Demo: Introduction to Ensembl

Ensembl

Homepage

The homepage of Ensembl is found at www.ensembl.org. It contains lots of information and links to help you navigate Ensembl:

On the right-hand panel you can see the current release number and what has come out in this release. To access old releases, scroll to the bottom of the page and click on View in archive site in the right-hand corner.

Click on the links to go to the archives. Alternatively, you can jump quickly to the correct release by adding e plus the release number in the URL. For example e98.ensembl.org jumps to Ensembl release 98.  
 
 

Available pangenomes

Pangenomes are available for:

• Canis lupus familiaris (Dog): 4 additional breeds
• Gallus gallus (Chicken): 2 additional breeds
• Mus musculus (Mouse): 15 additional strains
• Ovis aries (Sheep): 1 additional breed
• Rattus norvegicus (Norway rat): 3 additional strains
• Sus scrofa (Pig): 12 additional breeds

To view all available species in Ensembl, scroll back up to the top of the homepage and click the View full list of all species link underneath the coloured search block.

You can search for your species of interest (either the common or scientific name) using the search bar at the top right-hand corner of the table. Click on the common name of your species of interest to go to the species information page. We’ll click on Pig.

This is the species information page for Pig. Here you can see links to example features and to download flatfiles. Under the Genome assembly section, we can see that the species has data on an additional 12 breeds. Click on View list of breeds to see all available breeds in tabular form.

Species information

Let’s focus on the Genome assembly. Go back to the species information page and click on More information and statistics under the Genome assembly section.

Here you’ll find a detailed description of how to the genome was produced and links to the original source. You will also see details of how the genes were annotated.  
 
 

Ensembl Plants

Homepage

Let’s take a look at the Ensembl Plants homepage at plants.ensembl.org.

You will notice that the Ensembl Plants website is structured very similarly to the Ensembl main site. The only difference being the colour-coding.

You can navigate most of the taxa in the same way as you would with Ensembl.  
 
 

Available pangenomes in Ensembl Plants

Pangenomes are available for:

• Hordeum vulgare (Barley): 2 additional cultivars
• Oryza sativa (Rice): 15 additional cultivars
• Triticum aestivum (Wheat): 17 additional cultivars

To view all available species, go to the Ensembl Plants homepage and click the View full list of all species link underneath the coloured search block.  
 
 

Ensembl Rapid Release

Our newest genomes, such as those coming from the Darwin Tree of Life, are available on rapid.ensembl.org. Note that Ensembl Rapid Release has fewer features and tools available compared to Ensembl and Ensembl Genomes. Only gene annotation data is available, and variation and comparative genomics data is limited.

The Ensembl Projects page, lists all projects and collaborations that incorporate Ensembl gene annotation, including consortia with a focus on livestock and agriculture:

• AQUA-FAANG
• GENE-SWitCH
• BovReg
• NextGen

Available data, including genebuilds, from the Human Pangenome Reference Consortium (HPRC) can be accessed via projects.ensembl.org/hprc.  
 
 

1. How many coding and non-coding genes does pig have?

2. When was the current Sus scrofa genome assembly produced and by whom?

1. Which Gallus gallus (Chicken) breeds are available?

2. When was the genebuild of the Reg Jungle fowl last updated?

1. Are there any additional cultivars available alongside the Triticum aestivum (IWGSC) reference genome?

2. Find the description of the wheat assembly. Which institute provided the assembly and annotations?

3. How many coding and non-coding genes does the IWGSC assembly have?

4. Are there any other species of the genus Triticum available in Ensembl? If so, which species are they?

1. How many Oryza sativa genomes are available in Ensembl Plants?

2. How many cultivars are available for the Oryza sativa Japonica group?

3. What is the GCA ID of Oryza sativa (Geng/Japonica-trop2 var. Ketan Nangka)?

Demo: Exploring a genomic region in Pig

Searching for a region

Start at the Ensembl homepage, www.ensembl.org. In the species-specific search box, select Pig from the drop-down menu, enter 15:81890000-82000000 into the search box and click on Go. The format of your coordinates should be:
chromosome:start-end
You do not need to remove commas if there are any.

