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Demonstration Question: Using E-PCR

  Sample User Question
Analysis/Comments
Flow Chart
Step By Step Guide
  

Sample User Question back to top

How many unique STS markers exist within the sequence of the EDN1 mRNA sequence? Find the accession number for the RefSeq mRNA for EDN1 and use e-PCR to locate STS markers.

Note: Can you think of other ways to find this information? For this example, practice with the use of ePCR, then see if you can find another way to find the same information.

Analysis/Comments back to top

Identification of STS sites near or within a gene locus of interest provides the scientist with valuable, unique markers that can be used to specifically and sensitively identify that particular sequence within the entire genome.

Flow Chart back to top

  1. There are several ways to find the accession number for the EDN1 refseq mRNA including Entrez Gene and Entrez Nucleotide. Can you think of a way to link to that information from the MapViewer?
  2. E-PCR - allows you to search for known STS markers in a submitted sequence.

Step By Step Guide back to top

  1. Here's one way to find the mRNA for EDN1 - in the MapViewer, click on the gene name "EDN1" on the genes_seq map annotation to get to the Entrez Gene record. Scroll down to find the RefSeq section and locate the mRNA accession number "NM_001955."
  2. Go to the E-PCR page.
  3. Select Forward e-PCR
  4. Enter accession # for the mRNA.
  5. Submit the query.
  6. Examine the results.
  7. Note that you can find some STS marker information for a gene in its Entrez Gene record, though it is likely to include markers in the introns as well as the exons.

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