Expressed sequence tag
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An expressed sequence tag or EST is a short sub-sequence of a transcribed spliced nucleotide sequence (either protein-coding or not). They are intended as a way to identify gene transcripts, and are instrumental in gene discovery and gene sequence determination. The identification of ESTs has proceeded rapidly, with approximately 37 million ESTs now available in public databases (e.g. GenBank 7/2006).
An EST is produced by one-shot sequencing of a cloned mRNA (i.e. sequencing several hundred base pairs from both ends of cDNA clones taken from a cDNA library). The resulting sequence is a relatively low quality fragment whose length is limited by current technology to approximately 500 to 800 nucleotides. Because these clones consist of DNA that is complementary to mRNA, the ESTs represent portions of expressed genes.
ESTs can be mapped to specific chromosome locations using physical mapping techniques, such as radiation hybrid mapping or FISH. Alternatively, if the genomic sequence of the organism origin of the EST is available one can align their sequence to the genome.
At the current state of our knowledge of the human set of genes (2006) there is no experimental verification of the existence of thousands of genes for which however there are EST evidence. In this respect, ESTs become a tool to refine the predicted transcripts for those genes, which leads to prediction of their protein products, and eventually of their function. Moreover, the situation in which those ESTs are obtained (tissue, organ, disease state - e.g. cancer) informs of the conditions into which the corresponding gene is acting. Even though a gene might have only EST data, it is possible to use these sequences as a resource for designing probes for DNA microarrays that then can be used to determine the gene expression.
Some authors use the term "EST" to describe genes for which little or no further information exists besides the tag<ref>http://www.ncbi.nlm.nih.gov/dbEST/how_to_submit.html</ref>
[edit] References
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[edit] External links
- The NCBI Handbook, Part 3, Chapter 21 has a very nice overview.
- ECLAT a server for the classification of ESTs from mixed EST pools (from fungus infected plants) using codon usage
- EST3 a server for the classification of ESTs from mixed EST pools (from fungus infected plants) using nucleotide triples
- The current number of EST sequences in the GenBank division dbESTde:Expressed sequence tag
