the bottom image). Go into Simple features in the left-hand menu then select CpG islands. Click on the (i) button to find out more information.

   The CpG islands are determined from the genomic sequence using a program written by G. Micklem, similar to newcpgreport in the EMBOSS package. Save and close the new configuration by clicking on ✓ (or anywhere outside the pop-up window). There is one CpG island overlapping myo3b.

4. Click Share this page in the side menu. Copy the URL. Get your neighbour’s email address and compose an email to them, paste the link in and send the message. When you receive the link from them, open the email and click on your link. You should be able to view the page with the new configuration and data tracks they have added to in the Location tab. You might see differences where they specified a slightly different region to you, or where they have added different tracks.

5. Click Export data in the side menu. Leave the default parameters as they are (FASTA sequence should already be selected). Click Next>. Click on Text. Note that the sequence has a header that provides information about the genome assembly (USDA_OmykA_1.1), the chromosome, the start and end coordinates and the strand. For example:
   >3 dna:primary_assembly primary_assembly:USDA_OmykA_1.1:3:49195318:49199101:1

6. Click Configure this page in the side menu. Click Reset configuration. Click ✓.

1. Go to Ensembl Plants, select Triticum aestivum from the drop down menu then type TraesCS6D02G180200 into the search box. Click on the gene name link TraesCS6D02G180200 in the search results. Click on GO: Molecular function in the left-hand menu.

   There is one term listed: GO:0005515, protein binding.

2. Click on the transcript tab at the top of the page. Click on Exons in the left-hand menu.

   There are six exons. Exon 6 is longest with 485 bp, of which around one sixth is coding.

3. Click on either Protein Summary or Domains & features in the left-hand menu to view the data graphically or as a table, respectively.

   Leucine-rich repeats are predicted by many different methods, however each method predict the leucine-rich repeats at different positions.

(a) Go to plants.ensembl.org and type NCED2 into the search box, selecting Solanum locypersicum from the drop down menu. Click on the first result to go to the gene tab.

Click on the Show transcript table button if the transcript table is hidden. In the 4th column we see the protein length listed, 581 amino acids in length.

The location is listed at the top of the page, we can see that this is on Chromosome 8, between the base pairs 8,729,953 and 8,731,698, and on the forward strand.

(b) The gene description for this gene is ‘9-cis-epoxycarotenoid dioxygenase NCED2, chloroplastic’ which suggests the enzyme is localised to the chloroplast.

In the left-hand navigation panel, find the link to GO: Cellular location. We can see three results, chloroplast, plastid and chloroplast stroma, so this matches the gene description.

(c) Click on Gene expression in the left-hand navigation panel.

Darker shades of blue indicate higher expression. Hover your mouse over the heat-map to show a pop-up with the TPM (Transcripts Per Kilobase Million).

The 2cm fruit in the Tomato Genome Consortium has the highest expression at 103 TPM. You can also click on Filters at the top right and filter to high or medium expression.

(d) Click on the Gene gain/loss tree. You might find it easier to compare in the radial tree, click the two arrows icon at the top left of the image () to toggle to the radial view.

Look for the red lines, indicating the larger number of members and significant expansion. The number of members are listed just before the species name.

Brassica napus and Brassica juncea has the highest number of members in this gene family.

(e) Go to the transcript tab for this gene by clicking on the transcript ID Solyc08g016720.1.1 from the transcript table.

Find the Oligo probes link in the left-hand navigation panel. There is a single probe from Affymetrix, the AFFY TomGene, 20363698.

1. Go to the Ensembl Plants homepage (http://plants.ensembl.org/). Select C. canephora from the species list and type FUS3 in the search box. Click Go and click on the gene ID GSCOC_T00019208001. You can find the strand orientation and the location under Summary in the Gene tab.

   The C. canephora FUS3 gene is located on chromosome 7 on the forward strand.

2. Click on GO: Cellular component in the left-hand panel.

   The protein is located in the nucleus.

3. Click on Summary in the side menu.

   The gene description is Projected from Arabidopsis thaliana (AT3G26790) by UniProtKB/Swiss-Prot;Acc:Q9LW31.

4. Click on Show transcript table.

   The transcript is 1038 bp and the length of the encoded protein is 279 amino acids.

   Click on the transcript ID CDP16731 in the transcript table. You can find the number of exons in under in the summary information at the top of the page.

   It has 7 exons.

   Click on Sequence: Exons in the left-hand panel.

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

1. From the Ensembl Bacteria homepage, select Clostridium sporogenes by beginning to write the species name and selecting the species from the auto-complete list. Type PolC and click on the gene ID VT92_0235670. Click on GO: biological process in the left-hand panel.

   There are two terms listed: GO:0006260, DNA replication and GO:0006261, DNA-templated DNA replication.

2. Click on the transcript named OQP95999 or on the Transcript tab.

   OQP95999 is 4299 bp in length.

3. Click on either Protein Summary or Domains & features in the left hand menu to see graphically or as a table respectively.

1. Go to the Ensembl homepage. Select Chicken from the drop-down list in the blue box, enter MYH9 and click Go. In the search results page, click on Chicken reference in the left-hand panel to restrict your results to the reference genome only. Click on the first hit MYH9 (Chicken Gene, Breed: reference) to open the Gene tab. Look at the Location section in the gene summary at the top of the page.

   The gene is located on chromosome 1 on the forward strand.

   Now click on the Show transcript table button and focus on the Protein column in the Transcript table.

