Questions tagged [exons]
RNA Sequences corresponding to genomic regions which are retained in processed RNA (i.e., not spliced out).
23
questions
0
votes
0
answers
22
views
Availability of information on genes in Gnomad VCF data
Im new to gnomad and genetics in general and i was wondering does the gnomad genome data that is downlaoded in the vcf format on variants contains information of what is the nearest gene and is the ...
1
vote
0
answers
30
views
Location of Kozak Sequences
Are Kozak sequences always found within the first exon? I know that the first exon must be right next to the promoter so that RNA polymerase can start transcription, but just wondering how that would ...
- 111
1
vote
1
answer
866
views
Primers spaning exon-exon junctions
I am trying to choose which of two primers is most appropriate to use in qPCR, based on if the primer spans an exon-exon junction or not, where the primer that does span an exon-exon junction is ...
- 131
2
votes
1
answer
71
views
Are there any proteins assembled from non-adjacent parts of the genome?
Many proteins are assembled from multiple exons with the introns between adjacent exons being spliced out. But are there any proteins that have unrelated to them exons in the middle of their sequence?
...
- 43
1
vote
1
answer
92
views
Can a gene be split between different genomic locations several kb appart? [closed]
Can you have exons and introns of the same gene separated by hundred of kb in a genome? If so, how is the full mRNA assembled in such distance?
I'm working on plant mitochondria and I've seen an ...
- 41
4
votes
1
answer
622
views
What are an internal and external exons?
I read the book: Essential Genetics and Genomics It has a table summarizing the properties of the "typical" human gene:
It has a gene feature Size of internal exon,...
- 299
1
vote
0
answers
127
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!
- 11
2
votes
1
answer
1k
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 ...
- 3,098
0
votes
1
answer
25
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 ...
- 820
0
votes
1
answer
243
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 ...
- 56
2
votes
0
answers
61
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 (...
- 21
7
votes
1
answer
1k
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 ...
- 113
3
votes
0
answers
74
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 ...
- 31
1
vote
1
answer
85
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 ...
- 321
4
votes
2
answers
2k
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 ...
- 151
3
votes
1
answer
54
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?
- 71
1
vote
1
answer
38
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
1
answer
62
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
1
answer
155
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). ...
- 33
3
votes
2
answers
3k
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'...
- 141
5
votes
2
answers
1k
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 ...
- 51
9
votes
3
answers
231
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 ...
- 5,721
19
votes
3
answers
3k
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 ...
- 5,721