Press Enter or click Go to jump directly to the Region in detail page in Pig.

Region in detail

Click on the questionmark button button to view page-specific help. The help pages provide descriptions, labelled images and, in some cases, help videos to exaplin what you can see on the page and how to interact with it.

The Region in detail page is made up of three images, let’s look at each one in detail.  

Chromosome overview

The first image shows the chromosome overview:

You can jump to or highlight a different region by dragging out a box in the image using your cursor. Click and drag a box on the chromosome. A pop-up menu will appear.

If you want to move to the region, you can click on Jump to region (### bp). If you want to highlight it, click on Mark region (###bp). For now, we’ll close the pop-up by clicking on the X on the corner.  

Region overview

The second image shows a 1Mb region overview around our region of interest, which is marked in a red border. This view allows you to scroll back and forth along the chromosome.

You can also drag out and jump to or mark a region.

Click on the X to close the pop-up menu.

Click on the Drag/Select button to change the action of your mouse click. Click on the arrows to scroll along the chromosome by clicking and dragging your cursor within the region overview image. As you do this you’ll see the image below grey out and two blue buttons appear. Clicking on Update this image would jump the lower image to the region you scrolled to. We want to go back to where we started, so we’ll click on Reset scrollable image.

Region in detail view

The third image is a detailed, configurable view of the region.

Click on the Drag/Select option at the top right-hand corner to switch mouse action. Similarly to the region overview, you can select Drag, to scroll along the genome (the page will reload when you drop the mouse button). On Select you can drag out a box to highlight or zoom in on a region of interest.

Set your cursor action to Select, drag out a box around an exon and select Mark region.

The highlight will remain in place if you zoom in and out or move around the region. This allows you to keep track of regions or features of interest.  
 
 

Configuring the region view

We can edit what we see on this page by clicking on the blue Configure this page menu at the left.

This will open a menu that allows you to change the image.

You can put some tracks on in different styles; more details are in this FAQ: http://www.ensembl.org/Help/Faq?id=335.

Let’s add some tracks to this image. Add the All variants on genotyping chips - short variants (SNPs and indels) track in the pop-up menu. You can use the search bar to filter for the track, or you can select the track in the left-hand menu under Variation > Arrays and other. To enable the track, click on the square next to the track name and select the track style Normal.

Now click on the check icon in the top right-hand corner to save and close the menu. Alternatively, click anywhere outside of the pop-up menu. Wait for the Region in detail view to load. Once loaded, you should be able to see the track in the image. If the track does not appear in the image, no track features are present in your region of interest. You may need to scroll along the genome or zoom out to visualise a broader region.

We can also change the way the tracks appear by hovering over the track name then the cog wheel to open a menu. We can move tracks around by clicking and dragging on the bar to the left of the track name.

Sharing and exporting

Now that you’ve got the region view how you want it, you might like to show something you’ve found to a colleague or collaborator. Click on the Share this page button (either in the left-hand panel or at the top of the Region in detail view) to generate a URL. You can share the URL with your colleague, so that they can see the same view as you (including all the tracks and configurations you’ve added). The URL contains the Ensembl release number, so if a new release or even assembly comes out, your link will just take you to the archive site for the release it was made on.

You can also export the region image by clicking on the Export image button at the top of the Region in detail view, or export the data (i.e. the sequence or the annotation) by clicking on the Export data button in the left-hand panel.

To return this to the default view, go to click on Reset configuration at the top of the Region in detail view.  
 
 

1. Go to the region from 8,805,953 to 8,858,418 on pig chromosome 11.

2. Configure this page to turn on the Tandem repeats (TRF) track in this view. What is this track? How many TRF overlap this region?

3. Create a URL for this display. Email it to your neighbour.

4. Export the genomic sequence of the region you are looking at in FASTA format.

5. Turn off all tracks you added to the Region in detail page.

1. Go to the region from 38,111,022-38,265,293 on chicken chromosome 5. How many contigs make up this portion of the assembly (contigs are contiguous stretches of DNA sequence that have been assembled solely based on direct sequencing information)?

