7 votes
Accepted

Splicing and “the dominance of RNA-world”

This is a badly-worded phrase that means nothing in the context of the paragraph in which it occurs. There is no way the reader could be expected to understand it from this awful book on its own. ...
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6 votes
Accepted

Do transcripts always start and end with exons?

Most (almost all, AFAIK) mRNAs and lncRNAs start with exons for the reasons already mentioned by David. In a typical splicing event, the nucleotide that is 5' to the splice donor site (lets call it ...
  • 35.1k
5 votes
Accepted

What are an internal and external exons?

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....
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3 votes
Accepted

What percentage of RNA splicing happens during transcription?

I don't think it will be possible to give a conclusive answer to this question, because a) it's a matter of active research and b) the rate / percentage of transcripts that are fully spliced co-...
  • 4,316
3 votes

Why is an intron (or exon) still called intron (exon) if retained in (excluded from) mRNA?

You must know that: Introns are non-coding regions of an RNA transcript, or the DNA encoding it, that are eliminated by splicing before translation. An exon is any part of a gene that will encode a ...
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3 votes

Do transcripts always start and end with exons?

As far as I am aware, transcripts always start and end with exons. The reasons I wouldn’t expect otherwise (apart from my observations when examining Drosophila transcripts) are given below. As you ...
  • 22.7k
3 votes

Are there constraints on where intron/exon boundaries occur with respect to the triplet codons of the reading frame?

As pointed out by others this is not true. I just verified this for humans (annotations from gencode21). Methodology: Obtained the start points of the CDS for all genes For each exon of each gene, ...
  • 35.1k
2 votes

Exon skipping in mammals

You can see this review. There are several different types of alternative splicing (AS) events, which can be classified into four main subgroups. The first type is exon skipping, in which a ...
  • 35.1k
2 votes

Why aren't introns found on the ends of pre-RNA?

RNA splicing refers to a certain kind of RNA processing mechanism which leads to the excision and exclusion of some regions of the primary transcript. You should note that this is not the only method ...
  • 35.1k
2 votes

Are there constraints on where intron/exon boundaries occur with respect to the triplet codons of the reading frame?

Here is exon size data of some random gene (human ROR-gamma). Link: http://www.ncbi.nlm.nih.gov/nuccore/NM_005060.3 It gets cut at all three possible positions of codon: exon 2 30 exon 3 86 ...
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2 votes
Accepted

What's the difference between CREs and DHSs?

Cis-regulatory elements are simply DNA regions upstream or downstream of a gene that can affect its expression (basically they have to be in the same chromosome). DNAse-I hypersensitive sites (DHS) ...
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2 votes

Do transcripts always start and end with exons?

Thank you for a great question. I would like to start by clarifying some terminology. First, nascent RNA refers to an RNA molecule that is currently being transcribed and has not been processed. ...
2 votes
Accepted

How does the splicing enzyme recognize where to splice the introns?

There are two factors that involve the ability of enzymes to process RNA. 1) Structure see wikipedia 2) Binding affinitya Let's take a look at the splicing process: The active 'sites' (GU,A & AG)...
2 votes
Accepted

Why are there splice variants within the same organism? What might contribute to the need for the feature?

The reason is very simply to provide enough variation in a limited sized genome to produce the repertoire of proteins produced by the cells of multicellular organisms. It is also a matter of ...
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2 votes
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How big is the change in proteins due to alternative splicing?

For your first question, They can vary dramatically. I did not originally post as a formal answer because my statement below is hard to cite a source and would therefore be somewhat subjective, ...
  • 1,309
1 vote
Accepted

How is it determined which parts of an mRNA precursor are to be spliced?

Your question is a good one, and has given rise to decades of intensive research, which continues today. The short answer is that many factors are involved, ranging from sequences within the gene up ...
  • 1,699
1 vote

Can a gene be split between different genomic locations several kb appart?

Yes you can have exons and introns of the same gene separated by hundred (even thousands!) of kilobases. Here is an example for the human genome: "On average, there are 8.8 exons and 7.8 introns per ...
1 vote

What do these novel splicing sites mean?

A splice junction is formed from a pre-mRNA (or primary transcript) whenever an intron is removed, or spliced out. Two segments of RNA that used to be separated in the pre-mRNA are now ligated to ...
  • 3,432
1 vote

Are there constraints on where intron/exon boundaries occur with respect to the triplet codons of the reading frame?

As Alex M shows, many lengths of exons are 3n+1 or +2. It seems cells do not care about in-frame. In some cases, exon insertion by alternative splicing shift the frame and produce a short version of ...
  • 1,116
1 vote

How to predict the effect of a non coding SNP variant on the expressed protein?

You could try DeepSEA. It uses deep learning approach to predict function of noncoding SNVs. They use ENCODE and Roadmap Epigenomics for chromatin structure learning, 1KG for nonfunctional SNVs, HGMD ...
1 vote

How to predict the effect of a non coding SNP variant on the expressed protein?

A) Generate exon & transcript counts for your samples, library size + quantile normalize the data. B) Group samples into variant/wild-type categories C) Use wilcoxon's rank sum test to see if ...
1 vote

Are there constraints on where intron/exon boundaries occur with respect to the triplet codons of the reading frame?

I don't have time to find examples right now but no, it's not true. You often get cases like this (lower case letters represent the intron): ...
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1 vote

Why aren't introns found on the ends of pre-RNA?

RNA splicing begins with assembly of helper proteins at the intron/exon borders. These splicing factors act as beacons to guide small nuclear ribo proteins to form a splicing machine, called the ...
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