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Related Concept Videos

Leaky Scanning02:28

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 stands for...
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RNA editing is a post-transcriptional modification where a precursor mRNA (pre-mRNA) nucleotide sequence is changed by base insertion, deletion, or modification. The extent of RNA editing varies from a few hundred bases, in mitochondrial DNA of trypanosomes, to a just single base, in nuclear genes of mammals. Even a single base change in the pre-mRNA can convert a codon for one amino acid into the codon for another amino acid or a stop codon. This type of re-coding can significantly affect the...
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Point and Frameshift Mutations

Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
Alternative RNA Splicing02:18

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.
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Alternative RNA Splicing02:18

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.
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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. 
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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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AlterORF: a database of alternate open reading frames.

Inti Pedroso1, Gustavo Rivera, Felipe Lazo

  • 1Center for Bioinformatics and Genome Biology, Life Science Foundation, MIFAB and Andrés Bello University, Santiago, Chile and Department of Informatics, University of Santiago, Santiago, Chile.

Nucleic Acids Research
|December 22, 2007
PubMed
Summary

AlterORF is a new database detailing alternate open reading frames (ORFs) in prokaryotic genomes. This resource aids in improving genome annotation and identifying novel protein-coding genes.

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Genome annotation is crucial for understanding gene function.
  • Prokaryotic genomes contain numerous genes with potential for alternate open reading frames (ORFs).

Purpose of the Study:

  • To introduce the AlterORF database, a comprehensive resource for alternate ORFs.
  • To facilitate the identification of prokaryotic genes encoding proteins in multiple reading frames.
  • To enhance the accuracy of prokaryotic genome annotation.

Main Methods:

  • Compilation of alternate ORF data from 481 prokaryotic genomes.
  • Development of a searchable database containing over 1.5 million gene entries.
  • Implementation of a web interface for database access.

Main Results:

  • The AlterORF database provides information on over 1.5 million genes across 481 prokaryotic genomes.
  • The database successfully catalogs alternate open reading frames (ORFs).

Conclusions:

  • AlterORF serves as a valuable platform for prokaryotic genome annotation.
  • The database aids researchers in discovering novel protein-coding genes through alternate ORFs.