Biology

Beginning your Search:

  • Take note of the number of bases available to be searched in the database. This number increases daily as additions are made by scientists throughout the world. You can find this information displayed directly below the yellow box.

  • To search for your nucleotide sequence, check that the database is set to search for "nucleotide" in the gray bar at the top of the screen. This should already be visible, however, if it is not, just pull down the menu next to the word "Search" and select "nucleotide."

  • After the database is set to search for a nucleotide sequence you can type in the name of your gene of interest in the white search box at the top of the screen. For example, to look for the sequence to human beta-globin simply type "Human beta globin" in the search box.
  • Hit "Enter" to begin the search.

Finding what you need from your search results:

Depending on your gene of interest, you may get thousands of results and there is no guarantee that all of them are exactly what you are looking for. Be careful that the description given closely matches your gene. For example, your search for human beta-globin will include results for individual members of the globin gene family but these are not the genes you are looking for. Instead select the search result titled "human beta globin region on chromosome 11"

While you are looking through your results, take note of the different options listed for each entry in blue on the right side of the page. These are links that will provide you with additional information about your gene. These links will vary for each entry but you may see:

Taxonomy- If you do not specify a species when you conduct your search you may get

results from numerous different species many of which may be unfamiliar to you. Use this link to find out what species this search result is from.

Related Sequences-This link will provide you with other sequences related to the gene you searched for. These sequences may be from related genes in the same species or from the same gene in different species.

PubMed-If you would like to find publications of studies related to your gene of interest click on this link.

Protein- This link means that an amino acid sequence is available for your gene of interest.

OMIM- This option takes you to a second database called the "Online Mendelian Inheritance in Man." This is a catalog of human genes and genetic disorders.

Explore these different links to learn more about your gene!

Once you have found the correct search result for your gene of interest:

  • Click on the blue identification number for "human beta globin region on chromosome 11".
  • Scroll down the page and look at the different types of information that are available for this match
1. How many references are there for this database record?

2. How many nucleotides are sequenced in this record?

3. How many genes are found within this region of chromosome 11? How are these genes similar and dissimilar? (Hint: look in the "Comments" section)
  • The "Features" section provides a chronological, in-depth analysis of the nucleotide sequence. Scroll down this section until you come to entries for nucleotide 62137. This is the region of the sequence encoding the beta-globin gene.
4. Compare the CDS entries for wild-type beta-globin and beta-thalessemia. What is the difference between the two? How is this difference caused? (use information in the features section)
  • Make a table to compare the nucleotide size of Exons 1,2, and 3 in the beta-globin gene (starting at 62187) with those of the epsilon (19541), G-gamma (34531), A-gamma (39467), and delta (54790) globin genes.

5.What do you think occurred first during globin gene evolution: divergence from a common ancestor or the introduction of introns interrupting each globin gene? Why?

6.Predict the order in which you think the beta-globin family evolved. What gene family member served as a "common ancestor"?
  • Make a table to compare Introns 1 and 2 for each of the five genes and compare this table to the exon table.
7.Based on your data, is intron or exon size more free to evolve? Why?
  • At the end of the Comments section, immediately before the Features table, are listed the presumed sites where pre-mRNAs are cleaved and poly-adenylated. Using the nucleotide reference numbers given, check the actual DNA sequence to identify the nucleotides contained at these sites.
8.Can you derive a consensus sequence that signals for poly-adenylation to occur?

When you are finished, return to the Beta-thalessemia Menu Page to move on to the next section of the laboratory.