The Human Genome
Course Home Modules Schedule Exercises Comments Credits

Practice User Question : Upstream Region of a Gene

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

Sample User Question back to top

How can I find and download the 500bps of genomic sequence upstream of the human arylsulfatase B (ARSB) gene?

Analysis / Comments back to top

One of the major advantages of having the entire human genome sequence available is that it becomes extremely easy to find the genomic sequences surrounding a gene of interest. Often, a researcher wants to obtain the nearby genomic sequence because it contains important regulatory sites such as the promoter, transcription factor binding sites, ribosome binding sites, and other such elements. Now, a researcher can obtain the squence immediately from the databases with ease.

Flow Chart back to top

  1. Entrez Gene - Use Entrez Gene to learn more about the gene of interest and make certain that you are choosing the correct gene. Also, Entrez Gene provides a direct link to the MapView of the human genome sequence, specifically to the location of the particular gene of interest.
    Down Arrow
  2. Map Viewer - The MapViewer provides a graphic view of the human genome as well as links to the full sequence and the opportunity to download specific regions of the full sequence.

Step By Step Guide back to top

  1. Go to Entrez Gene and type in the name of the gene arylsulfatase B; specify human[organism]. Click on the record accession # to see the full record.
  2. Link to the MapViewer.
  3. In the MapViewer: Click on the 'dl' (download) link in the annotation of the master map: Genes_seq. If this is not the master map, use the 'Maps & Options' dialog box to make Genes_seq the master map.
  4. Specify an additional 500 basepairs upstream: adjust by -500. Note: use the orientation arrow on the Genes_Seq map annotation to identify where the 5' end is. This is extremely important as genes can occur on both DNA strands of the chromosome such that some appear as though they are going "backwards" by the chromosome numbering system. Be certain you know where the 5' and 3' ends of the gene are located. The arrow on the Genes_seq map will always give you that information and using a ruler on the Genes_seq map will give you approximate numerical locations for the 5' and 3' ends that will help you know which end to add the additional 500bp.
  5. Click on the 'Change Region/Strand' button.
  6. Click on 'Save to Disk'. This will save the entire genomic sequence of this gene plus 500 base pairs upstream.
  7. Note that you could, by calculating and entering the appropriate location numbers, download just the 500 upstream basepairs alone.

Human Genome Return to Slides (*.html or *.mht format)
Return to Exercises List		 Revised 07/12/2007