Introns/Exons - Sequence analysis (Mar/10/2008 )
Hello,
I have done PCR, sequenced my products and found polymorphisms in my sequences. Now my boss has asked me to label my sequence into exons and introns, ORFs etc but I do not how to do this. Is there a programme or website that I can use? I know exons are the coding regions and stop codons end them but do i have look through sequence by eye and where does coding start?
Thank you very much for any help.
JillyBee x
I have done PCR, sequenced my products and found polymorphisms in my sequences. Now my boss has asked me to label my sequence into exons and introns, ORFs etc but I do not how to do this. Is there a programme or website that I can use? I know exons are the coding regions and stop codons end them but do i have look through sequence by eye and where does coding start?
Thank you very much for any help.
JillyBee x
Try Ensembl Genome browser (http://www.ensembl.org/index.html) or UCSC genome browser (http://genome.ucsc.edu/). These websites let you search after sequences, and can show you sequence information including exons, introns, translation to protein, alignments, etc.
Here are some additional sites that might be of help. Have not tried all of these, but some of them are quite nice.
Orf prediction sites
Splice site prediction sites
Good luck!
hello jillxca
there is a previous post in the dna methylation forum finding exon (should be in the bioinformatics i think, same as this one) that could give you a hint of where to find your intros - exons. bioinformatics is a resource only, not the solution to the actual issues.
cheers.
tj
I have another question about intron/exons that I am curious if anyone could help me with.
I have been working on a phylogeny project for a gene that my lab is currently studying, and what I have found is that this gene has a tandem duplicate within 100kb of sequence (ie. they are both on the same BAC). Interestingly the tandem duplicate has an intron which is non-homologous and cannot be aligned.
I have been scouring the literature looking for similar cases but cannot seem to find any reference to this phenomenon.
How does a non-homologous intron arise?
Anyone have any ideas?
Thanks a bunch.
my first guess would be an insertion of a retrotransposon (or multiple) in one of the introns. Have you checked for a difference in the presence of repetitive elements in the introns? Do you have an idea how long ago the duplication took place?
i support the idea of repetitive element insertion in your tandem duplicate. you could also look for siRNA generation. or experimentally check the expression levels of one or the other copy.
cheers.
Thank you for your thoughts on this matter.
The duplication I'm looking at is pretty old and probably predates the diversification of this plant family, making it at least 25MYA. One of the paralogous genes was retained and is expressed while the other is a pseudogene and has been subjected to a number of frameshift mutations. This copy, as far as we can tell, is not expressed, not even partially.
Are there any programs one can use to find retrotransposon repetitive elements? What kind of signature should I look for?
You can use Repeatmasker (http://www.repeatmasker.org/cgi-bin/WEBRepeatMasker) to identify (and mask) repetitive elements. There are a number of plant species available which you can select. Depending on the origin of your sequence, it may be in the list or not. Otherwise I would take its closest relative.
If the duplication occurred that long ago, it's quite likely that you have had insertion of repetitive elements in the intronic sequences, leading to a strong divergence between the introns of the paralogs.