<p>These suggestions are based on your comment that you have the gene sequence.</p>

<p>For a statistical approach, you could formulate a null model and show that the sequence similarity you observe is much higher than expected under the null model, but reasonable under your exon shuffling model. Ideally, you would show this individually for each exon, to convince the reader about the exons' disparate origins. I'll propose a reasonable null model, though suggestions are gladly accepted here. Pick a random gene, assume it's built using exon shuffling, and search the rest of the transcriptome for sequences that best substantiate that argument. </p>

<p>For an evolutionary approach, you could search for orthologs (homologues? I never remember the difference) of your gene in other species. Hopefully, the results would show that your gene formed more recently than the exons it's built out of. If your gene actually has some other origin, maybe you'll find out it's older than some of its putative components. This can't exactly "confirm" your hypothesis, but it will test your hypothesis and just be generally a cool thing to try.</p>

CC BY-SA 3.0
2017-11-05T21:31:53.310Z
2017-11-05T21:31:53.310Z
eric_kernfeld
<p><em>Note: this question has also been asked on <a href="https://www.reddit.com/r/bioinformatics/comments/6udxef/how_to_confirm_a_gene_is_derived_by_exon/?st=j6hk7ejm&amp;sh=885530b6" rel="nofollow noreferrer">reddit</a></em></p>

<p>I'm trying to confirm that the sequence of a novel gene is derived by exon shuffling between several different genes. I have the promoter sequence, gene sequence, and mRNA (with defined exon/intro boundaries). I've tried performing several database searches with the sequences, but each search produces a set of different unrelated hits. How would one go about using this info to confirm the exon shuffling hypothesis? Any tips are appreciated. Thanks!</p>

CC BY-SA 3.0
2017-08-18T06:48:27.377Z
The best proof is showing it in the wet lab. Try to clone your shuffled exon gene (cDNA made from mRNA), and sequence it the old fashion way (Sanger).
benn
<ngs><sequence-analysis><molecular-genetics>
How to confirm exon shuffling in a gene?
# How to confirm exon shuffling in a gene?

(Asked by: username_0 on 2017-08-18)

*Note: this question has also been asked on [reddit](https://www.reddit.com/r/bioinformatics/comments/6udxef/how_to_confirm_a_gene_is_derived_by_exon/?st=j6hk7ejm&sh=885530b6)*

I'm trying to confirm that the sequence of a novel gene is derived by exon shuffling between several different genes. I have the promoter sequence, gene sequence, and mRNA (with defined exon/intro boundaries). I've tried performing several database searches with the sequences, but each search produces a set of different unrelated hits. How would one go about using this info to confirm the exon shuffling hypothesis? Any tips are appreciated. Thanks!

**Tags:** ngs, sequence-analysis, molecular-genetics
> **Comments:**
> **username_1**: The best proof is showing it in the wet lab. Try to clone your shuffled exon gene (cDNA made from mRNA), and sequence it the old fashion way (Sanger).  

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## 1 answers

### Answer by username_2 on 2017-11-05. Score: 1

These suggestions are based on your comment that you have the gene sequence.

For a statistical approach, you could formulate a null model and show that the sequence similarity you observe is much higher than expected under the null model, but reasonable under your exon shuffling model. Ideally, you would show this individually for each exon, to convince the reader about the exons' disparate origins. I'll propose a reasonable null model, though suggestions are gladly accepted here. Pick a random gene, assume it's built using exon shuffling, and search the rest of the transcriptome for sequences that best substantiate that argument.

For an evolutionary approach, you could search for orthologs (homologues? I never remember the difference) of your gene in other species. Hopefully, the results would show that your gene formed more recently than the exons it's built out of. If your gene actually has some other origin, maybe you'll find out it's older than some of its putative components. This can't exactly "confirm" your hypothesis, but it will test your hypothesis and just be generally a cool thing to try.


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