   The transcript ENSGALT00010036169.1 (MYH9-209) produces the longest protein at 1,960 amino acid residues.

2. Gene Ontology maps terms to a protein in three classes: biological process, cellular component, and molecular function.

   Meiotic spindle organisation, cell morphogenesis, and angiogenesis are some of the roles associated with the MYH9 gene.

3. Click on ENSGALT00010036169.1 in the Transcript table to open the corresponding Transcript tab. Look at the About this transcript section in the transcript summary at the top of the page.

   The transcript has 41 exons.

   Click on the Exons link in the left-hand side menu. In the Sequence column of the Exon table, look for any UnTranslated Regions (UTRs) which coloured in orange.

   Exon 1 is completely untranslated, and exons 2 and 41 are partially untranslated. You can also see this in the cDNA view if you click on Sequence: cDNA in the left-hand menu.

   Click on External References: General identifiers in the left-hand menu. Look for UniProtKB in the External database column.

   A0A1D5PM19.34 from UniProt matches the translation of the Ensembl transcript. Click on A0A1D5PM19.34 to open the corresponding UniProt entry in a new browser tab.

4. In the left-hand menu, look for External References: Oligo probes.

   There are probes from Affy and Agilent that can be used to monitor expression of this transcript.

1. Go to the Ensembl homepage. Select Pig from the drop-down list in the blue box, enter TRAF3 into the text box and click Go. In the search results page, click on Pig reference in the left-hand panel to restrict your results to the pig reference only. Click on the first hit TRAF3 (Pig Gene, Breed: reference) to open the Gene tab. Look at the Location section in the gene summary at the top of the page.

   The TRAF3 gene is located on the forward strand.

   Now look at the About this gene section in the gene summary at the top of the page.

   TRAF3 has 4 transcripts.

   Click on the Show transcript table button underneath the gene summary. Focus on the Protein column in the transcript table.

   The transcript ENSSSCT00000101908.1 (TRAF3-201) produces the longest protein at 573 amino acid residues in length.

2. Gene Ontology maps terms to a protein in three classes: biological process, cellular component, and molecular function.

   Some of the GO terms associated to the TRAF3 gene are: regulation of cytokine production and proteolysis (biological process), protein kinase and metal ion binding (molecular function), and cytoplasm and endosome (cellular component).

3. Click on ENSSSCT00000101908.1 in the transcript table. Under the summary information at the top of the page, focus on the About this transcript section.

   This transcript has 11 exons.

   Click on the Exons link in the left-hand side menu. In the Sequence column of the Exon table, look for any UnTranslated Regions (UTRs) which coloured in orange.

   Only exon 11 is partially untranslated. You can also see this in the cDNA view if you click on Sequence: cDNA in the left-hand menu.

   Click on External References: General identifiers in the left-hand menu. Look for UniProtKB in the External database column.

   A0A4X1TTD0.19 and A0A8W4FAU5.6 from UniProt match the translation of the Ensembl transcript. Click on the IDs to open the corresponding entry in UniProt.

4. In the left-hand menu, look for External References: Oligo probes.

   The link is greyed out, which means that no commercial oligo probes are available to monitor expression of this transcript.

5. Go to the Ensembl homepage by clicking on the Ensembl logo in the top left-hand corner of any page. Select Pig from the drop-down list in the blue box, enter TRAF3 into the text box and click Go. In the search results page, click on Pig berkshire in the left-hand panel to restrict your results to the Berkshire breed only. Click on the first hit TRAF3 (Pig Gene, Breed: berkshire) to open the Gene tab. Look at the Location section in the gene summary at the top of the page.

   The TRAF3 gene is located on the forward strand in the Berkshire breed.

   Now look at the About this gene section in the gene summary at the top of the page.

   TRAF3 has 5 transcripts in the Berkshire breed.

   Click on the Show transcript table button underneath the gene summary. Focus on the Protein column in the transcript table.

   The transcript ENSSSCT00065038580.1 (TRAF3-205) produces the longest protein at 573 amino acid residues in length.

6. The Ensembl canonical transcript in the pig reference genome is 6,677 bases in length. The Ensembl canonical transcript in the Berkshire breed is 6,340 bases in length. This suggests that the TRAF3 Ensembl canonical transcript in the reference has more/larger UTRs compared to the Berkshire breed. To compare, you can open the Sequence: Exons pages in the Transcript tab in both breeds and look at the length of the UTR (coloured in orange).

1. Start at the homepage and enter BA00369602 into the search box and select Triticum aestivum from the drop-down list. Click on the Gene ID BA00369602 in the search results to get to the variation homepage.

   Under Synonyms, you can see that the variant is also known as AX-94448191 in CerealsDB.

2. Click on Genes and regulation.

   The variant is a missense variant on TraesCS2D02G303800, where it gives a glycine to aspartic acid (G/D) change at transcript position 406.

3. Click on Sample genotypes. Scroll down the table to see if there are any cultivars with the A allele in the genotype column.

   All of the cultivars listed have the genotype G|G.

1. Select Phaseolus vulgaris from the Species search drop-down menu and search for PHAVU_001G219900g. In the results page, you can click on the coordinates 1:48,238,848-48,245,168 to go straight to the Location tab. Scroll down to the Region in detail view. The variation track (phaseolus_vulgaris_eva_PRJEB18671) is shown at the bottom of the view.

   If you don’t see the Variation - All sources track, click Configure this page on the left-hand panel, search for the track in the pop-up menu and enable the track by clicking on the square next to the track name. Close the pop-up window and wait for the track to load.

