Module 4: Splicing
Questions:
- List two ways in which the histograms are similar.
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List one way that the histograms differ (other than color).
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Recall that our other evidence (see Module 3) indicates that tra-RA extends from 9,851 to 10,846. How many gaps do you see in the histograms in this interval?
How many exons do you see?
Q5. Do females or males make more transformer mRNA or do they express it at about the same level?
Q6. Using the information you’ve gathered so far, make a diagram of the tra-RA (female specific) isoform with 3 exons and 2 introns. Represent exons as rectangular boxes, and introns as lines that connect the boxes. Number each exon and intron (start from left with ‘exon 1’).
Q7. Where is the promoter in relation to the exons and introns? Mark the putative Transcription Start Site with a bent arrow, pointing in the direction of transcription.
Q8. What is the coordinate of the last nucleotide in the female tra-RA exon 1?
Q9. What are the first two nucleotides of the female tra-RA intron 1?
Q10. What are the last two nucleotides of the female tra-RA intron 1?
Q11. What is the coordinate of the first nucleotide in the female tra–RA exon 2?
Q12. What are the last three nucleotides of the female tra–RA exon 2?
Q13. What is the coordinate of the last nucleotide in the female tra-RA exon 2?
Q14. What are the first two nucleotides of the female tra-RA intron 2?
Q15. What are the last two nucleotides of the female tra-RA intron 2?
Q16. What is the coordinate of the first nucleotide in the female tra-RA exon 3?
Q17. Using the information you’ve gathered so far, make a graphical picture of the tra-RA (female specific) isoform with 3 exons and 2 introns. Number each exon and intron. Add the coordinates for first and last nucleotide of the exons that you have found so far. Add the sequences of the splice donor and splice acceptor sites at the appropriate locations.
Q18. Where do you think the promoter is located in relation to your gene model? What evidence do you have to support your idea, using the evidence tracks we have displayed (Base Position, RNA-Seq Coverage, Exon Junctions)?