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Published on: April 22, 2021
WebScipio: Reconstructing alternative splice variants of eukaryotic proteins
Klas Hatje1, Björn Hammesfahr, Martin Kollmar
1Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen 37077, Germany.
Nucleic Acids Research
|May 17, 2013
Summary
WebScipio reconstructs gene structures from protein sequences and genome assemblies, now including alternative splicing variants using EST and cDNA data. This tool aids genomic and proteomic research by detailing gene structures for over 1100 species.
Area of Science:
- Genomics
- Proteomics
- Bioinformatics
Background:
- Accurate exon-intron structures are crucial for genomics and proteomics.
- Previous versions of Scipio and WebScipio enabled gene structure reconstruction.
- Gene structure analysis is vital for understanding protein families and single genes.
Purpose of the Study:
- To enhance WebScipio with a module for mapping expressed sequence tag (EST) and cDNA data.
- To identify all types of alternative splice variants.
- To improve the service for biologists studying gene structures, alternative splicing, and tandem gene duplicates.
Main Methods:
- Reconstruction of gene structures using protein sequences and genome assemblies.
- Prediction of mutually exclusive spliced exons and tandemly arrayed gene duplicates.
- Mapping of EST and cDNA data to reconstructed gene structures.
Main Results:
- The updated WebScipio server provides access to ~3400 genome assembly files from >1100 eukaryotic species.
- A new module allows for the identification of alternative splice variants.
- Gene structures can be analyzed graphically and at the nucleotide level.
Conclusions:
- The enhanced WebScipio offers improved functionality for gene structure analysis, including alternative splicing.
- The web server provides daily updated eukaryotic genome data.
- WebScipio is a user-friendly, freely available resource for biological research.
Related Concept Videos
02:18Alternative 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...
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...
02:18Alternative 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...
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...
01:32RNA 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...
01:32RNA Splicing
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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...
02:32Exon 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...
Exon shuffling follows “splice frame rules.” Each exon has three reading...