2. Zoom in around the first exon of this gene by drawing a box in the respective region (you can change your mouse action by clicking the Drag/Select icons at the top right-hand corner of the view). Note the gene is on the reverse strand (this is signified by the < sign next to the transcript name, and it is located below the Contigs track), so the first exon will be on the right hand side of that image. The variation legend is shown at the bottom of the page, telling you what the colours mean.

   There are four missense variants within the region; 1:48244305:C_T:PRJEB18671, 1:48244362:T_G:PRJEB18671, 1:48244426:G_A:PRJEB18671, 1:48244435:T_A:PRJEB18671.

   Missense variants are shown in yellow. Click on the variants to get additional information on that variant including location. You can zoom into the region if the variant block is too small to click.

   The variants are found at 1:48244305, 1:48244362, 1:48244426, 1:48244435.mSNPs are tagged with ambiguity codes (zoom into the region if you cannot see this). You can find a useful IUPAC ambiguity code guid on the bioinformatics.org website.

1. Select Solanum lycopersicum from the Species search drop-down menu and search for Solyc02g084570.3. In the results page, you can click on the coordinates 2:48284598-48288482 to go straight to the Location tab. Scroll down to the Region in detail view. The variation track is shown at the bottom of the view.

   If you don’t see the Variation - All sources track, click Configure this page on the left-hand panel, search for the track in the pop-up menu and enable the track by clicking on the square next to the track name. Close the pop-up window and wait for the track to load.

2. Zoom in around the last exon of this gene by drawing a box in the respective region (you can change your mouse action by clicking the Drag/Select icons at the top right-hand corner of the view). Note the gene is on the reverse strand (this is signified by the < sign next to the transcript name, and it is located below the Contigs track), so the last exon will be on the left hand side of that image. The variation legend is shown at the bottom of the page, telling you what the colours mean.

   The types of variants seen in that region are 3’ UTR, missense, synonymous and splice region variants.

   Splice region variants are shown in orange. Click on the variants to get additional information on that variant including location. You can zoom into the region if the variant block is too small to click.

   The variants are found at 2:48285642 and 2:48285640-48285641. Note that the two variants overlap: one is a SNP and the other is an indel. SNPs are tagged with ambiguity codes (zoom into the region if you cannot see this). You can find a useful IUPAC ambiguity code guid on the bioinformatics.org website. Single-letter ambiguity codes are given when two or more possible nucleotides may be represented at a single base locus.

1. Go to Ensembl Fungi, click on View full list of all species. You can sort the table by column. Click on the Variation database column to sort the table by species with variation data.

   The table shows that we have 8 fungi species currently with variation databases.

2. Click on Fusarium oxysporum in the table and on the species page search for FOXG_13574T0. From the Gene tab, click on Variant table in the left-hand panel. You can use the filter at the top right-hand corner of the table tmp_10_6610.

   The alleles are C/T, where C is the reference allele.

3. Click on tmp_10_6610 in the table to open the Variant tab. Then click on Genotype frequency from the menu on the left-hand side of the page.

   The most frequent allele at this position is C with a frequency of 0.850.

4. Click on Sample genotypes in the menu on the left.

   The table shows that sample 909454 has the C|T genotype and 909455 has the T|T genotype.

(a) Go to the Ensembl homepage.

Type rs10731268 in the Search box, then click Go. Click on rs10731268.

(b) Click on Genes and Regulation in the side menu (or the Genes and Regulation icon).

rs10731268 falls within 2 genes: ENSGALG00010028562 and ENSGALG00010028568 (HGNC: MLLT1). This variant has a missense consequence in seven transcripts of the ENSGALG00010028562 gene, and downstream gene variant consequence in three transcripts of the ENSGALG00010028568 (HGNC: MLLT1) gene.

(c) Click on Citations in the left hand side menu.

This variant is mentioned in the paper ‘Identification and characterization of genes that control fat deposition in chickens’ from 2013 by D’Andre et al. Click on the PubMed ID 24206759 to go to the paper.

(d) Click on Phylogenetic Context in the side menu. Select Alignment: 17 sauropsids EPO and click Go.

Japanese quail, Duck, Golden Eagle, Common canary and Zebra finch all have an A in this position. This suggests that A may be the ancestral allele.

(a) Go to the Ensembl homepage.

Type rs81219178 in the Search box, then click Go.

Click on rs81219178 (Pig Variant, Breed: reference).

Click on Genes and regulation in the left-hand menu or on the icon.

The variant causes a D->N amino acid change (Aspartic acid -> Asparagine). The SIFT score of 0.01 predicts that this change will have a deleterious effect on the protein.

(b) This variant affects one transcript (ENSSSCT00000091644.1) of ENSSSCG00000051798 gene and it has the missense consequence.

(a) Go to the Ensembl homepage.

Select Search: Sheep and type CD72. Click Go.

Click on novel gene (Sheep Gene, Breed: texel) to go to the Gene tab.

In the left-hand menu, click on Variant table to see the full list of variants described for this gene.

Filter the table for: Consequences > missense variant to see which variants cause changes in the amino acid sequence.

There are 23 missense variants.

(b) Click on the heading SIFT of the table to sort the column.

Five missense variants have been predicted to be deleterious by SIFT, shown by the red SIFT scores. Their IDs are: rs593145093, rs1088269383, rs1093464070, rs422891390 and rs597376323.

(a) Please note there is more than one way to get this answer. Either go to the Variant Table for the Atlantic salmon hs6st2 gene, and filter variants to the missense variants, or search Ensembl for 25:3426821:C_A:PRJEB34225 directly.

