By Wolfsberg Tyra G., Wetterstrand Kris A., Guyer Mark S., Collins Francis S., Baxevanis Andreas D.
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Extra resources for A user's guide to the human genome
9). Differences exist at the ends of the EST, but the sequences are identical in the region surrounding the putative missing exon. An alternatively spliced mRNA is more likely to be of biological significance when it changes the sequence of the encoded, wildtype protein. To determine whether EST BE798864 could encode a protein different from that of the known gene (RAB9P40), one can simply compare the two sequences directly against each other using the NCBI’s BLAST 2 Sequences tool. First, open a new web browser window, because information from the above search will be needed here; this will prevent having to use the browser’s Back and Forward keys excessively and is a good general rule when using multiple web tools.
Click on the track labeled Fgenesh++ Gene Predictions to go to a summary page describing the prediction (Fig. 3). The region has sequence similarity to the pendrin gene (which was already known at the beginning of the example). The size and the beginning- and endpoints of the prediction are given, and it is indicated that the prediction lies on the minus strand; this was also indicated in Fig. 2 by the left-pointing arrows in the intronic regions. To obtain the sequence, click on Genomic Sequence.
For purposes of this example, consider the gene encoding pendrin (PDS), a protein associated with developmental abnormalities of the cochlea, sensorineural hearing loss and diffuse thyroid enlargement (goiter). From the UCSC home page, choose Human from the pulldown Organism list, and click on Browser. The user is now at the Human Genome Browser Gateway. The search in this case is simple: select Dec. 2001 from the assembly pull-down menu, type pendrin into the position box, and then click Submit.