2. Zoom in on ESRRB gene.

3. Turn on the RefSeq GFF3 annotation track as Expanded with labels.

4. Save this image in PDF format.

1. Go to the region from 28,400,000 to 28,988,000 on cow chromosome 12.

2. Configure this page to turn on the CpG islands track in this view. What is this track? Are there any CpG islands near the BRCA2 gene? What are their values?

3. Zoom in on the BRCA2 gene.

4. Create a URL for this display. Email it to your neighbour. Open the link they sent you and compare. If there are differences, can you work out why?

5. Export the genomic sequence of the region you are looking at in FASTA format.

6. Turn off all tracks you added to the Region in detail page.

1. Go to the region 18:7146000-7409000 in the Texel Sheep genome. What genes are found in this region? What strand are they on?

2. Zoom into the start of the first exon of the gene on the left. Zoom in until you can see the genome sequence as coloured bases.

3. Turn on the tracks for translated sequence and start/stop codons. Can you find the start codon? What does this tell you about the gene?

1. Go to 2D:378720500-378780600 in Triticum aestivum (wheat).

2. How many genes are in this region? What strand are the genes on? What are the gene IDs for these genes?

3. What tracks can you see that show gene structure? Where did the different tracks come from?

4. Export the genomic sequence for this region.

5. Can you view the genomic alignments of the homoeologous regions? What are the different formats you can export the image as?

Go to the Ensembl Plants homepage and do the following:

1. Go to the region between 405000 and 453000 on chromosome 1 in Oryza sativa Japonica.

2. Turn on the AGILENT:G2519F-015241 microarray track. Are there any oligo probes that map to this region?

3. Highlight the region around any reverse strand probes you can see. Do they map to any Ensembl transcripts?

Demo: The Gene tab

If you click on any one of the transcripts in the Region in detail image, a pop-up menu will appear, allowing you to jump directly to that gene or transcript.

Searching for a gene

Another way to go to a gene of interest is to search directly for it.

We’re going to look at the NSDHL gene in Sus scrofa (Pig). From www.ensembl.org, select Pig from the drop-down menu in the blue box. Enter NSDHL into the search box and click the Go button.

Your search results include hits in all available Pig genomes. You can filter your results by breed in the left-hand panel. We want to restrict our results to entries in the Pig reference only. Under Restrict breeds to: in the left, click on Pig reference.

In your filtered search results, click on NSDHL (Pig Gene, Breed: reference) or the Ensembl ID ENSSSCG00005019191 to open the Gene tab:

Viewing the gene sequence

Let’s walk through some of the links in the left hand navigation column. How can we view the genomic sequence? Click Sequence in the left-hand panel.

The sequence is shown in FASTA format. Take a look at the FASTA header:
>primary_assembly:Sscrofa11.1:X:123905599:123929717:1

The FASTA header always starts with a > followed by sequence information. Broken down, the information in the FASTA header is as follows:
>[primary_assembly:Sscrofa11.1]:[X]:[123905599]:[123929717]:[1]

• [primary_assembly:Sscrofa11.1] = name of the genome assembly
• = chromosome
• [123905599] = start coordinate
• [123929717] = end coordinate
• [1] = forward strand (-1 refers to reverse strand)
   

Exons are highlighted in orange within the genomic sequence. Variants can be added with the Configure this page button found in the left-hand panel. Click on the button to open a pop-up menu. Add the options Show variants: Yes and show links and Line numbering: Relative to this sequence.

Save and close the pop-up menu by clicking on the check icon in the top right-hand corner.

You can download this sequence by clicking in the Download sequence button found above the sequence.

This will open a pop-up menu that allows you to pick the sequence format. You can download the sequence in plain FASTA or richt-text format (RTF), which includes all the coloured annotations and can be opened in a word processor. This button is available for all sequence views.

Viewing the gene function

To find out what the protein does, have a look at Gene Ontology (GO) terms from the Gene Ontology consortium. There are three categories of GO terms:

• Biological process (what the protein does)
• Cellular component (where the protein is)
• Molecular function (how it does it)

Click on GO: Biological process in the left-hand panel to view GO terms associated with NSDHL.

Viewing gene information in external databases

Can our gene be found in other databases? Click on External references in the left-hand menu.

