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Exon-Intron™ database

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Also listed as: ExInt™
Related terms
Background
Methods
Research
Implications
Limitations
Safety
Future research
Author information
Bibliography

Related Terms
  • Chromosome, database, disease, DNA, Exon-Intron, expression, exon, gene, intron, PCR, polymerase chain reaction, RNA, splicing.

Background
  • Exon-IntronT (ExIntT) database is an electronic database that stores information about the exons and introns of genes. An exon is the part of a gene that stores information for making proteins, while an intron is a part of a gene that does not contain this information. In the DNA sequence of a gene, exons and introns are typically found next to each other.
  • DNA (deoxyribonucleic acid) is located in a compartment of the cell called the nucleus and is packaged in structures called chromosomes. Human cells contain 46 chromosomes, and each chromosome has hundreds of genes. Genes contain the instructions for making the proteins that perform all of the functions in the human body. Chromosomes also contain many other regulatory sequences that control how much of a gene will be made, when it will be made, and where in the body it will be made.
  • Expression refers to the process of converting a gene into a functional product. Cells express genes by making mRNA (messenger RNA), and RNA (ribonucleic acid) is then converted into proteins. Each gene produces its own unique mRNA. A gene is described as being expressed if mRNA for that gene is found in a cell. Measuring the amount of different RNAs in a cell can tell researchers how much of each gene is expressed by that cell. When a cell produces a specific mRNA, cellular proteins remove the introns from the mRNA and connect the exons to each other. This process is called splicing.
  • DNA contains four different chemical compounds called bases: cytosine, thymine, guanine, and adenine. In any given person, these bases are found in a particular order along the chromosomes, and it is the order of these bases that stores information for making genes. The order of these bases is distinct for each gene. Specific sequences of bases also provide information on where introns in a gene start and stop.
  • The ExIntT database stores information for sequences of introns and exons and where in each gene those introns and exons are located. The database also contains information on the intron nucleotide sequence, the amino acid sequence of the corresponding protein, and the position of the introns at the amino acid level.
  • Understanding the locations or sequences of introns may be important to researchers for several reasons. For example, some human diseases may be caused by mutations that affect the removal of introns. If introns are not removed from mRNA, the mRNA may produce proteins that do not function properly, which may lead to disease. Studying introns may help researchers better understand how a disease is caused or how intron sequences or locations may be used to help clinicians diagnose a disease.

Methods
  • The Exon-IntronT (ExIntT) database is an Internet database that is free to use and available to the general public.
  • The ExIntT database can be used to search for the exons and introns of human genes. Exons and introns of genes from other model organisms that researchers commonly use in experiments, such as mice, flies, and worms, can also be found in the database.
  • An individual may search the database in a variety of different ways: by using a gene name, the length of a DNA sequence, or a Genbank® identifying number (Genbank® is another Internet database where the sequence information of DNA is stored). Additionally, individuals may search the database using a specific DNA sequence, which may also be found in Genbank.
  • After a gene of interest is searched for, ExIntT generates a graphical representation of the DNA sequence of the gene. This graphical representation shows how many introns and exons are in the gene, how large they are, and where they are located. By clicking on the exons or introns, a user can see the specific DNA sequence of the exon or intron.

