On your computer, use a web browser to access GenBank: . Once there, find a nucleotide sequence for the human , sometimes called the “Christmas factor” (F9) gene. In other words, find a DNA sequence for the gene that encodes the coagulation factor IX protein. This is found by using the search area at the top of the GenBank web page. You are looking for a specific “accession”—a sequence submission record—with the accession ID: . To summarize, we need to find the nucleotide sequence for the human , sometimes called the “Christmas factor” (F9) gene. To do this we: genes (like F9) are composed of messenger RNA (mRNA)-coding sequences called (expressed portions of DNA sequence) and intervening sequences called (the name emphasizes their intervening role). Intron sequences in pre-mRNA are non-coding and are removed before transcription to mRNA. The exons are then joined together (concatenated) and comprise mature mRNA. The process of removing introns and reconnecting exons is called ‘splicing.’ Mature mRNA is comprised of coding sequence (CDS) and untranslated regions (UTR) at 5′ and 3′ ends
. Coding sequence is made up of —the portion of mRNA that codes for amino acids. The amino acid coding portions (CDS), along with other gene features, are annotated on the left side of the description in GenBank records. For example, you will see something similar to this in the annotations for the F9 gene: The actual line on the GenBank page will be much longer (i.e. containing more than just the ranges for two exons) but the first two ranges match exactly what is given above. The word in a GenBank record is analogous to a function in Python. It is an instruction to slice out and join (concatenate) the segments separated by commas within parentheses. The resulting string represents the amino acid coding sequence (CDS). Assuming we have the entire F9 gene sequence stored in a variable , the example above could be written in Python as: Python indexes start at 0, but GenBank annotations start at 1. Notice how the coordinates differ between the GenBank record example and the Python code above. Failure to adjust indexes correctly is a common situation in computer science and the bugs related to this are known as