Bhavi Patel 10/14/11 Bioinfomatics LabDuring our experiment we created an annotated DNA sequence of a gene that expressed Glioma cancer, which is childhood brain cancer in Homo sapiens (humans). In our DNA sequence, we were able to identify and label the 5UTR, 3UTR, the coding sequence, the start codon, the stop codon, the TATA box, the CCAAT box, and TF binding sites. The 5UTR is foundbefore the coding sequence in mRNAs, while the 3UTR is found at the end (Vocabulary list) Thecoding sequences are sequence of bases in an mRNA that is an open reading frame, while the start codon is a specific sequence that indicates the beginning of a sequence and the stop codon indicates the end of a sequence (Vocabulary list). The TATAA box is a sequence right in front of the site for the transcription of the gene, while the CCAAT box is in front of the TATAA box and helps us to find the beginning of the gene (Vocabulary list). Our construct expresses the Contortrostain toxin which is found in Agkistrodon contortrix contortrix on mature and smooth cell types. The rationale for this design was to have the Contortrostatin toxin, 5UTR, 3UTR, the coding sequence, the start codon (ATG), the stop codon (TAA,TAG, or TGA), the TATAA box (GTATAAAGGCGAG), the CCAAT box (TCAGCCAATCAGTG), and TF binding sites, all on the Homo sapien DNA molecule that we created, because we wanted to see if by having toxin targeting glioma in childhood brain cancer whether or not we would be able to get rid of it completely. The accession number we choose on PubMed for the coding sequence is AF212305. The criteria we used for choosing a sequence from PubMed, was that it had to be Agkistrodon contortrix contortrix and it had to have the Contortrostatin toxin on the "Nucleotide" database in PubMed. The transcription factor binding sites that we choose were MEF2A and SRF because both of these binding sites were found on our “correct” promoter sequence, in addition to this MEF2A which binds to CTATTTATAG, is found smooth muscle and SRF which binds to GCCCATATATGG is found in mature cells and since both of these are found in a child’s brain we used them as our transcription factor binding sites. We determined that this was the “correct” promoter sequence because our promoter sequence had everything we had to label, which includes the 5UTR, 3UTR, the coding sequence, the start codon (ATG), the stop codon (TGA), the TATA box (GTATAAAAGGCGAG), the CCAAT box (TCAGCCAATCAGTG), and TF binding, therefore we knew that it could work in an organism. If there was another transcription factor binding sites in our construct it would cause the transcription binding factors in our construct to be expressed less frequently because the other transcription factor binding site wouldalso be expressed, which in the end is effecting our construct. There are many potential difficulties in using this construct in a clinical setting, for instances, the construct is not completely accurate because the construct was only 90% accurate when we created it and in addition to this both healthy and unhealthy cells can be effected in both negative and positive ways, which is not good for an organism. Therefore using this construct is not recommended in clinical settings.References:http://bcrc.bio.umass.edu/intro/content/bioinformatics-vocabulary-list