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Exploring the GSCOC_T00019208001 gene in Coffea canephora (Robusta coffee)

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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.