(b) Once you’re in the Variation tab, click on the Genes and regulation link or icon.

This SNP is found in four transcripts from two genes. It is a missense variant in hs6st2 gene and an intron variant, and downstream gene variant in ENSSSAG00000118991.

(c) Select Population genetics from the side menu.

From the Frequency data table, the PRJEB34225 allele frequencies shows that C is the major allele (95% of all population) compared to A (5% of all population).

Go to Ensembl Plants and click on Tools at the top of the page. Click on Variant Effect Predictor and select Oryza sativa Japonica Group from the Species menu.

Either click on Choose file and select the file to upload it, or directly paste the URL into the Or provide file URL: box. Click Run at the bottom of the page. When your job is done, click View results.

1. The number of affected genes and transcripts is shown in the Summary statistics table at the top.

   8 genes and 8 transcripts are affected by these variants.

2. Use the filters to view only missense variants. The filters are found above the detailed results table in the middle. Select Consequence and is from the drop-down menus. Then type missense_variant into the boxe. Add to apply your filter.

   1 variant is a missense variant. It causes a leucine to arginine (L/R) at position 16 change in the gene OS09G0103500. The SIFT score is 0.01 (Deleterious low confidence). Refere to this link for more information on SIFT (https://sift.bii.a-star.edu.sg/).

Go to any Ensembl Plants page and click on Tools in the navigation bar at the top of the page. Click on Variant Effect Predictor and change your species to Triticum aestivum by clicking on Change species.

Enter a descriptive name for your VEP job. If you have downloaded the variant file to your local machine, click on Choose file to upload. Alternatively, you can paste the URL for the file into the Or provide file URL: box. Click Run at the bottom of the page. When your job is done, click View reesults.

1. 20 variants were analysed, of which 1 is novel.

2. Only 1 gene is affected by variants in this file. The gene has 2 transcripts and both are affected by the variants.

3. You can find a list of calculated variant consequences and their impact here.

   Yes, the novel variant results in a stop_lost in TraesCS3A02G301400.1 and is a downstream_gene_variant for TraesCS3A02G301400.2.

4. Use the filters to view only variants with HIGH impact (you may need to add the column under Show/hide columns at the top of the table if you cannot find it). The filters are found above the detailed results table in the middle. Select Impact and is from the drop-down menus. Then type HIGH into the box; this will autocomplete. Click Add.

   There are 3 variants with high impact and all three are stop altering. Missense variants are not classified as high impact, because they do not always have significant impacts on protein functions. Usually the protein is still produced. In contrast, stop altering variants affect the protein length, and therefore likely affect the protein function.

5. At the top right of the table there is an option to download data. Click on VCF for the All option. Open the VCF file you have downloaded in a text editor. You can see that VEP adds annotation in the INFO column of the VCF file.

Go to any Ensembl Plants page and click on Tools in the navigation bar at the top of the page. Click on Variant Effect Predictor and change your species to Triticum aestivum by clicking on Change species.

Enter a descriptive name for your VEP job. Paste the variants in VCF format into the text box. Click Run at the bottom of the page. When your job is done, click View reesults.

1. Only 1 gene is affected by variants in this file. The gene has 1 transcript which is affected by the variants.

2. Use the filters to view only variants with HIGH impact (you may need to add the column under Show/hide columns at the top of the table if you cannot find it). The filters are found above the detailed results table in the middle. Select Impact and is from the drop-down menus. Then type HIGH into the box; this will autocomplete. Click Add.

   There are 2 variants with high impact (var1 ands var3). One is a start lost (although also a start retained variant), the other is a splice donor variant. Missense variants are not classified as high impact, because they do not always have significant impacts on protein functions. Usually the protein is still produced. In contrast, start/stop altering variants affect the protein length, and therefore likely affect the protein function.

3. At the top right of the table there is an option to download data. Click on VCF for the All option. Open the VCF file you have downloaded in a text editor. You can see that VEP adds annotation in the INFO column of the VCF file.

Go to the Variant Effect Predictor (VEP) under Tools on the top banner of any Ensembl page.

Copy the following into the Paste data text box: 6 23650222 23650222 A/C + var1, 6 23645685 23645685 C/A + var2, 1 51237121 51237121 C/T + var3,

Note that this is the Ensembl default format (chr start end reference/alternate alleles). For additional formats accepted by VEP, have a look here: http://www.ensembl.org/info/docs/tools/vep/vep_formats.html

Click Run.

(a) In the Results table, you’ll see that the variants fall into three genes.

(b) The consequence terms are listed in the Consequence column and Consequences (all) chart and include intron_variant, regulatory_region_variant, upstream_gene_variant and downstream_gene_variant.

(c) Variant 3 at 1:51237121-51237121 with T allele affects regulatory feature ENSR00000006264 (promoter).

Go to the Variant Effect Predictor (VEP) under Tools on the top banner of any Ensembl page.

Copy the following into the Paste data text box:

3 71541903 71541903 C/A
18 24867 24867 G/A
23 153938 153938 C/T
22 10699690 10699690 C/G
1 48884151 48884151 A/G

Note that this is the Ensembl default format (chr start end reference/alternate alleles). For additional formats accepted by VEP, have a look here: http://www.ensembl.org/info/docs/tools/vep/vep_formats.html

Click Run.

(a) In the Results table, you’ll see that the variants fall into nine genes (one is intergenic).