This page contains corresponding links to the gene in other projects, such as NCBI gene (formerly Entrezgene), Reactome gene and UniProtKB.  
 
 

Demo: The Transcript tab

Let’s now explore one transcript/isoform/splice variant. Click on the Show transcript table button at the top of the page.

Have a look at the largest one, NSDHL-201.

If we were to only choose one transcript to analyse, we would choose this one because it has the Ensembl Canonical flag. The Ensembl canonical transcript is a single, representative transcript identified at every locus. You can read more about canonical transcripts in the Genebuild documentation page.

Click on the transcript ID ENSSSCT00000048661.3 to open the corresponding to view more information. This opens the corresponding Transcript tab. The left-hand menu provides several options for the transcript NSDHL-201. You can find any protein-related information in the Transcript tab, if the transcript is protein-coding.
 

Transcript evidence

For detailed information on the support for this transcript, click on Supporting evidence.

Viewing the transcript sequence

Exon sequence

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

You may want to change the display (for example, to show more flanking sequence, or to show full introns). In order to do so click on the Configure this page button in the left-hand panel and change the display options accordingly.

cDNA sequence

Click on Sequence: cDNA in the left-hand panel to see the spliced transcript sequence.

UnTranslated Regions (UTRs) are highlighted in dark yellow, codons are highlighted in alternating white and light yellow, and exon sequences are shown in alternating black and blue colours (highlighting where another exon begins). Variants are represented by highlighted nucleotides and clickable IUPAC ambiguity codes representing the variation above the sequence.  

Protein information

Click on Protein Information: Protein summary to view domains from Pfam, Superfamily, AlphaFold DB, and more.

Clicking on Domains & features shows a table of this information.

Transcript information in external databases

Click on External References: General identifiers in the left-hand panel. This page shows corresponding information in other databases such as the European Nucleotide Archive (ENA), UniProtKB and Reactome.

1. Find the TRAF3 (TNF receptor associated factor 3) gene in the pig reference, and go to the Gene tab.
   • Which strand of the genome is this gene located?
   • How many transcripts are there of the gene?
   • Which transcript produces the longest protein and how long is the protein sequence?

2. What are some functions of TRAF3 according to the gene ontology (GO)? Have a look at the Ontologies pages for this gene.

3. In the transcript table, click on the transcript ID for TRAF3-201, and to open the corresponding Transcript tab.
   • How many exons does it have?
   • Are any of the exons completely or partially untranslated?
   • Is there an associated sequence in UniProt? Have a look at the General identifiers for this transcript.

4. Are there microarray (oligo) probes that can be used to monitor the expression of TRAF3-201?

5. Now find the TRAF3 gene in the Berkshire pig breed.
   • Which strand of the genome is this gene located?
   • How many transcripts are there of the gene?
   • Which transcript produces the longest protein and how long is the protein sequence?
6. How do the Ensmebl canonical transcripts differ between the pig reference and the Berkshire breed?

1. Find the MYH9 (myosin, heavy chain 9, non-muscle) gene in the chicken reference, and go to the Gene tab.
   • On which chromosome and which strand of the genome is this gene located?
   • Which transcript produces the longest protein and how long is the protein sequence?

2. What are some functions of MYH9 according to the Gene Ontology consortium? Have a look at the GO pages for this gene.

3. In the transcript table, click on the transcript ID for MYH9-209, 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 UniProt? Have a look at the General identifiers for this transcript.
4. Are there microarray (oligo) probes that can be used to monitor ENSGALT00010036169.1 expression?

Start in the Ensembl Plants homepage and select the Triticum aestivum IWGSC genome to answer the following questions:

1. What GO: Molecular function terms are associated with the Wheat gene TraesCS6D02G180200?

2. Go to the transcript tab. How many exons does it have? Which one is the longest? Approximately, how much of that is coding?

3. What domains can be found in the protein product of this transcript? What prediction method(s) identified these domains?

