Pseudoexons

Abstract

A pseudoexon is a potential exon in intronic regions of pre‐mRNA that is not normally spliced into mature mRNA. It contains sequences similar to 5′ and 3′ splice‐site consensus sequences, but is not recognized by the cellular splicing machinery.

Keywords: intron–exon; pseudoexon; exon inactivation; splicing; silencer

Figure 1.

Distribution of conserved splice sites of real introns in six organisms. In these logo graphs, the information content ranges from zero to two. Zero signifies no conservation (all four nucleotides have equal probability of use) and two indicates the maximum degree of conservation (one nucleotide is present).

Figure 2.

Example of a pseudoexon, formed in intron 6 between exons 6 and 7 (open boxes) of the human gene encoding the growth‐hormone receptor (GHR): the pseudoexon sequence (6ψ) is located between the bar signs (‘|’) and is indicated in bold. Underlined letters indicate the base that when mutated activates the pseudoexon, which leads to pathological insensitivity to growth hormone. The mRNAs for both normal and mutant genes are shown above the genes (thick lines indicate exons in mature mRNAs).

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References

Gromoll J, Weinbauer GF, Skaletsky H, et al. (1999) The Old World monkey DAZ (deleted in azoospermia) gene yields insights into the evolution of the DAZ gene cluster on the human Y chromosome. Human Molecular Genetics 8: 2017–2024.

Huang CH, Xie SS, Socha W and Blumenfeld OO (1995) Sequence diversification and exon inactivation in the glycophorin A gene family from chimpanzee to human. Journal of Molecular Evolution 41: 478–486.

Long M and Deutsch M (1999) Association of intron phases with conservation at splice site sequences and evolution of spliceosomal introns. Molecular Biology of Evolution 16: 1528–1534.

Long M, de Souza SJ, Rosenberg C and Gilbert W (1998) Relationship between ‘proto‐splice sites’ and intron phases: evidence from dicodon analysis. Proceedings of the National Academy of Sciences of the United States of America 95: 219–223.

Metherell LA, Akker SA, Munroe PB, et al. (2001) Pseudoexon activation as a novel mechanism for disease resulting in atypical growth‐hormone insensitivity. American Journal of Human Genetics 69: 641–646.

Saxena R, Brown LG, Hawkins T, et al. (1996) The DAZ gene cluster on the human Y chromosome arose from an autosomal gene that was transposed, repeatedly amplified and pruned. Nature Genetics 14: 292–299.

Schneider TD and Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Research 18: 6097–6100.

Schneider TD, Stormo GD, Gold L and Ehrenfeucht A (1986) Information content of binding sites on nucleotide sequences. Journal of Molecular Biology 188: 415–431.

Sun H and Chasin LA (2000) Multiple splicing defects in an intronic false exon. Molecular and Cellular Biology 20: 6414–6425.

Vilches C, Pando MJ and Parham P (2000) Genes encoding human killer‐cell Ig‐like receptors with D1 and D2 extracellular domains all contain untranslated pseudoexons encoding a third Ig‐like domain. Immunogenetics 51: 639–646.

Further Reading

Burge CB, Tuschl T and Sharp PA (1999) Splicing of precursors to mRNAs by the spliceosomes. In: Gesteland RF and Cech TR, Atkins JF (eds.) The RNA World, 2nd edn. pp. 525–560. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Stephens RM and Schneider TD (1992) Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. Journal of Molecular Biology 228: 1124–1136.

Web Links

GenBank Database. This is a sequence database run by National Center for Biotechnology Information, National Institutes of Health, USA. It collected all publicly available DNA sequences http://www.psc.edu/general/software/packages/genbank/genbank.html

Deleted in azoospermia (DAZ). LocusID: 1617. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=1617

Growth hormone receptor (GHR). LocusID: 2690. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=2690

Glycophorin B (GYPB). LocusID: 2994. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=2994

Hypoxanthine phosphoribosyltransferase 1 (HPRT1). LocusID: 3251. LocusLink: http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=3251

Deleted in azoospermia (DAZ). MIM number: 400003. OMIM: http://www.ncbi.nlm.nih.gov/htbin‐post/Omim/dispmim?400003

Glycophorin B (GYPB). MIM number: 111740. OMIM: http://www.ncbi.nlm.nih.gov/htbin‐post/Omim/dispmim?111740

Growth hormone receptor (GHR). MIM number: OMIM: http://www.ncbi.nlm.nih.gov/htbin‐post/Omim/dispmim?600946

Hypoxanthine phosphoribosyltransferase 1 (HPRT1). MIM number: 30800. OMIM: http://www.ncbi.nlm.nih.gov/htbin‐post/Omim/dispmim?308000

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How to Cite close
Long, Manyuan(Jul 2006) Pseudoexons. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0005089]