(b) The consequence terms are listed in the Consequence column and Consequences (all) chart and include intron_variant, upstream_gene_variant, missense_variant, and downstream_gene_variant.

(c) The most frequent coding consequence is missense_variant. This is shown in one of the pie charts above the table.

Go to www.ensembl.org and click on the Variant Effect Predictor link on the homepage. Click Launch VEP.

Choose Atlantic salmon as the species and enter the five variants from the exercise.

Note: Variation data input can be done in a variety of formats. See more details here http://www.ensembl.org/info/docs/variation/vep/vep_formats.html

Click Run.

When your job is listed as Done, click View Results.

(a) Five variants were analysed, none of these variants are novel.

(b) Only one gene (cdc16) is affected by these variants. It has ten transcripts, all of which are affected.

(c) Yes. These variants have the missense_variant, intron_variant and downstream_gene_variant consequences for the different transcripts of cdc16 gene.

(d) At the top right of the table there is an option to download data. Click on VCF for the All option. Open the VCF file you have downloaded in a text editor. You can see that VEP adds annotation in the INFO column of the VCF file.

Go to Ensembl Plants. Look for the main search box highlighted in green. Select Oryza sativa Japonica Group from the drop-down box and type in Lsi1. Click Go and click on the gene ID Os02g0745100.

1. Go to Plant Compara: Orthologues on the left-hand panel.

   Liliopsida has 24 1-to-1 orthologues, the only group with 1-to-1 orthologues. This group is synonymous with Monocotyledon, so the group that contains the grasses. Eudicotyledons has the highest number of 1-to-many orthologues, indicating that this gene has been duplicated in the eudicots.

2. Use the search box in the top right-hand corner of the Selected orthologues table and enter Triticum aestivum, the table should automatically filter.

   There are 3 results, one for each component (A,B,D). Note that these are considered 1-to-1 orthologues, rather than 1-to-many. This is because these genes arose in wheat by hybridisation (allopolyploidy), rather than duplication (autopolyploidy).

3. Click on Compare regions (found in the 3rd column below the gene identifier) from the 2nd result for component 6B. This takes us to the Location tab. Scroll down to the bottom of the page.

   Both genes have 5 exons and the same structure. This looks unusual because the gene in rice is on the forward strand, while the gene in wheat is on the reverse strand. This is reflected in the crossing green links between the pink alignment blocks.

4. Click on the Gene tab at the top of the page and click on Gene gain/loss tree in the left-hand panel.

   Significant expansions are shown with red branches, and the number of genes in the family shown in the count next to the image and species name. We can see that Echinochloa crus-galli (Cockspur grass) has 25 members in this group.

We can change the tree to radial view by clicking on the icon with two arrows at the top left of the image.

Go to plants.ensembl.org, choose Zea mays and search for Zm00001d015746. Click through to the Gene tab view.

On the gene tab, click on Orthologues at the left side of the page to see all the orthologous genes.

These are the orthologues in the Liliopsida:

• 20 1-to-1
• Seven 1-to-many
• Two many-to-many

The percentage of identical amino acids in the sorghum protein (the orthologue) compared with the gene of interest. i.e. maize Zm00001d015746 (the target species/gene) is 82.07%. This is known as the Target %ID. The identity of the gene of interest (maize GRMZM2G144081) when compared with the orthologue (the sorghum gene, the query species/gene) is 81.69% (the query %ID).

Note the differences in the values of the Target and Query % ID reflects the different protein lengths for the genes.

Go to the Ensembl Plants homepage, select Triticum aestivum from the Species drop-down and search for TraesCS4D02G040400. Click through to the Gene tab. On the Gene tab, click on Plant Compara: Orthologues at the left-hand side of the page to see all the orthologous genes.

1. These are the orthologues in the Liliopsida:

   • 24 1-to-1
   • 9 1-to-many
   • 0 many-to-many

2. Filter the table by entering Secale cereale in the filter box on the top right-hand corner of the table.

   The percentage of identical amino acids in the rye protein (the orthologue) compared with the gene of interest (i.e. wheat RHT1; the target species/gene) is 98.71%. This is known as the Target %ID. The identity of the gene of interest (wheat RHT1) when compared with the orthologue (the rye gene, i.e. the query species/gene) is 97.91% (the query %ID).
   Note the differences in the values of the Target and Query % ID reflects the different protein lengths for the genes.

3. Click on View Sequence Alignments in the Orthologue column. Select View Protein Alignment from the pop-up menu. Click on the green Download homology button above the table and select Nexus. Click on Download or Download Compressed to save the alignment on your local machine.

4. Go to Plant Compara: Gene tree in the left-hand menu. You can find the gene tree ID above the phylogeny.

   The gene tree ID is EPlGT00940000163877.

5. You can find some summary statistics below the gene ID.

   There are 418 speciation nodes and 149 duplication nodes.

1. Go to the Ensembl Plants homepage. Select Triticum aestivum from the Species drop-down, enter TraesCS2D02G080000 in the search box and click Go. Open the Gene tab.

   The gene description is as follows: Ascorbate peroxidase, ROS homeostasis, Chloroplast protection, Carbohydrate metabolism, Plant architecture, Fertility maintenance. This was projected from Oryza sativa (Os07g0694700).

2. Go the Location tab in the top left-hand corner. Click on CConfigure this page in the side menu. Open Comparative genomics: BLASTz/LASTz alignments in the pop-up menu. Turn on the tracks for Arabidopsis thaliana, Zea mays (corn) and Sorghum bicolor (great millet) in the Normal style. Save and close the pop-up menu

   There is alignment across most of the coding regions, with some gaps occurring in all 3 species. These gaps map with the intronic regions of the T. aestivum gene.

