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A Tale of Three Gene Annotations

Explore discrepancies in gene annotations in Glycoside Hydrolase Family 9 enzymes, analyzing start codon variations and Shine-Delgarno sequence presence. How different databases handle these variations and how to identify the correct start codon. Learn how to navigate such discrepancies while examining the genome.

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A Tale of Three Gene Annotations

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  1. A Tale of Three Gene Annotations Nick Carney

  2. JGI Gene 2500587691 RAST/SEED JGI Manatee

  3. The SEED Manatee JGI Manatee The SEED JGI

  4. Shine-Delgarno? • No Shine-Delgarno sequence immediately in front of start codons • The only suggested Shine-Delgarno comes far after the beginning of the gene

  5. The Possible Protein

  6. Alignment

  7. Glycoside hydrolase family 9 • Group of enzymes that hydrolyze glycosidic linkages in carbohydrates • Classified into families based on how similarities • Family 9 • Endoglucanase • Cellobiohydrolase http://pfam.sanger.ac.uk/structure?id=1rq5

  8. Resolution? How do all three databases come up with a different start codon? How do we truly know which is the correct start codon? How do we deal with this as we examine the genome?

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