11
votes
Accepted
Can exons be located outside of the coding sequence?
Yes, of course. Exons are not limited to the protein coding regions. Many UTRs are in exons. In fact, you even have various cases of UTRs being multiple exons, and being spliced.
What is strange in ...
- 10.6k
8
votes
Can exons be located outside of the coding sequence?
Those are the untranslated regions (UTRs). All mRNAs have a 5' UTR and a 3' UTR. These give the ribosome something to grab onto and often contain important regulatory sites such as miRNA target sites.
- 1,779
5
votes
Accepted
5
votes
Accepted
On the same strand, for the same gene, can exons be overlapping?
I'm not quite sure what you're asking, but pretty much anything can happen in terms of exons and transcripts:
Two different genes encoded on different strands can share the same genomic region as an ...
- 15.1k
4
votes
Accepted
Availability of information on genes in Gnomad VCF data
This question has gone through some iterations and commentary, so I've decided to just answer it, though it's more of a "homework" question. What you need to do is to look at the VCF file, ...
- 4,252
2
votes
Pipeline for extracting gene from multiple genomes for use in HyPhy selection analyses?
Okay well, because you're using HYPHY, you're going to need a gene tree of every gene you intend to analyze. This requires you to understand the homology relationships between the genomes at hand. ...
- 347
2
votes
Get gene exons from UCSC browser by HGNC name
If you need a 3-column BED, you can just use standard Unix tools:
...
- 6,605
2
votes
Accepted
Get gene exons from UCSC browser by HGNC name
You could grab exons via Gencode v27 (hg38) GFF annotations and convert them to BED via BEDOPS convert2bed/gff2bed:
...
- 3,184
2
votes
Can exons be located outside of the coding sequence?
Although the explanation that UTR (untranscribed) regions can consist of multiple exons covers most situations, I think it is good to mention stop codon readthrough.
This would result in a CDS (...
- 445
2
votes
Accepted
Find the genomic locations of exons of certain human gene
Perhaps you could use this (assuming hg38) as a lookup table:
...
- 3,184
2
votes
Extract only exon regions from GFF/GTF file with input bed regions
Bedtools intersect will do this:
By far, the most common question asked of two sets of genomic features is whether or not any of the features in the two sets “...
- 15.1k
1
vote
1
vote
What is the tP statistic from ANGSD?
While I can't explain it to you directly, you might check out the section on theta estimators in Korneliussen et al. (2013) which is cited on the above ANGSD wiki page. The equation for this estimator ...
- 31
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