Stack Exchange Network

Stack Exchange network consists of 175 Q&A communities including Stack Overflow, the largest, most trusted online community for developers to learn, share their knowledge, and build their careers.

Visit Stack Exchange

Questions tagged [exons]

RNA Sequences corresponding to genomic regions which are retained in processed RNA (i.e., not spliced out).

1
vote
0answers
81 views

Can you splice out the first and last exon from pre-mRNA?

I think the answer is no because there are no introns before the first exon or after the last exon, although I am not sure if this assumption is correct. Thanks!
0
votes
1answer
175 views

Clarification on RefSeq Genes track on IGV

The following picture is a snapshot of the RefSeq Genes track (collapsed) on IGV. I know that the bold blue line indicates exons and the thin one indicates introns. However, I cannot find what the ...
0
votes
1answer
22 views

Which matched normal(s) to use when computing CNAs from exome data with a Read-Depth approach

I want to use a Read-Depth algorithm to call copy number alterations (CNAs) from Whole Exome Sequencing data (WES) of a specific tumor. I have a set of WES tumor samples, some of which also have the ...
0
votes
1answer
132 views

Confirming exon shuffling in a gene

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 ...
2
votes
0answers
53 views

Can elementary alternative splicing events be combined in more complex events?

I'm a computer scientist who is trying to understand alternative splicing. As the title says, I'm here to ask you if, from a biological point of view, elementary/basic alternative splicing events (...
6
votes
1answer
957 views

Whole Genome Sequencing vs Whole Exome Sequencing

I am working on a project where I want to discover causative genes for a certain disease I may have. I was wondering whether to get WGS or WES to perform this experiment:- I am looking at SNP's and ...
3
votes
0answers
64 views

What are the reasons which make intron detection uncertain?

Intron/exon sequence detection seems to involve statistical prediction which can at best deliver a guess (until experimentally confirmed) as to where the splice site is. What are the reasons why ...
1
vote
1answer
74 views

Is there a good site or software to see if a primer pair spans an exon junction?

I am going to perform some RT-qPCR tests to validate an experiment.  I'm currently in the process of ordering primers, and I would like to get them from the Harvard Primer Bank since these have been ...
4
votes
2answers
1k views

Can intron become exon in alternative splicing?

From this image We can see several exons that are actually introns in other genes. It's not a really a different gene, it's an alternative splicing of a gene. My background is not biology so is it ...
1
vote
0answers
36 views

Is intron removal coordinated?

Are the introns present in a nascent rna molecule removed simultaneously or are they removed in some sort of sequential fashion or is removal completely random?
1
vote
1answer
32 views

A question on exclusion of study participants for an Exome genotyping array

I'm reading a paper that used whole exome sequencing on an African American and European populations to discover novel low frequency and rare variants associated with lipid levels & the risk of ...
1
vote
1answer
53 views

Investigating rare variants in ethnically different populations (European ancestry & African ancestry)

If you are investigating low-frequency and rare variants for a complex trait using exome sequencing, why would one consider using different populations (African ancestry and European ancestry) ...
1
vote
1answer
117 views

Omics integration questions [closed]

Let's say that I have a population of Mus musculus in the lab. I divide it in a control group and a test group. The test group is constantly subjected to a stress (example: elevated UV radiation). ...
3
votes
2answers
2k views

Detecting Introns and Exons

I know that when RNA is transcribed from the original strand of DNA it contains introns and exons, and that the introns are spliced out of the strand to provide genetic diversity. However, what I don'...
5
votes
2answers
940 views

How to find Exons in mRNA Computationally

I'm having trouble finding a method to find exons in the original DNA sequence used to create the mRNA, even given the sequence of the mRNA, as I cannot find a way to reliably identify the beginning ...
9
votes
3answers
209 views

What are the limiting factors for gene length and number of exons?

I recently downloaded gene annotations for Homo sapiens from Ensembl for some bioinformatic analysis. The vast majority of the gene annotations have 20 exons or less, although there are some that have ...
17
votes
3answers
2k views

Is exon order always preserved in splicing?

Are there any cases in which the splicing machinery constructs an mRNA in which the exons are not in the 5' -> 3' genomic order? I'm interested any such cases, whether they involve constitutive or ...