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6

WES, almost certainly. First of all, the vast majority of phenotype-causing variants are found in exons. For most analyses that are looking into disease causing mutations, WGS is pointless. It only makes your analysis harder and doesn't actually add anything useful. If you know you're interested in CNVs, that's different. CNV detection is hard in general ...


5

Yes, the internal exons are those that aren't at the ends, which are often referred to as terminal exons1. However, exons are sequences of nucleotides that are incorporated into the mature mRNA — i.e. they don't have to be (entirely) protein coding. It is probably simplest to think of exons as being the transcribed regions that are not introns — i.e. ...


5

There are references in the literature to the phenomenon of "exon scrambling" which seems to be what you are asking about, but the prevailing view is that the evidence for this process, which comes from comparing EST sequences with genome sequences, can be explained by cloning artefacts occurring during EST characterisation. Certainly I agree that there is ...


4

The only information you are missing is a way to identify the splice sites. There are many ways of doing what you need. The simplest, assuming you are sure of the origins of the mRNA, is to use a BLAST flavor, either plain BLASTn or, even better, BLAT, to compare your mRNA sequence to the genome of interest. BLAT really should be all you need if the mRNA ...


3

I think that you are talking about trans-splicing. This does indeed happen. It is fairly common in protist organisms, though in humans it is quite rare. For more information about how this process works, including mechanisms in vertebrate organisms, see this paper. Here is one model from that last paper for how it works:


3

Quick answer: we don't really know. As WYSIWYG said, splice sites do have a sequence signature. The image below (taken from [1]) shows the consensus for human acceptor and donor sites: In the images above, the size of a nucleotide represents its frequency at that location. As you can see, there is a clear signal around the splice sites and this signal is ...


2

There are some signature sequence which mark intron-exon boundaries. Usually introns start with a GU and end with an AG. But this feature per-se is not sufficient for splicing; there are other cis-elements such as exon/intron splicing enhancers/silencers [ESE/ESS; ISE/ISS]. Refer this article. Also, there are protein regulators of splicing such as SR ...


2

You should ask this question over at biostars.org -- and could use a bit more clarity. Do you actually have RNA-seq data that you want to use to find the exon/splicing structure of an mRNA? First step would be to use a splicing-aware aligner. A few free ones are: STAR TopHat GSNAP Let us know why that wouldn't do what you want when you re-ask this ...


2

If there is a such a site, I have never encountered it. Since you say you have the genomic coordinates for each primer it seems to me like all you need is a list of the genomic coordinates of every transcribed exon in the human genome. Assuming that is correct then you are in luck because such lists do exist in the form of a GFF3 file. You should be able to ...


2

Most of the transcripts you show have different transcription start sites. In other words, this happens because of alternative transcription start sites. So this is not typical alternative slicing. Some genes have different transcriptional start sites, but the case you show has exceptionally many start sites.


2

Should I use genomics or/and exomics or/and epigenomics? Depends on what you want to look at. Whole genome sequencing will give you all the mutations. If you are interested only in the coding part of the genome then you can go for exome sequencing. Though, exome sequencing will save your time and resources considerably, you may lose out a lot of relevant ...


1

The thinnest blue line is intron, so not in your transcript. The medium thickness segment is untranslated exon, the thickest blue segment is translated.


1

For the detection of somatic copy nuber alterations it is best to compare each tumour sample with its matched normal. If you want to call CNVs for all your tumour samples and some don't have matched normals, then pooling together all the normal BAMs to create a reference may be the best way to standardise your calling.


1

It's not clear what is 'several database searches with the sequences'. The most obvious solution is blasting your sequence so you can see which part can't be aligned and then blasting the rest. You can choose different implementations (megablast of blastn) and play with algorithm parameters because it may not work for you as-is. But it will work as-is if you'...


1

If a portion of sequence ends up in the mature RNA, it is by definition not an intron (save for abnormal splicing events and rare intron retention). Specific to your question, it seems each form is under the control of its own promoter. This means that A8 will have to splice out the first exons of all other forms (this would be exon skipping). On the other ...


1

When you design the arrays, you need to have probes on the surface complementary to the sequence you want to detect. Depending on what you want to detect, you need to design these probes with known sequence on a known position. If you want to detect single nucleotide polymorphisms (SNP), then you need a library of known SNPs on your ChIP, which are basically ...


1

Too long for a comment, but sort of: Mainly you do this because these populations have segregated long time ago and developed differently, so it is more likely to identify these polymorphisms. It is also helpful to use populations for this which mixed not too much with other populations (thats why north-americans are usually not used here, as America was ...


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