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Exploring a genomic region in Oryza sativa Japonica (rice)

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Exploring a genomic region in Oryza sativa Japonica (rice)

Go to the Ensembl Plants homepage and do the following:

  1. Go to the region between 405000 and 453000 on chromosome 1 in Oryza sativa Japonica.

  2. Turn on the AGILENT:G2519F-015241 microarray track. Are there any oligo probes that map to this region?

  3. Highlight the region around any reverse strand probes you can see. Do they map to any Ensembl transcripts?

  1. Go to the Ensembl Plants homepage. Select Oryza sativa Japonica from the Species drop-down list and type 1:405000-453000. Click Go.

  2. Click on Configure this page to open the menu. You can find the AGILENT:G2519F-015241 track under Oligo probes in the left-hand menu, or by using the Find a track box at the top right. Turn on the track as Normal then save and close the menu. As the AGILENT:G2519F-015241 track is stranded, it appears at the top and bottom of the view.

    There are 5 probes mapped to this region on the positive strand and one probe on the reverse strand.

  3. Drag a box around the reverse strand probe then click on Mark region to highlight.

    The highlighted region maps to two transcripts: Os01t0107900-02 and Os01t0107900-01