3. Click on Comparative Genomics: Region Comparison in the left-hand menu. Go to the Select species or regions button and add A. thaliana. Save and close the menu.

   The gap in the alignment translates to the intronic regions of the T. aestivum gene.

4. Go to Comparative Genomics: Alignments (text) and select A. thaliana from the Alignment drop-down. Click on the green Download alignment button and select ClustalW. Download the file to your local machine either in a compressed format, or as it is by clicking the green Download button above the file format preview.

Go to Ensembl Plants. Select Arabidopsis thaliana from the drop-down box and type in AT1G50180. Click Go and click on the gene ID AT1G50180.

1. Go to Plant Compara: Orthologues on the left-hand panel.

2. Filter for Coffea canephora using the filter option in the top right hand corner of the table.

   Coffee has 25 many-to-many orthologues.

3. Click on View Sequence Alignments then cDNA (found in the 3rd column below the gene identifier) for the GSCOC_T00030728001 gene. This takes us to the Orthologue Alignment page.

   Click on Download Homology to download the alignment in ClustalW format

1. Go to the Ensembl homepage, select Chicken from the drop-down list in the blue search box, enter BRAF and click Go. Open the **Gene tab and click on Comparative Genomics: Orthologues at the left-hand panel to see all the orthologous genes.

   There 25x 1:1 and 1x 1:many orthologues in sauropsida.

   Find Green anole in the Selected orthologues (you can use the filter in the top right-hand corner).

   The percentage of identical amino acids in the Green anole protein (the orthologue) compared with the gene of interest. i.e. chicken BRAF (the target species/gene) is 84.42%. This is known as the Target %id. The identity of the gene of interest (chicken BRAF) when compared with the orthologue (Green anole BRAF, the query species/gene) is 94.67% (this is the Query %id).

   Click on the View Sequence Alignments link in the Orthologue column of the Selected orthologues table and select View Protein Alignment in the pop-up menu. To download the alignment, click on the Download homology button and select the CLUSTALW file format in the pop-up menu.

2. Click on Comparative Genomics: Genomic alignments in the left-hand panel. Click on Select an alignment and add Human in the pop-up menu. In the table, select Block 1 to view the largest block of aligned sequence (this will lead you to the Location tab). Click on Display full alignment. In the alignment, sequences coloured in red are exons.

   There is a gene in both species in this region. You can find where the start and stop codons are located if you Configure this page and select Codons: START/STOP codons in the options.

Note: You can visualise the alignment in the genomic context in the Comparative Genomics: Region Comparison page (blue lines connect homologous genes between species). Go to Select species or regions, add Human and close the pop-up menu. Click on Configure this page. In the pop-up menu under Comparative features category, enable the Join genes option. You may need to zoom out on the Region in detail view to see blue lines connecting all the homologous genes between chicken and human genes in that region.

1. Search for the DBH(ENSSSCG00000005742) gene in the Pig (SScrofa11.1) reference and switch to the Location tab. Click on Alignments (image) in the left-hand panel. Under Alignment, click on the Select alignment button to open a pop-up menu. Enable the 16 pig breeds EPO-Extended alignment, then close the menu.

   All 12 big breeds as well as cow, horse and sheep have an alignment at this region. This can also be seen in the Alignments (text) page, where the exons are coloured in red.

2. You can export the alignments from either the Alignments (images) or Alignments (text) pages. Click on the blue Download alignments button at the top of the page. From the pop-up menu, select File format: CLUSTALW. You can Preview the alignment in a new browser tab, or Download the file to your local machine.

3. Click on Region in detail in the left-hand panel. In the pop-up menu, go to the Comparative genomics section and turn on the following tracks:
   • Multiple alignments: 16 pig breeds EPO-Extended
   • Conservation score for 16 pig breeds EPO-Extended
   • Constrained elements for 16 pig breeds EPO-Extended

   Close the pop-up menu and find the tracks in the Region in detail view.

   The 16 pig breeds EPO-extended track shows that the entire region for the DBH gene can be aligned among the big breeds and related agricultural species. The Constrained elements and Conservation score tracks show where the conserved sequence is located in the alignment. Regions where constrained elements are found are regions with high GERP scores. Higher conservation regions (i.e. constrained elements) match up with exonic regions (exons tend to be highly conserved) of the gene. Note that there are intronic regions that seem to be fairly conserved across the species available.

4. For both 16 way GERP elements and 91 way GERP elements tracks, click on the track name to open the pop-up menu. Hover over the i icon with your cursor to find a track description.

   The 16 way GERP elements track shows the 16 pig breeds EPO-Extended multiple whole-genome alignment. The 91 way GERP elements track shows the 91 eutherian mammals EPO-Extended multiple whole-genome alignment.

   You can move the 91 way GERP elements track closer to the 16 way GERP elements track to make any comparisons easier.

   You will notice that constrained elements match-up with exonic regions in the genome.

   Click on the track name and open the information tab in the pop-up menu. Click on the GERP conservation score link.

   This opens the documentation page for the multiple whole-genome alignment calculations.

1. Open the Gene tab for the PLAG1 gene (ENSSSCG00000006247) in the pig reference (Sscrofa11.1) genome. In the left-hand panel, click on Comparative Genomics: Breeds: Orthologues to explore orthologues in pig breeds.

