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Exploring a gene in Magnaporthe oryzae

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Exploring a gene in Magnaporthe oryzae

We’re going to look at the gene ATG8 in Magnaporthe oryzae in Ensembl Fungi. This gene is involved in autophagy, and targeted silencing of this gene inhibits infection (you can find further info in Wilson and Talbot, Nature Reviews Microbiology volume 7, pages 185–195 (2009)).

  1. Find the genomic sequence of the M. oryzae ATG8 gene. How many exons does the gene have?

  2. Which biological processes annotated by Uniprot are associated with this gene?

  3. How many transcripts does the gene have? Download the cDNA sequence in FASTA format to your computer.

  4. Are there any entries of the gene in external databases? If so, which ones?

  1. From the Ensembl Fungi homepage, type ATG8 into the Search for a gene search bar, click the drop-down menu and select Magnaporthe oryzae and click the Go button. Click on the gene ID MGG_01062, which will open the Gene tab. Go to Sequence in the left-hand panel. ATG8 exons are in red font.

    The ATG8 gene has 3 exons.

  2. Go to Ontologies: GO: Biological process in the left-hand panel.

    The ATG8 gene has 2 Uniprot annotation GO terms associated with it: Autophagy and protein transport.

  3. Click on Show transcript table underneath the gene summary information at the top of the page.

    The gene has 1 transcript (MGG_01062T0).

    Click on Sequence: cDNA in the left-hand panel. You can export the sequence by clicking the Download sequence button, which will open a pop-up menu. Select FASTA from the drop-down list and select cDNA only. You can download the sequence as is or, if you have a large sequence, you can download the compressed file.

  4. Click on External References: General identifies in the left-hand panel. You will find hyperlinks to entries in external databases under the Database identifier column.

    Yes, there are entries in the Magnaporthe comparative DB, NCBI gene and WikiGene.