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RNA Splicing

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...

Alternative RNA Splicing

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...

Alternative RNA Splicing

Alternative RNA Splicing

Pre-mRNA Processing: RNA Splicing

Pre-mRNA Processing: RNA Splicing

Leaky Scanning

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...

pre-mRNA Processing

pre-mRNA Processing

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl...

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Related Experiment Video

Updated: Jan 15, 2026

ACT1-CUP1 Assays Determine the Substrate-Specific Sensitivities of Spliceosomal Mutants in Budding Yeast

ACT1-CUP1 Assays Determine the Substrate-Specific Sensitivities of Spliceosomal Mutants in Budding Yeast

Published on: June 30, 2022

Precursor RNA structural patterns at SF3B1 mutation sensitive cryptic 3' splice sites.

Austin Herbert¹, Abigail Hatfield¹, Alexandra Randazza¹

¹Department of Genetics and Biochemistry, Center for Human Genetics, Clemson University, Clemson, South Carolina, USA.

|October 8, 2025

Summary

This summary is machine-generated.

The SF3B1 K700E mutation common in blood disorders alters splice site recognition. SF3B1-sensitive cryptic sites have weaker, flexible sequences, distinguishing them from SF3B1-resistant sites.

Keywords:

3’ splice site RNA structure SF3B1 cryptic splice site myelodysplastic syndrome spliceosome

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Last Updated: Jan 15, 2026

ACT1-CUP1 Assays Determine the Substrate-Specific Sensitivities of Spliceosomal Mutants in Budding Yeast

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Published on: June 30, 2022

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Using the E1A Minigene Tool to Study mRNA Splicing Changes

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Published on: April 22, 2021

Area of Science:

Molecular Biology
Genetics
RNA Splicing

Background:

SF3B1 is crucial for spliceosome function, particularly 3' splice site selection.
The SF3B1 K700E mutation is prevalent in myelodysplastic syndromes and other blood disorders.
Mutant SF3B1 utilizes cryptic 3' splice sites, but their distinct properties remain unclear.

Purpose of the Study:

To identify and characterize SF3B1-sensitive cryptic 3' splice sites.
To determine sequence and structural features differentiating SF3B1-sensitive from SF3B1-resistant splice sites.
To understand how SF3B1 mutations impact alternative splicing.

Main Methods:

Bioinformatic analysis to identify SF3B1-sensitive and resistant cryptic splice sites.
Sequence analysis of polypyrimidine tracts and canonical splice site strength.
Chemical probing to assess RNA structural accessibility of splice sites.
Comparative analysis of RNA structural flexibility.

Main Results:

Identified 192 SF3B1-sensitive and 2800 SF3B1-resistant cryptic 3' splice sites.
SF3B1-sensitive sites feature extended polypyrimidine tracts and weaker flanking canonical splice sites.
RNA structural analysis revealed similar accessibility patterns but less pronounced differences in SF3B1-sensitive sites, indicating greater flexibility.

Conclusions:

SF3B1-sensitive splice junctions possess unique sequence and structural properties.
These junctions contain weak, poorly differentiated splice sites that are susceptible to altered recognition by mutant SF3B1.
Findings provide insight into the molecular mechanisms of SF3B1-mediated splicing defects in blood disorders.