Part D: Corroborate predictions using Entrez

The BLAST search in Part C showed that the gene annotated in Part B is likely to be C. elegans gene enu-3.6. In this section, we will corroborate this finding by comparing our gene to an annotated sequence for C. elegans chromosome III, NCBI Entrez database entry NC_003281.10.

This tutorial is not dependent on the previous tutorials, so you can start from within the currently open GeneQuest project, or begin with a new, empty GeneQuest project.

1. Select File > Open Entrez Sequence.

2. Enter NC_003281.10 in the dialog box, keep the default database selection (nucleotide), and then click OK.

3. When prompted, click Save. This saves a local copy of the sequence and opens it as a new GeneQuest document, using the default method set.

4. In the Method Curtain, expand the Features method by clicking the plus sign or triangle to its left. There are over 30,000 features in the list.

5. To sort the features by name, use Sites & Features > Sort Features > Name.

6. Locate and select the enu-3.6:CDS feature and drag it to the Assay Document

7. Choose Edit > Go to Location and search for location 10751000. Zoom in as needed.

8. Double-click on the feature to open it in the Feature Editor.

9. Compare this known feature you created in Part C of this tutorial. In both cases, exon 1 is 116 bp in length; exon 2 is 560 bp; exon 3 is 146 bp; and exon 4 is 134 bp. This is good evidence that the gene found and annotated in Part C is the enu-3.6 gene.

This is the end of the tutorial.