User Question 6: Analysis of Exonic SNPs
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| Sample User Question:
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Germ line mutations in the BRCA1 gene (U14680) lead to the predisposition
to breast and ovarian cancer. A single point mutation, a G to T
substitution in exon 18 at nucleotide 5199 (codon 1694) has been
observed in a group of breast and ovarian cancer patients. This
mutation changes a glutamic acid to a stop codon (Glu 1694 ter).
Further study revealed that instead of expressing any transcript with
exon 18 containing stop codon, the mutant allele produces
only mRNA in which the entire exon 18 has been skipped.
Explain the cause of this exon-skipping phenomenon.
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| Flow Chart |
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- Entrez Nucleotide - Find the nucleotide sequence for a gene by searching with Genbank accession number
- ESE Finder -Analyze the exonic sequence to find the presence of Exonic Splicing Enhancer Element (ESE)
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| Step By Step Guide |
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- Entrez Nucleotide
- Enter "U14680" in the search box and Click on "GO"
- Click on "U14680"
- Scroll down to the "Feature" section and go to "Exon" number 18
- Click on "Exon" and select "FASTA" from "Display" drop-down menu, click on "Display"
- ESE Finder
- Copy FASTA sequence of exon 18 from previous step and paste into the text box
- Click on "Send" button (e.g., what option to select)
- Repeat the above steps with the mutated sequence where T will replace G at position 6
- Compare the "ESE Finder analysis results" for both the wild type and mutated sequence
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