Questions tagged [splicing]

Splicing is a modification of an RNA after transcription, in which intervening nucleotide sequence sequences (introns) are removed and the remaining sequences (exons) are joined.

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Intein Splicing

Currently I am trying to read and understand this paper on intein splicing. https://sci-hub.tw/https://www.ncbi.nlm.nih.gov/pubmed/22001202 However, I'm a little confused with Figure 4. Why do the ...
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What do these novel splicing sites mean?

I'm sure that the anwser is obvious for some of you but I just endend my internship where we found novel splice junctions (junctionseq; RNAseq data) (see the attached file) and I have some ...
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Can you splice out the first and last exon from pre-mRNA?

I think the answer is no because there are no introns before the first exon or after the last exon, although I am not sure if this assumption is correct. Thanks!
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Meaning of acceptor/donor splicing sites? [closed]

What is the meaning of acceptor and donor in acceptor site and donor site expressions in the context of RNA splicing. Note that I know the biological meaning of these concepts. I am just intrigued by ...
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How big is the change in proteins due to alternative splicing?

How different can the proteins be that are coded from the same DNA-sequence but undergoe alternative splicing? What I am trying to wrap my head around is why we are so fixated with the DNA-sequences ...
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Can nerves in the human body be spliced with a form of electric wire?

This may be a ridiculous question, and is hypothetical, but I'd like a well-supported answer. Is it possible to splice copper wire (for example) into the human nervous system? Would the charge ...
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Can elementary alternative splicing events be combined in more complex events?

I'm a computer scientist who is trying to understand alternative splicing. As the title says, I'm here to ask you if, from a biological point of view, elementary/basic alternative splicing events (...
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Splicing and “the dominance of RNA-world”

This is a paragraph from my textbook. The significance of such complexities is now beginning to be understood. The split-gene arrangements represent probably an ancient feature of the genome. ...
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non-coding RNA modelling in silico

I've been trying to model a non-coding RNA molecule which binds to a RNA binding protein. I found the DNA sequence for ncRNA from NCBI. I did not find the RNA seq of the same. Hence my doubt is, ...
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How often does pre-mRNA processing lead to midstream off-frame errors in eukaryotic mRNAs?

As I understand it, the splicing of introns from pre-mRNAs is not incredibly precise. I've only ever seen nucleotide position ranges given in any description of the involved processes. Since there is ...
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Do transcripts always start and end with exons?

I realized that in all cases of "RefSeq Genes" annotations of hg19 I looked at spliced transcripts start (and end) with an exon. From the annotation there is no evidence of any sequence upstream or ...
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What's the difference between CREs and DHSs?

I would like to know what's the difference between cis-regulating elements and DNase I–hypersensitive sites, in order to produce a meaningful segregation of non coding elements affecting gene ...
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How to predict the effect of a non coding SNP variant on the expressed protein?

I am writing a paper for non coding SNPs on patients with metastatic breast cancer. Having used a specific gene panel (NGS) of approximately 60 genes, I'm currently running out of ideas on what to ...
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877 views

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

When the DNA from the nucleus is transcribed to an mRNA, the mRNA is spliced by an enzyme before it goes outside through the nuclear pore. What is the name of this enzyme and how does it recognize ...
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574 views

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

I only know splice variants are produced by different combinations of introns and exons. I wish to know why there is a need of such function. Perhaps using the same amount of DNA sequence to produce ...
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Are there constraints on where intron/exon boundaries occur with respect to the triplet codons of the reading frame?

I did a quick search (here and elsewhere) and couldn't find anything on this subject. If all introns in a given primary transcript were spliced out in the same way, then this wouldn't matter. But ...
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Exon skipping in mammals

I've heard from several sources that the predominant form of alternative splicing (at least in mammals) is exon skipping. However, my personal evidence is only anecdotal: I've heard it and read it, ...
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Why aren't introns found on the ends of pre-RNA?

We recently learned in genetics class that exons always cap the ends of nascent RNA. I have been trying to figure out the reason why introns can't instead be found on the ends instead of exons. The ...
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Trimming of tRNA precursors

From Molecular Biology of the Cell (4th edition) by Bruce Alberts et al. (Chp 6, Pg 338) : Both bacterial and eucaryotic tRNAs are typically synthesized as larger precursor tRNAs, and these are ...
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What are some examples of genes that code for multiple proteins?

The title pretty much says it all. It is widely taught that a gene in a eukaryotic system could produce more than one protein due to post-transcriptional modification, but I do not believe I have come ...
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How cotranscription events affect splicing?

I want to know how and how often does cootranscription takes place? Can transcription regulators influence splicing during cotranscription?
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What regulates these two methods of splicing?

Alternative splicing can shuffle the exon order and select from the exon sequence of a single gene site to provide a combinatorial selection of possible transcription products from the one gene. Can ...
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Are some non-coding RNA spliced?

Are some non-coding RNA spliced like mRNA? I tried to find some information but I don't find anything...
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Altering the human genome

I recently had a conversation with a rather unusual gentleman who was, let's say, more than a little partial to conspiracy theories. He has this idea that governments are lowering "nanowires" from ...
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What are limiting factors for intron length?

For predicting genes from a sequenced genome, you need to set a maximum intron length. How long can introns get in animals? Is there some limit?
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What are the mechanism binding histone code with alternative splicing?

There are some bioinformatical considerations showing that there is a significant correlation of some between histone code and alternative splicing; but what are the hypothesis about the underlying ...
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Is exon order always preserved in splicing?

Are there any cases in which the splicing machinery constructs an mRNA in which the exons are not in the 5' -> 3' genomic order? I'm interested any such cases, whether they involve constitutive or ...