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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...

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...

Pre-mRNA Processing: RNA Splicing

Pre-mRNA Processing: 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

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...

Exon Recombination

Exon Recombination

The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon has three reading...

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Related Experiment Video

Updated: Jul 17, 2026

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression

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Published on: March 29, 2019

SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level.

Junichi Sugahara¹, Nozomu Yachie, Yasuhiko Sekine

¹Institute for Advanced Biosciences, Keio University, Tsuruoka, 997-0017, Japan.

In Silico Biology

|February 6, 2007

Summary

A new program called SPLITS efficiently identifies intron-containing and split transfer RNA (tRNA) genes in archaea. This tool aids in discovering novel tRNA genes within large genomic datasets.

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Area of Science:

* Molecular Biology
* Genomics
* Bioinformatics

Background:

* Archaea exhibit unique tRNA precursor structures, including introns in diverse gene locations (cis-spliced tRNA) and split tRNA genes requiring trans-splicing.
* Existing genome projects generate vast archaeal sequence data, but comprehensive methods for identifying these complex tRNA types are lacking.

Purpose of the Study:

* To develop a robust computational methodology for the genome-wide identification of intron-containing and split tRNA genes in archaea.
* To address the limitations in current tRNA gene searching strategies for archaeal genomic data.

Main Methods:

* Developed SPLITS, a program designed to search for various tRNA gene types, with a focus on intron-containing and split tRNAs.
* SPLITS identifies the bulge-helix-bulge motif characteristic of archaeal pre-tRNA introns to delineate and remove intronic sequences.
* Intron-removed sequences are subsequently processed by tRNAscan-SE for accurate tRNA gene prediction.

Main Results:

* SPLITS achieved 100% accuracy in predicting known tRNAs with single introns at unconventional sites and known split tRNAs.
* The program demonstrated 85.7% accuracy in identifying tRNAs with double introns.
* Successfully identified novel tRNA genes, demonstrating its utility in post-genome project analysis.

Conclusions:

* SPLITS provides a comprehensive and effective solution for identifying diverse tRNA gene structures in archaeal genomes.
* The tool significantly enhances the discovery of novel tRNA genes, particularly complex cis- and trans-spliced variants.
* SPLITS is freely available, facilitating further research in archaeal genomics and tRNA biology.