Demo: comparative genomics

Gene tab: homologues and gene trees

Homologues across different species

Let’s explore homologues of the BRCA2 gene in the pig (Sscrofa11.1) reference genome. Search for the gene and go to the Gene tab. Homologues can be found under Comparative Genomics in the left-hand menu. If there are no orthologues or paralogues, the option will be greyed out. Paralogues is greyed out for BRCA2 indicating that there are no paralogues. Click on Comparative Genomics: Orthologues to see the available orthologues. Select the species set Laurasiatheria to show carnivores, ungulates and insectivores only in the Orthologue table at the bottom.

Let’s look at the Cow orthologue.

Links from the orthologue allow you to view alignments of the orthologous proteins and cDNAs. In the table, click on View Sequence Alignments under the Orthologue header and then click on View Protein Alignment in the pop-up menu.

Homologues across different pig breeds and other livestock species

Let’s explore homologues of the BRCA2 gene across different pig breeds and other livestock species. Click on Comparative Genomics: Breeds: Orthologues to see the available orthologues. In the table, use the filter in the top right-hand corner and enter *Pig. This filters the table to include only pig breeds.

Let’s look at the Pig - Hampshire orthologue.

Links from the orthologue allow you to view alignments of the orthologous proteins and cDNAs. In the table, click on View Sequence Alignments under the Orthologue header and then click on View Protein Alignment in the pop-up menu.

Gene trees across different species

Click on Comparative Genomics: Gene tree to display the current gene in the context of a phylogenetic tree used to determine orthologues and paralogues.

You can change the gene tree display by using the View options below the image or the Configure this page button on the left-hand panel. You can also click on the individual nodes in the phylogeny to open a pop-up menu for other display options. Grey funnels indicate collapsed nodes. You can expand them by clicking on the node and selecting expand this sub-tree from the pop-up menu.

You can download the tree in a variety of formats. Click on the Export image button above the phylogeny to download the image in various formats.

Click on the Export button above the phylogeny to download the phylogeny or alignments in various formats.

Gene trees across different pig breeds and other livestock species

Click on Comparative Genomics: Breeds: Gene tree to display the current gene in the context of a phylogenetic tree across different pig breeds and other livestock species.

You can change the gene tree display by using the View options below the image or the Configure this page button on the left-hand panel. You can also click on the individual nodes in the phylogeny to open a pop-up menu for other display options. Grey funnels indicate collapsed nodes. You can expand them by clicking on the node and selecting expand this sub-tree from the pop-up menu.

Location tab: alignments and synteny

Pairwise and multiple whole-genome alignemnts

Conservation scores and constrained elements

Let’s look at some of the comparative genomics views in the Location tab. Go to the region 15:81873000-82000800 in the pig (Sscrofa11.1) reference genome. This region contains the HoxD cluster which is involved in limb development and is highly conserved between species.

You can turn on Genomic Evolutionary Rate Profiling (GERP) conservation scores and constrained elements. GERP scores assess the conservation of genomic elements across species. Positive scores represent highly-conserved regions in the genome (which suggest critical functional regions in the genome), while negative scores represent highly-variable regions. Constrained elements highlight these highly conserved regions. You can read more about conservation scores and constrained elements in the Ensembl comparative genomics documentation.

Click on the Configure this page button in the left-hand panel. In the pop-up menu, go to Comparative genomics: Conservation regions in the left-hand panel and turn on the tracks for Constrained elements for 16 pig breeds EPO-Extended and Conservation score for 16 pig breeds EPO-Extended on the right. Save and close the menu.

You can now see the conservation scores in pale pink. These were used to determine the peaks indicated in the constrained elements track in dark pink. This track indicates regions of high conservation between species, considered to be “constrained” by evolution.  

Pairwise whole-genome alignments

Let’s look at individual species comparative genomics tracks. Click on the Configure this page buton . In the pop-up menu, go to Comparative genomics: BLASTz/LASTz alignments in the left-hand menu. Here, you can enable alignments between closely related species. Let’s visualise genomic alignments of species with differing relatedness to the pig reference:

• Pig - Largewhite (Sus scrofa) - LASTz net
• Chacoan peccary (Catagonus wagneri) - LASTz net
• Human (Homo sapiens) - LASTz net

Save and close the menu.

