Genome 371 Lecture 3 - Genome 371 Lecture 3 1/26/11 4:15 PM...

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1/26/11 4:15 PM Genome 371 Lecture 3 Page 1 of 13 http://courses.washington.edu/au371mkr/resources/lecture_notes/lecture_03.html Lecture 3 Mendelian inheritance 8 Oct 2010 Lecture 3 handout (pdf) Subscribe to podcast: Slide 1 Slide 2 Home Course mechanics Help hours Calendar Syllabus Lectures, Podcasts Quiz Sections Practice problems Exams GoPost Send email to class Useful links The Gradiator
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Genome 371 Lecture 3 Page 2 of 13 http://courses.washington.edu/au371mkr/resources/lecture_notes/lecture_03.html Slides 3 and 4 Follow-up to QS1 homework: As discussed in class and in quiz section, the approach we used (of looking for open reading frame) is only one test in a battery of tests to identify genes in "unknown" sequence. But, looking for open reading frames can run into problems with complex genomes in which exons are small and introns are large--so the open reading frame that is contained in the gene may be broken up into such small pieces, it's hard to recognize that they are even there. The sequence represented on the left is one such example -- it is a portion of the human separase gene, so there should be an ORF, but there are so many introns, we can't recognize the ORF pieces just based on looking for a start. ..stop codon pattern. One approach that complements the ORF search is to look for sequence conservation. We would expect that because exons contain the coding portions of genes, they will be conserved across species (especially for genes involved in fundamental cell biological processes); in contrast, introns would largely be free to mutate and change over time. Therefore, sequences that are conserved stand out as likely having some function. In fact, as you can see from this diagram, the conserved sequences match up remarkably well with the locations of exons. Additionally, as you saw in quiz section, genes such as tRNA genes will not be detected when we look for open reading frames. However, we do expect them to be conserved, so by looking at sequence conservation we should be able to detect such genes. Slide 5
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Genome 371 Lecture 3 - Genome 371 Lecture 3 1/26/11 4:15 PM...

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