   PLAG1 orthologues have been identified in all 12 available pig breeds: Bamei, Berkshire, Hampshire, Jinhua, Large white, Meishan, Pietrain, Rongchang, Tibetan, Wuzhishan and USMARC.

2. Stay in the Comparative Genomics: Breeds: Orthologues page and look for the Pig - Tibetan entry in the Orthologues table. Click on View Sequence Alignments and select View cDNA Alignment in the pop-up menu. This will lead you to the sequence alignment between the pig reference PLAG1 gene and the orthologue in the Tibetan breed. Click on the ? icon above the alignment to open the corresponding help page and find a description of the data (including descriptions of the conservation codes and summary statistics).

   The alignment is in ClustalW format and the asterisk (*) is a conservation code that denotes the aligned nucleotides are identical in both sequences.

   In the **Type: 1-to-1 orthologues table, look for the column **% identity (cDNA).

   The % identity (cDNA) describes the number of identical nucleotides between the two sequences in the alignment. The % identity (cDNA) between the pig reference and the Tibetan breed is 99%, meaning 99% of the cDNA sequence alignment is identical.

3. In the left-hand panel, click on Comparative Genomics: Breeds: Gene tree. Above the gene tree image, you can find some summary statistics.

   There are 16 genes in the gene tree.

   In the gene tree, look for PLAG1, Pig (coloured in red) in the tree and find the closest branch.

   The most closely related orthologue is the PLAG1 gene in the Berkshire breed. Clicking on PLAG1, Pig - Berkshire opens more details on the orthologue including the Ensembl ID (ENSSSCG00065079212) and strand (reverse).

4. Click on the Export button at the top of the gene tree image. In the pop-up menu, select File format: Newick (you can find a preview of each file format underneath) and Preview the file on your browser.

1. From the Ensembl homepage, choose European seabass from the drop-down list and search for pax6b. Click through to the Gene tab view. Click on Comparative Genomics: Orthologues at the left side of the page to see all the orthologous genes.

   From the summary table, we can see that the European seabass has 52 1-to-1 orthologues and 9 1-to-many orthologues in the ray-finned fishes species list.

2. Search for Gilthead seabream in the orthologues table below.

   The percentage of identical amino acids in the Gilthead seabream protein (the orthologue) compared with the gene of interest, i.e. the European seabass pax6b (the target species/gene), is 99.78%. This is known as the Target%id.

The identity of the gene of interest (European seabass pax6b) when compared with the orthologue (Gilthead seabream pax6b, the query species/gene) is 99.78% (the Query %id).

Note that any difference in the values of the Target and Query %id reflects the different protein lengths for the two orthologues. In the case of the European seabass and Gilthead seabream, the identity is the same as both proteins are 457 amino acids long.

1. Click on the View Sequence Alignments link in the Orthologue column to View Protein Alignment in ClustalW format.

   Conserved amino acids are indicated by asteriks (*). You can find more information about the ClustalW format in our help pages. There is no difference between the N-terminus and C-terminus. The sequence is conserved around both termini.

Click New. Choose the Ensembl Plants Genes database. Choose the Triticum aestivum genes dataset.

Click on Filters in the left panel. Expand the GENE section by clicking on the + box. Select Input external references ID list - RefSeq peptide ID(s) and enter the list of IDs in the text box (either comma separated or as a list). HINT: You may have to scroll down the menu to see these.

Count shows 68 genes (the hybridisations and whole genome duplications in wheat’s evolutionary history means that many RefSeqs are duplicated across the genome)..

Click on Attributes in the left panel. Select the Features attributes page. Expand the Gene section by clicking on the + box. Select Gene name from the Gene section. Expand the External section by clicking on the + box. Select RefSeq Peptide ID from the External References section.

Click the Results button on the toolbar. Select View All rows as HTML or export all results to a file.

1. 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 Plants Genes database and Triticum aestivum genes (IWGSC) dataset. Now, filter for the genes with NCBI Gene ID only:

2. Click on Filters in the left panel, expand the GENE section by clicking on the + box. Select with NCBI Gene ID under Limit to genes (external references)…. 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 92 Genes.

   Now filter further for genes that are protein-coding by selecting Gene type – protein_coding and click again on Count.

   This still gives you 92 Genes, meaning that all genes you have previously filtered are protein-coding.

   Finally, filter for genes that have a signal peptide domains. Expand the PROTEIN DOMAINS AND FAMILIES section by clicking on the + box. Select Transmembrane helices – Only under Limit to genes….

   There are 79 genes on the bread wheat genome that contain NCBI Gene IDs and protein coding with signal domains.

3. Go to Attributes on the left-hand panel. Select Sequences from the options on the right. Expand the SEQUENCES section by clicking on the + box and select Peptide. Select the appropriate header information from the HEADER INFORMATION section: Gene description and Source of gene name.

4. 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.

Go to plants.ensembl.org and click on the link Tools at the top of the page. Click on BioMart.

Click New. Choose the Ensembl Plants Genes database. Choose the Hordeum vulgare genes (MorexV3_pseudomolecules_assembly) dataset.

Click on Filters in the left panel. Expand the GENE section by clicking on the + box. Enter the gene list in the Input external references ID list box. Select Gene stable ID(s) [e.g. HORVU.MOREX.r3.1HG0000030] from the drop-down menu.

Click on Attributes in the left panel. Select the Homologues attributes page. Expand the ORTHOLOGUES section by clicking on the + box. Select Triticum aestivum gene stable ID.

Click Results.