From the alignment, we can see that the most distantly related species (Human) has the largest number of gaps in the alignment. If you compare the alignment region that contains a lot of gaps (marked above) with the 16 way GERP elements track, you’ll notice that this region does have any constrained elements, and therefore suggests that the genomic sequence is highly variable across species.

We can also look at the sequence alignment itself. Click on Alignments (text) in the left-hand panel. Click on Select another alignment and add Pig - Largewhite in the pop-up menu. Click Apply to save and close the menu.

You will see a list of the regions aligned, followed by the sequence alignment. Exons are shown in red.

To compare with both contigs visually, go to Comparative Genomics: Region Comparison in the left-hand menu.

To add a species to this view, click on the blue Select species or regions button. Choose Pig - Largewhite from the list then close the menu.

You can configure this view for both species. Click on Configure this page and look in the top left of the menu.

The drop down allows you to configure each species separately.  

Synteny

Synteny describes the conserved order of genes in a sequence alignment between two species. We can view large-scale syntenic regions from our chromosome of interest. Click on Comparative Genomics: Synteny in the left-hand menu.

Multiple whole-genome alignments

We are going to look at the PLAG1 gene in the pig reference (Sscrofa11.1) genome and explore its gene tree and homologues.

1. Have orthologues been identified in any pig breeds? If so, which ones?

2. Open the cDNA sequence alignment against the Tibetan breed. What does the asterisk (*) symbol mean in the alignment? What is the % identity (cDNA) and what does the number stand for?

3. Let’s look at the PLAG1 breed gene tree. How many genes are depicted in the gene tree? According to the gene tree, which orthologue is the most closely related to the pig reference PLAG1 gene? What is the Ensembl ID of the orthologue and what strand is it located on?

4. Export the gene tree in Newick format.

Go to www.ensembl.org to find the DBH gene on the reference pig genome (Sscrofa11.1).

1. Go to the Location page for this gene. View the Alignments (image) and Alignments (text) for the 16 pig breeds EPO-Extended. Do all the pig breeds show a gene in these alignments?

2. Export the alignments in ClustalW format.

3. Go to the Region in detail view and turn on the 16 pig breeds EPO-Extended multiple alignment, conservation score and constrained elements tracks. Are there any differences between the conservation score and constrained elements tracks?

4. Compare the 16 way GERP elements track and the 91 way GERP elements track that is already turned on by default.

   • What is the difference between the two tracks?
   • Which regions of the gene do most of the constrained element blocks match-up to?
   • How can you find more information on how the constrained elements track was generated?

1. Let’s explore the orthologues of the chicken BRAF gene.
   • How many orthologues are predicted for the chicken BRAF in sauropsida (birds and reptiles)?
   • How much sequence identity does the Anolis carolinensis (Green anole) protein have to the chicken one?
   • Export the protein alignment in Clustal format.
2. Look at the orthologue in human. Is there a genomic alignment between human and chicken? Is there a gene for both species in this region?

Go to Ensembl Plants and answer the following questions:

1. How many orthologues are predicted for the Triticum aestivum (wheat) gene RHT1 (gene ID TraesCS4D02G040400) gene in Liliopsida?

2. How much sequence identity does the Secale cereale (rye) protein have to the maize one?

3. Download the alignment in Nexus format.

4. Open the gene tree for the wheat RHT1 gene. What is the gene tree ID?

5. How many speciation and duplication nodes does the phylogeny have?

In any of the sequence views shown in the Gene and Transcript tabs, you can view variants on the sequence. You can do this by clicking on Configure this page from any of these views.

Let’s take a look at the Gene sequence view for MCM6 in chicken. Search for MCM6 and go to the Sequence view.

If you can’t see variants marked on this view, click on Configure this page and select Show variants: Yes and show links.

Find out more about a variant by clicking on it.

You can add variants to all other sequence views in the same way.

You can go to the Variation tab by clicking on the variant ID. For now, we’ll explore more ways of finding variants.

To view all the sequence variations in table form, click the Variant table link at the left of the gene tab.

You can filter the table to only show the variants you’re interested in. For example, click on Consequences: All, then select the variant consequences you’re interested in.

You can also filter by SIFT, or click on Filter other columns for filtering by other columns such as Evidence or Class.

