High School Outreach: Bioinformatics
Using Bioinformatics to Learn
About Your Plant Lines
U.W. Madison
NSF Plant Genomics: Cell Wall Biogenesis
NSF: DBI 0077719
After you have described the Phenotype of your plant line and
have photographed it, you can now investigate what is known
about the gene in which T-DNA has been inserted
From the your line number and the line key, find the Salk number for your
sample. On the internet go to the T-DNA Express:The SIGnAl
Arabidopsis Gene Mapping Tool (http://signal.salk.edu/cgibin/tdnaexpress). Type your Salk number in the cDNA/T-DNA Box.
Submit
Search for the Salk number and the gene number on the map
(see arrows). Note under the gene number is a representation
of the gene with introns and exons.Where is the beginning
and end of the gene? Where is the T-DNA inserted?
The gene number tells you a lot about the gene. What
chromosome is it on? What genes are next to it? What other
information do you think we could obtain from this diagram?
You may want to come back to this screen and play with
some of the possibilities but for the time being, click on the
gene (in this example At3g11130)
This is a resource for looking up more information on
At3g11130 (or any other gene you might have chosen). Click
on NCBI
Note the position of your gene on chromosome 3. There are
other resources listed in the column on the left and also just
below the chromosome graphic which you could investigate.
Return to the previous screen
Click on TAIR
This site gives you information on the possible function of a gene
(clathrin vesicle coat) and where in the cell it functions (endomembrane
system). There is a lot more here one could to investigate.
Go to the mips web site: http://mips.gsf.de/proj/thal/ . There are a
number of thing you could investigate on this page. For now, click on
MAtDB
Click on Searches. Again there is a lot more in the left hand
column one could investigate
Type in gene code for your gene (in our example At3g11130)
in the search by entry code box. Click Search.
Here we have the predicted function of this gene base on
either direct studies or from gene of other species which have
a similar DNA sequence. Click on DNA sequence.
This is the unspliced DNA sequence of our gene, i.e. it includes introns
and exons. The introns are small case symbols and the exons are bold
capital symbols. Now click protein sequence.
This shows the linear order of amino acids which result from the
transcription and translation of our gene. Check with your teacher for the
key to the amino acid symbols. Click on 3D structure.
This is a list of polypeptides similar to the clathrin of our
gene. These can be compared in various ways to our gene
product and can be rendered as a 3D model. Click on 1BPO
Click on 1BPO
Click on Download/Display File
Click on PDB none
Click on OK
Click Save
The PDB file you have downloaded can now be rendered into a 3D
model using programs like RasMol 2.6 or SwissView. The is a ribbon
representation of the heavy B chain of the rat Clathrin using SwissView
Go to the search engine google (www.google.com) and type
in Cazy. Click Search. Click on CAZY- Carbohydrate-Active
EnZymes
This site looks at genes and the carbohydrate gene family
they are related to. Type in gene number (At3g11130) and
click search
This gene does not produce a product that is directly related to
carbohydrate biosynthesis or disassembly but may be involved in the
transport of a gene product involved in one of these processes. As a
result we don’t get any information in this search.