Alternative Splicing

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Module 6: Alternative Splicing

Investigation 1, step 4:

Q1. Given that exons are shown by the black blocks, and introns are shown by lines in the FlyBase Genes track, what does this tell us about the first intron of tra-RB compared to tra-RA?

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Investigation 1, step 5:

Q2. Given what you know about the initiation of translation, which of the 3 possible reading frames is used for both the tra-RA and tra-RB products?

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Q3. Give the coordinate for the last base of the first exon for tra-RA.

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Q4. Give the coordinate for the last base of the first exon for tra-RB.

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Q5. What is the consensus sequence for the 5’ splice site (donor site)?

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Q6. What are the coordinates for the 5’ splice site in tra-RA?

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Q7. What are the coordinates for the 5’ splice site in tra-RB?

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Q8. What is the phase at this splice site?

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Investigation 1, step 6:

Q9. What are the coordinates for the first base of the second exon in tra-RB?

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Q10. What is the consensus sequence for the 3’ splice site?

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Q11. What are the coordinates for the 3’ splice site in intron 1 of tra-RB?

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Q12. What phase do we anticipate?

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Q13. Given this, what is the reading frame for tra-RB exon2?

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Q14. Does this make sense, given the location of stop codons?

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Investigation 1, step 7:

Q15. What are the coordinates for the first base of the second exon in tra-RA?

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Q16. What is the consensus sequence for the 3’ splice site?

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Q17. What are the coordinates for that sequence in intron 1 of tra-RA?

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Q18. Given the phase at the donor site, what phase are we looking for here?

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Q19. Given this, what is the reading frame for RA exon 2?

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Q20. Does this make sense, given the location of stop codons?

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Investigation 1, step 8:

Q21. From your analysis of the RA isoform of tra in Module 5, how many amino acids does the tra-RA protein product have?

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Now look at the tra-RB isoform:

Q22. Write down the coordinates for exon 1.

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Q23. Given the reading frame that you established for tra-RB, does translation continue through exon 2, or is it terminated by a stop codon?

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Q24. Write down the coordinates for the translated portion of exon 2.

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Q25. How many amino acids does the tra-RB protein have?

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Q26. Is it likely that tra-RB could play the same functional role played by tra-RA?

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Investigation 2:

Use what you learned in Module 5 to construct a gene model for tra-RB. Locate the start codon, splice sites, and the stop codon. Construct the gene model below.

Q27. Coordinate for start of translation: ______________

Q28. Coordinate for last base of exon 1: ______________

Q29. Coordinate for first base of exon 2: ______________

Q30. Coordinate for last base of exon 2: ______________

Q31. Coordinate for first base of exon 3: ______________

Q32. Stop codon coordinates: ______________

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