WormBase tutorial

Table of Contents

1. Introduction to WormBase
2. Part 1: Finding your Gene
3. Part 2: Examining the Sequence Summary
4. Part 3. Other Information on the Gene
5. Part 4. Links from the Home Page
6. Part 5. Other Genes to Explore

Part 2: Examining the Sequence Summary

1. Next we are going to examine the gene and amino sequence in more detail. Click on the "Sequence Summary" link in the yellow bar near the top of the page. You should see a summary of the gene's sequence, with much of the same information that we saw on the gene summary page. Although it may seem repetitive to have this information again, it is often helpful to have familiar informational landmarks as you negotiate these complex databases. Notice that the gene name is now listed as B0412.2 because we are examining the sequence.

2. The picture of the gene model shows the introns as lines and the exons as pink boxes. daf-7 has five exons (and thus four introns). The gray boxes at the beginning of exon 1 and the end of exon 5 are the 5' and 3' untranslated regions (UTR), which may not be present for all genes. The diagram also shows the expected PCR products from using these primer pairs, ones that were listed under the Reagents field on the Gene Summary page.

3. Scrolling down, you can see the nucleotide sequence of the gene. The yellow and orange highlights with the capital letters are the exons. The gray nucleotides in lower case letters are the 5' untranslated region and the 3' untranslated regions, while the black nucleotides in lower case letters with no highlighted background are the introns. The first sequence is the unspliced transcript; the second is the mature mRNA.
   
   There is no functional difference between yellow and orange exons; the colors simply make it easier to distinguish adjacent exons when comparing the unspliced and spliced transcripts.

4. Scrolling even further, you can see the predicted amino acid sequence (its conceptual translation). There are also links to do rapid BLAST searches against two C. elegans specific databases in order to find genes and proteins with related sequences.

5. The exact locations of the exons are given by the table at the bottom of the page. This table shows both the position of the exons with respect to the start codon for the gene and with respect to the beginning of the sequence on the cosmid B0412.
   
   The bottom of the page lists the known cDNA clones for the gene, which can be obtained by an investigator who wants to study the gene further.