4. Consider the following gene structure: 2 3 4 120* 150 . 100 190 Exons are num

Question

4. Consider the following gene structure: 2 3 4 120* 150 . 100 190 Exons are number (1-4) and sizes are given (e.g. exon 1 is of size 120 nts). The transcript can initiate (begin) at either arrow and exons 2 and/or 3 can be spliced out (noted by dotted splice junctions) (a) (2pt) How many possible isoforms of this gene could exist? (b) (4pt) For each isoform, list the junction spanning RNA-seq read that would support its existence (c) (4pt) It was noted in class that longer read lengths will reduce the need for isoform inference algorithms. Assuming only single end reads, what is the shortest read length that would guarantee the ability to unambiguously identify all isoforms of this gene? For this question we require that a junction read must capture at least 5 bp of each adjacent exon

Explanation / Answer

A and b : There are five isoforms of gene would exist. One is when transcription starts from 1st transcription site and transcribes all exons 1, 2, 3 and 4. Second when transcription starts from 2nd initiation site and transcribes exons 2, 3 and 4. The others being:

3rd = 1,3,4

4th= 1, 4

5th= 2, 4

C: The shortest read length would be 10bp long. which is in between 1st and 2nd exons.

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