The table contains lots of information about the variants. You can click on the IDs here to go to the Variation tab too.

You can also see the phenotypes associated with a gene. Click on Phenotype in the left hand menu.

Let’s have a look at variants in the Location tab. Click on the Location tab in the top bar.

Click on Configure this page and open Variation from the left-hand menu.

There are various options for turning on variants. You can turn on variants by source, by frequency, presence of a phenotype or by individual genome they were isolated from. You can also turn on QTLs, which cover a locus without being associated with a specific variant. Turn on the following variation tracks.

• All variants on genotyping chips - short variants (SNPs and indels)
• Phenotype annotations (QTLs)

Click on a variant to find out more information. It may be easier to see the individual variants if you zoom in.

Let’s have a look at a specific variant, which happens to fall within the MCM6 gene: rs14625781.

The easiest way to find this variant is if we put rs14625781 into the search box. Click through to open the Variation tab.

The icons show you what information is available for this variant. Click on Genes and regulation, or follow the link at the left.

This variant is found in three transcripts of the MCM6 gene, and is missense in two. SIFT predicts that it is unlikely to affect protein function of either (Tolerated).

Let’s look at population genetics. Either click on Explore this variant in the left hand menu then click on the Population genetics icon, or click on Population genetics in the left-hand menu.

We can see data from EVA study PRJEB44919 showing the frequency of the alleles and genotypes. We can see what animals these genotypes were actually observed in by going to Sample genotypes.

Click on Phylogenetic context to see the variant in other species.

We can see that other birds also have the C alleles as a reference whereas Anolis_carolinensis has an A allele.

(a) Find the page with information for the chicken SNP rs10731268.

(b) What gene(s) does rs10731268 fall within? What is its effect?

(c) Have any papers been written mentioning rs10731268? What are they about?

(d) What allele is at this position in other birds? What is the likely ancestral allele?

The human gene MC4R has been associated with obesity. The SNP rs81219178 has been identified as a variant in the pig MC4R gene.

(a) What is the amino acid change caused by rs81219178 in MC4R of the pig? Is the change likely to alter the protein function?

(b) How many transcripts does this variant affect? What are the consequences of this variant?

We have identified seven variants in pig:
rs319195925, rs80805426, rs81267388, rs80854621, rs711163915, rs321793337, rs792403417

We will use the Ensembl VEP to determine:

• If the variants have been annotated in Ensembl already
• If genes are affected by the variants

Go to the front page of Ensembl and click on Variant Effect Predictor in the Tools section or click on VEP in the top header.

This page contains information about the VEP, including a link for downloading the script version of the tool. Click on the Launch VEP button to open the input form.

Lets input the variants data in VCF format:
Chromosome Position Name Reference Alternative

Put the following into the Input data box:

9 9580742 rs319195925 T C
1 213701082 rs80805426 C A
15 83361856 rs81267388 A G
1 159538854 rs80854621 A G
14 50574184 rs711163915 C A
14 50571223 rs321793337 G A
14 50571474 rs792403417 C T

The VEP will detect automatically that the data is in VCF format.

There are further options that you can choose for your output. These are categorised as Identifiers, Variants and frequency data, Additional annotation, Predictions, Filtering options and Advanced options. Let’s open all menus and take a look.

Hover over the options to see definitions.

When you have selected everything you need, scroll right to the bottom and click Run.

The display will show you the status of your job. It will say Queued, then automatically switch to Done when the job is done, you do not need to refresh the page. You can save, edit, share or delete your job at this time. If you have submitted multiple jobs, they will all appear here.

Click on View Results once your job is done.

In your results you will see a graphical and table summary of the data as well as a table with the detailed results.

We have identified a few variants associated with body size in chicken (bGalGal1.mat.broiler.GRCg7b):

chr 6, genomic coordinate 23650222, alleles A/C, forward strand
chr 6, genomic coordinate 23645685, alleles C/A, forward strand
chr 1, genomic coordinate 51237121, alleles C/T, forward strand

(a) Which genes and transcripts do these variants map to?

(b) What are the consequence terms for these variants?

(c) Which regulatory feature is affected by the variants?