Research
  • Information obtained from the Exon-IntronT (ExIntT) database may be useful in a variety of contexts.
  • Studying diseases: Some human diseases may be caused by mutations that affect the removal of introns. When a cell produces a specific mRNA, cellular proteins remove the introns from the mRNA and connect the exons to each other. This process is called splicing. If introns are not properly removed from mRNA, the mRNA may produce proteins that do not function properly, which may lead to disease.
  • For example, retinitis pigmentosa is a genetically inherited eye disease that may lead to impaired vision and eventually blindness. Mutations in a gene called TULP1 that affect the proper splicing of the gene have been shown to cause the disease. The ExIntT database may be used to better understand how specific mutations may affect the structure of a gene or the mRNA and lead to abnormal protein production.
  • Diagnosing diseases: For many diseases, researchers have identified genetic mutations that are responsible for causing the disease. If a patient displays symptoms of a particular genetic disease, genetic testing may be used to help diagnose that patient by detecting the abnormal DNA. The ExIntT database may help to design specific genetic tests for diagnosing a patient. For example, the ExIntT database could be used to study the DNA sequence near the genetic mutation. This may help in designing probes (short sequences of DNA that can be used to detect a specific sequence) for polymerase chain reaction (PCR) experiments. PCR is a method that uses proteins called enzymes and nucleic acid probes called primers to amplify and detect genes and is commonly used in genetic testing to screen for mutations.
  • Studying evolution: The ExIntT database may be used by researchers to study the evolution of genes. This is because as genes evolve, the number of or DNA sequence of their exons and introns may change. For example, researchers may use the ExIntT database to look for differences in the same gene between humans and chimpanzees. Using the sequence information in the database, researchers may be able to identify changes in the human version of the gene that were not present in the chimpanzee version. These changes may result in differences in the protein made by the gene, which have the potential to influence human traits.

Implications
  • The Exon-IntronT (ExIntT) database contains a large amount of information about the intron and exon sequences of genes. By storing this information in one central location, this database makes it easier for researchers to find information. This may help speed up research on evolution and disease and may facilitate the design of genetic tests for diagnosing disease.

Limitations
  • The Exon-IntronT (ExIntT) database can tell a researcher which exons and introns a gene has, but it may not be able to provide definitive information regarding how evolutionary changes or mutations involving exons and introns affect the function of a gene. If researchers identify a specific genetic mutation or change in the DNA sequence of a gene, they may need to perform additional experiments to better understand how the mutation affects the function of the protein encoded by that gene.

Safety




Future research
  • Because the Exon-IntronT (ExIntT) database contains a large amount of information, it will be useful in helping researchers perform future experiments. For example, as new genetic mutations are identified and linked to diseases, the ExIntT database may be helpful in designing genetic tests to detect those mutations in patients. Additionally, as DNA from more species is sequenced, the ExIntT database may be useful in helping to understand how genes evolved in different organisms.

Author information
  • This information has been edited and peer-reviewed by contributors to the Natural Standard Research Collaboration (www.naturalstandard.com).

Bibliography
  1. Abbasi AH, Garzozi HJ, Ben-Yosef T, et al. A novel splice-site mutation of TULP1 underlies severe early-onset retinitis pigmentosa in a consanguineous Israeli Muslim Arab family. Mol Vis. 2008 Apr 21;14:675-82.
  2. Baralle D, Baralle M. Splicing in action: assessing disease causing sequence changes. J Med Genet. 2005 Oct;42(10):737-48.
  3. The Biotechnology Online School Resource. .
  4. ExInt Database Homepage. . Accessed August 5, 2008
  5. National Center for Biotechnology Information. .
  6. Natural Standard: The Authority on Integrative Medicine. .
  7. Sakharkar M, Long M, Tan TW, et al. ExInt: an Exon/Intron database. Nucleic Acids Res. 2000 Jan 1;28(1):191-2.
  8. Sakharkar M, Passetti F, de Souza JE, et al. ExInt: an Exon Intron Database. Nucleic Acids Res. 2002 Jan 1;30(1):191-4.
  9. Shepelev V and Fedorov A. Advances in the Exon-Intron Database (EID). Brief Bioinform. 2006 Jun;7(2):178-85.

Copyright © 2011 Natural Standard (www.naturalstandard.com)


The information in this monograph is intended for informational purposes only, and is meant to help users better understand health concerns. Information is based on review of scientific research data, historical practice patterns, and clinical experience. This information should not be interpreted as specific medical advice. Users should consult with a qualified healthcare provider for specific questions regarding therapies, diagnosis and/or health conditions, prior to making therapeutic decisions.

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