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The Ensembl Data Platform)

Course Details

Lead Trainer
Aleena Mushtaq
Event Date
2026-05-05
Location
 
Description
Work with the Ensembl Outreach team to get to grips with the new Ensembl Data Platform.

Materials

CC-BY 4.0 logo

Demos and exercises

Visualising data in the Ensembl platform

Exploring the GSCOC_T00019208001 gene in Coffea canephora (Robusta coffee)

The gene for TF-B3 domain-containing protein (GSCOC_T00019208001) is a known master regulator of somatic embryogenesis, an important factor in stable genetic transformation and successful plant regeneration of coffee trees expressing the Bacillus thuringiensis (Bt) toxin Cry10Aa to induce Coffee Berry Borer (CBB) resistance.

  1. Find the Coffea canephora GSCOC_T00019208001 gene on Ensembl. On which chromosome and which strand of the genome is this gene located?

  2. Can you find information on the protein family/sub family and the position of its domain?

  3. How long is this gene’s transcript (in bp)? How long is the protein it encodes? How many exons does it have?

  4. List the matches for this gene in other biological databases.

  1. Go to the Ensembl website (https://beta.ensembl.org/). Select Robusta coffee AUK_PRJEB4211_v1 from the species selector app and search for GSCOC_T00019208001. Click Find a gene on the right hand side panel and enter the gene ID, click on the gene ID GSCOC_T00019208001 and then click on the Entity viewer icon. You can find the strand orientation and the location at the top of the transcript feature.

    The C. canephora GSCOC_T00019208001 gene is located on the forward strand at chromosome 7:772,198-774,571.

  2. Click on the Gene function tab at the top.

    The protein family (PANTHER) and domain name (PFAM) are displayed on the right-hand side of the view.

  3. Click on the Transcripts tab.

    The canonical transcript CDP16731 is 1038 bp long and the length of the encoded protein is 279 amino acids. This transcript (CDP16731) has 7 exons.

  4. Click on External references on the right-hand side menu.

    The external references or xrefs for the gene and its transcripts are listed in this panel.

Finding orthologous genes for disease resistance gene in Arabidopsis thaliana

Resistance to the leaf rust delivered by SH3 factor(s) is well-grounded as specially durable. In 2023, Paula Cristina da Silva Angelo et al (https://doi.org/10.1016/j.pmpp.2023.102111) reported that the Arabidopsis thaliana gene AT1G50180 is an important gene in the SH3 locus conferring diseae resistance.

Search Ensembl for the gene AT1G50180 in Arabidopsis thaliana (Thale cress) TAIR10.

  1. Find homologous genes for AT1G50180 .

  2. How many results can you see? Which species gene is closest to AT1G50180 when you consider protein similarity and coverage?

  3. Download the protein sequence for transcript AT1G50180.1.

Go to Ensembl Select Arabidopsis thaliana (Thale cress) TAIR10 from the species selector app and search for AT1G50180. Click Find a gene on the right-hand side panel and enter the gene ID, click on the gene ID AT1G50180 and then click on the Entity viewer icon.

  1. Click on the Gene relationships tab on the top. The Gene relationships panel shows a table that lists genes homologous to your gene of interest.

  2. Homologous genes share a common ancestor, being separated or ‘split’ by a speciation event or a gene duplication event. The % Protein similarity is the percentage of identical amino acid residues aligned against each other. Whereas, the % coverage is the percent of query which is in local alignment with the respective reference.

  3. Click on the Down arrowhead button on the right-hand side. Select cDNA from under All transcripts and finalise your export by clicking on the Download button.