Gene reports

You will each be assigned a gene during your recitation section early in the semester. This is your personal gene throughout the semester and you will be given questions to answer about your gene, the answers to which will be found through your own research, on NCBI web pages and in journals in the library. You will give an oral presentation on your gene at an assigned recitation session during the second half of the course. More details about the gene assignment will be given during the first review session. Your oral presentation will be graded and will represent 10% of your final grade.

Link to NCBI database

Gene assignment 4

For your gene, identify:

1. General structure of your gene
1. How many introns and exons? How long are they? Where are they?
2. Find the genomic DNA sequence and the mRNA sequence.
   You may not want to print the whole sequence if it is large, but you should be able to find it. (To get the mRNA, you may need to use the cDNA sequence (which is a DNA copy of the mRNA)).

3. In the genomic DNA sequence, see if you can find the
1. First base of transcript
2. upstream promoters (eg. TATAA box) (This is hard, because promoters do not always have the concensus sequence. But see if there is something around -35 bp).
3. End of the transcript
4. Poly A signal (also hard. should be about 60 bases upstream from the end of the transcript).
5. Intron splicing sequences (two bases at beginning and end of each intron)
6. Start codon
7. Stop codon

You should be able to find all of this from the NCBI database (http://www.ncbi.nlm.nih.gov/).

If you use the "gene" search as before, you will probably find some links near the bottom to a DNA copy of the mRNA sequence and hopefully a genomic (DNA) sequence under "related sequences".

Many of the sequences are annotated to show the locations of introns and exons etc.

See some Hints and an example.

Gene assignment 3

1. Find the map position of your gene. Which chromosome is it on? Try to find the recombinational map position (in cM) as well as the physical location (number of the starting base pair). Often that information will be provided for you in the "GENE" database, near the top of the entry for your gene.
   Click on the "Map Viewer" (if available for your gene) and explore the chromosomal region around your gene. What are some other nearby genes? Try zooming in to eh sequence level, and out to the whole chromosome. For some organisms, only one of those types of maps may be available. For other genes, the NCBI database may not list the map position, but you may be able to find it if you search some of the first papers about your gene. Finally, if you are researching a Drosophila gene or an Arabidopsis gene, you might try the more specialized databases for those organisms: www.flybase.org and www.arabidopsis.org.
   Example: If you look in the NCBI database at the vermilion locus of Drosophila you can find a heading "Genomic context" near the top of the page. There this says that the gene is on the X chromosome at band position 9F11. Just above that, you can see that the reference sequence begins at base pair number 10,769,208. Both of those are physical map positions. This database does not give a genetic (or recombinational) map position. However, if you look up the same gene in the Drosophila database ( http://www.flybase.org/.bin/fbidq.html?content=maploc&FBgn0003965) you can find that its recombinational map position is at 33.0 cM.

1. Read chapters 5 and 6 of the tutorial in the solutions manual (pp 415-420).
2. Your second assignment is to find 3 recent papers about your gene. What does the gene do? What are some of the questions people are studying? For many genes you can use the PubMed database (as described in your tutorial) to find papers about it. For others you might need to try some of the resources on the library web page. I particularly recommend the "Web of Science" database.

Gene assignment 1: I have randomly assigned each student a gene to research. Which is my gene?

To get started, you should

1. Read the first two chapters of the genomics tutorial in your Solutions Manual (pp 393-404)
2. Find their gene in the database, figure out what it does, and what organism(s) is it in.

There will be another short gene assignment next week.