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.