7

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. Normally I would not think it the role of this site to remedy deficiencies in text books. However, as this involves some interesting questions I will try to read ...


6

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 pre-donor) and the one that is 3' to the acceptor site (lets call it post acceptor) are joined together and the intronic sequence between them is removed. If ...


6

There are a large number of ways a protein variant can be produced by post translational modification. The question may seem obvious, but its really quite broad. I can start this out. I doubt I know all the ways a single transcript can produce variant proteins. A detailed description might be more like a review article than an answer here. First, ...


5

The answer is not simple - @shigeta mentioned a few mechanisms leading to single gene-to-multi protein relationships - and the answer is certainly not short (there are thousands of these genes). But anyway "alternative splicing" seems to be the primary mechanism according to this article, so rather than listing all alternatively splicing genes, here are the ...


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. ...


4

Trimming = removing RNA sequences from one end. Splicing = removing introns and joining exons back together.


4

Just for balance, here is an example of a single protein being constructed from two primary gene products (two separate genes involved) via protein splicing.


3

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 part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. Now, about the exceptions, alternative splicing: Here, ...


3

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-transcriptionaly is almost certainly not constant but will depend on a lot of factors & regulatory mechanisms. Another important detail is that this analysis / ...


3

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 will be aware, the spliceosome (at least for mRNA) is a highly sophisticated multi-component ribonuclear protein complex, and has functions to both splice out ...


3

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, calculated the distance between the CDS start and exon end Obtained the remainder after dividing this value by 3 (modulo) Commands: Command-1: awk 'BEGIN{...


2

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 type of exon known as a cassette exon is spliced out of the transcript together with its flanking introns (see the figure, part a). Exon skipping accounts for ...


2

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 by which such a thing can happen; Endo-ribonucleases can clip the ends of the transcript and this happens in the case of tRNA-processing. But as "splicing" ...


2

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 exon 4 142 exon 5 513 exon 6 122 exon 7 133 exon 8 108 exon 9 111 exon 10 110 Alernatively spliced isoform B of this gene gets different first exon. ...


2

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) are regions of chromatin that get digested during the DNAse treatment because they are exposed i.e. not protected by a protein (complex). The protein complex can ...


2

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. Processing can include the splicing out of introns or polyadenylation at the 3' end, for example. Mature RNA is (typically) spliced and polyadenylated. Second, ...


2

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) need to be in spatial proximity (point one), and the enzyme needs to be able to bind there, aka forming hydrogen bonds with the nucleotides, which is mostly ...


2

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 efficiency and reduced energy consumption. Consider that on average there are about 100,000 unique protein types being produced in a human cell [1], but the human ...


2

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, although I am pretty confident in the assertion. It is based on my own experience in both GWAS and EWAS literature reading. My research concerns methods for ...


1

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 to chromatin-level changes. De Conti et al. in their review "Exon and intron definition in pre-mRNA splicing" (2012 DOI: 10.1002/wrna.1140) note: Most ...


1

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 gene. About 80% of the exons on each chromosome are < 200 bp in length. < 0.01% of the introns are < 20 bp in length and < 10% of introns are more ...


1

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 each other, forming a junction of two exons. RNA-Seq reads that span such a splice junction site would not align very well to the genomic sequence, however if you ...


1

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 gene product or introduce premature stop codon (PTC). When PCT is recognized in cells, the spliced transcript is quickly degraded. This is called nonsense ...


1

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 for noncoding regulatory mutations, GRASP (Genome-Wide Repository of Associations between SNPs and Phenotypes) for noncoding eQTL and US National Human Genome ...


1

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 there are differences in exon inclusion or overall expression. Remember that 3'UTR variants can also imply differential degradation by miRNA. Tools like TargetScan ...


1

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): ACCTGTaccttgcaacttgcatAGCTGAC Which would be spliced to: ACCTCTGAC Note that the second codon consists of one nucleotide from exon1 and two from exon2. I'll try and update this with real world examples, but I can ...


1

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 spliceosome. These animation is showing this happening in real time. see> http://education-portal.com/academy/lesson/rna-splicing-of-introns-exons-and-other-forms-...


1

Co-transcriptional splicing (CTS) is very widespread. Different studies (which are done on different cell types) report different frequencies of CTS. Most of them report a frequency of ~0.8 in different cells except for mouse liver which was reported to have a frequency of 0.45 This is the article that summarizes these different studies. Can transcription ...


Only top voted, non community-wiki answers of a minimum length are eligible