Click the New button on the toolbar, choose the Ensembl Plants Genes database and Solanum lycopersicum genes (SL2.40 (ITAG2.3)) dataset.

Click on Filters in the left panel and expand the REGION section. Under Multiple regions enter 6:21394819-21397868.

Click on Attributes in the left panel, select the Variation attribute and under VARIANT ASSOCIATED INFORMATION, tick Variant_name and Variant alleles.

1. Go to BioMart (you can find a shortcut in the navigation bar at the top of any Ensembl Plants page) and click New. Choose the Ensembl Plant Genes database. Choose the Arabidopsis thaliana genes (TAIR10) dataset.

2. Click on Filters in the left panel. Expand the GENE. Enter the gene list in the Input external references ID list box. Select Gene Name from the input options dropdown list.

3. Click on Attributes in the left panel. Select the Homologues attributes at the top of the page. Expand the GENE section. Select Gene Name. Expand the ORTHOLOGUES [A-E] section. Select Coffea canephora gene stable ID.

4. Click Results. Select View: All rows as HTML.

   All genes have a homologue in coffee.

On the Ensembl homepage, click on the BioMart link on the toolbar.

Start with all genes in chicken by choosing the Ensembl Genes database, then Gallus gallus genes dataset.

Now, filter for the genes on the 20 chromosome only:

Click on Filters in the left panel, expand the REGION section by clicking on the + box. Select Chromosome – 20.

Now click the Count button on the toolbar.

This will give you 473 / 24356 Genes.

Now filter further for genes that are protein-coding by expanding the GENE section (simply click on the + box). Then select Gene type – protein_coding and click again on Count.

This now gives you 332 / 24356 Genes.

Finally, filter for genes that encode proteins that contain transmembrane domains. Expand the PROTEIN DOMAINS section by clicking on the + box. Select Transmembrane helices – Only.

There are 69 genes on chromosome 20 in chicken that are protein coding and contain transmembrane domains.

Now you can specify the attributes to be included in the output (note that a number of attributes will already be selected by default). Click on Sequences, then Protein. The sequence will be exported as FASTA format.

Have a look at a preview of the results (only 10 rows of the results will be shown):

Click the Results button on the toolbar.

If you are happy with how the results look in the preview, output all the results by selecting Export all results to, then choose the Compressed web file (notify by email), click on _Unique results only, enter your email address in the appropriate box and click on Go.

As with all BioMart queries you must select the dataset, set your filters (input) and define your attributes (desired output). For this exercise:
Dataset: Ensembl genes in chicken
Filters: Transmembrane proteins on chromosome 9
Attributes: Ensembl gene and transcript IDs and Associated gene names

Go to the Ensembl homepage (https://www.ensembl.org) and click on BioMart at the top of the page. Select Ensembl genes as your database and Chicken genes (bGalGal1.mat.broiler.GRCg7b) as the dataset. Click on Filters on the left of the screen and expand REGION. Change the chromosome to 9. Now expand PROTEIN DOMAINS AND FAMILIES, also under filters, and select Limit to genes …, choosing With Transmembrane helices from the drop-down and select Only. Clicking on Count should reveal that you have filtered the dataset down to 143 genes.

Click on Attributes. Under Features expand GENE. Select Gene name.

Now click on Results. The first 10 results are displayed by default; display all results by selecting All from the drop-down menu above the table.

The output will display the Ensembl gene ID, Ensembl Transcript ID and associated gene names of all proteins with a transmembrane domain on chicken chromosome 9. If you prefer, you can also export as an Excel sheet by using the Export all results to XLS option.

(a) Click New. Choose the Ensembl Genes database. Choose the Chicken genes dataset.

Click on Filters in the left panel. Expand the GENE section by clicking on the + box. Select Input microarray probes/probesets ID list - AFFY Chicken probe ID(s) and enter the list of probeset IDs in the text box (either comma separated or as a list).

Count shows three genes match this list of probesets.

Click on Attributes in the left panel. Select the Features attributes page. Expand the GENE section by clicking on the + box. In addition to the default selected attributes, select Gene name and Gene description. Expand the EXTERNAL section by clicking on the + box. Select AFFY Chicken probe from the Microarray probes/probesets section.

Click the Results button on the toolbar. Select View All rows as HTML or export all results to a file. Tick the box Unique results only.

Your results should show that the 2 probes map to 2 Ensembl genes.

(b) Don’t change Dataset and Filters – simply click on Attributes.

Select the Sequences category. Expand the SEQUENCES tab by clicking on the + box. Select Flank (Transcript) and enter 2000 in the Upstream flank text box. Expand the HEADER INFORMATION tab by clicking on the + box. Select Gene description and Gene name in addition to the default selected attributes.

Note: Flank (Transcript) will give the flanks for all transcripts of a gene with multiple transcripts. Flank (Gene) will give the flanks for one possible transcript in a gene (the most 5’ coordinates for upstream flanking).

Click the Results button on the toolbar.

(c) You can leave the Dataset and Filters the same, and go directly to the Attributes section:

Click on Attributes in the left panel. Select the Homologues category. Expand the GENE tab by clicking on the + box. Select Gene name. Unselect Transcript stable ID and Transcript stable ID version. Expand the ORTHOLOGUES [A-E] tab by clicking on the + box. Select Duck gene stable ID, Duck chromosomes/scaffold name, Duck chromosome/scaffold start (bp) and Duck chromosome/scaffold end (bp).

Click the Results button on the toolbar. Select View All rows as HTML or export all results to a file.

Your results should show that for each chicken gene, one duck orthologue has been identified.