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Exploring the CCD7 gene in Arabidopsis thaliana

  1. Find the Arabidopsis thaliana CCD7 gene on Ensembl Plants. On which chromosome and which strand of the genome is this gene located?

  2. Where in the cell is the CCD7 protein located?

  3. What is the source of the assigned gene name?

  4. How many transcripts does it have? How long is its longest transcript (in bp)? How long is the protein it encodes? How many exons does it have? Are any of the exons completely or partially untranslated?

  1. Go to the Ensembl Plants homepage (http://plants.ensembl.org/). Select A. thaliana from the species list and type CCD7 in the search box. Click Go and click on the gene ID AT2G44990. You can find the strand orientation and the location under Summary in the Gene tab.

    The A. thaliana CCD7 gene is located on chromosome 2 on the forward strand.

  2. Click on GO: Cellular component in the left-hand panel.

    The protein is located in the chloroplast and plastid.

  3. Click on Summary in the side menu.

    The gene name is assigned and imported from NCBI gene (formerly Entrezgene).

  4. Click on Show transcript table.

    There are 3 transcripts. The longest one is 2005 bp and the length of the encoded protein is 622 amino acids.

    Click on the transcript ID AT2G44990.3 in the transcript table. You can find the number of exons in under in the summary information at the top of the page.

    It has 6 exons.

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

    The first and last exons are partially untranslated (sequence shown in orange). This can also been seen from the fact that in the transcript diagrams on the Gene Summary and Transcript Summary pages the boxes representing the first and last exon are partially unfilled.