Module 5: Translation
Questions:
Q1. First examine reading frame 1. Are there any stop codons in the reported exon? _______ If there are early stop codons, do you think this is the reading frame used during translation?__________________
Q2. Examine reading frame 2. Are there any stop codons in this reading frame within the exon? _________
Q3. Examine reading frame 3. Are there any stop codons in the reported exon? _______
Q4. Using the evidence above, which reading frame maintains an Open Reading Frame (ORF) across exon2 of tra-RA? _________________ Is this the same reading frame as that used for exon 1? _________
Q5. Give the coordinates for the entire start codon for tra-RA. (start codon coordinates should be three consecutive numbers, for example: nucleotides 212-214).
________________________
Q6. Which reading frame should we follow along to see the predicted amino acid sequence of tra-RA? _____________
Q7. Zoom out to see the entire exon. Are there any stop codons in this reading frame in the first exon? _______________
Q8. Give the coordinates for the very last base of the first exon. __________________
Q9. Knowing that exon 1 ends with a partial codon of 1 base, what reading frame is being used in the second exon? _____
Q10. Based on the evidence you see in the browser, give the coordinates for the first base of the second exon of tra-RA. _____
Q11. Do you observe an appropriate splice acceptor site just upstream within the intron? ________
Q12. Give the coordinate of the base prior to the 5’ splice site of intron 2 _________________
Q13. How many bases are left in the codon before the splice site, i.e. is this phase 0, phase 1, or phase 2? ______________________
Q14. Locate the 3’ splice site of Intron 2. Give the coordinate of the first base in exon 3 for tra-RA ________________
Q15. Which reading frame is being translated in the final exon? _________________
Q16. Give the coordinates for the bases in the stop codon. ______________________
Q17. Let’s consolidate all the data we found above in one place:
Gene model for tra-RA
Coordinate for start of translation: ____________________
Coordinate for last base of exon 1: ____________________
Coordinate for first base of exon 2: ____________________
Coordinate for last base of exon 2: ____________________
Coordinate for first base of exon 3: ____________________
Stop codon coordinates: ____________________
Take the coordinate information above to draw a map of tra-RA using rectangles to represent exons and connecting lines to represent introns. Label the ends of the exons with the appropriate coordinates and indicate the transcription start site for the tra-RA initial transcript. Below this map, provide a map of the processed mRNA after intron removal. Below this map, indicate the regions that are translated into a protein. Give precise coordinates. Color coding may be helpful.
Q18. To cement your knowledge of gene structure, you could construct a similar map of the spd-2 gene. How many exons does this gene have? _______How many introns? _____ How many isoforms? _______ Use the same approach to determine the coordinates for the exons, and the coordinates for the coding region (another name for the region that is translated).