Ensembl TrainingEnsembl Home
More ▼
Finding orthologous genes for disease resistance gene in Coffea canephora (coffee)

<- Back to exercise page

Finding orthologous genes for disease resistance gene in Coffea canephora (coffee)

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 Plants for the gene AT1G50180 in Arabidopsis thaliana.

  1. From the gene tab, go to the Arabidopsis thaliana AT1G50180 gene Orthologues page under Plant Compara.

  2. Reduce the orthologues table to look only at Coffea canephora (coffee) orthologues. How many results can you see?

  3. Download the cDNA alignment in ClustalW format for the alignment between the Arabidopsis thaliana AT1G50180 gene and the Coffea canephora GSCOC_T00030728001 gene.

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