RNAinfo: Splicing signals Genefinding Splice site consensus
ESEs Genome Annotation Alternative Splicing RNA links

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This is Steve Mount's web page for gene annotation and splice site selection. The page was inspired by my review article in the American Journal of Human Genetics (PubMed; Journal)

I provide links on gene annotation (including cDNA alignment), genefinding, splicing signals (including splice site prediction), and specific comments on splice site consensus, ESEs and microexons. These pages, collectively accessible as www.RNAinfo.org, are a bit out of date right now (April, 2005) but under active revision.

mis-annotated gene


A list of selected documented microexons is available. Very small exons, or microexons, pose special problems for gene annotation. They are difficult to recognize using computational genefinding methods, and can even confound the alignment of cDNA and genomic sequences. Furthermore, because microexons are very often the site of alternative splicing, an understanding of how they are recognized (and regulated) is key to understanding gene expression.
References to genes with very small exons:

A conserved 9 nt. exon in invertase described by Simpson et al. 2000. Requirements for mini-exon inclusion in potato invertase mRNAs provides evidence for exon-scanning interactions in plants. RNA 6:422-433.

A 6 nt. exon in troponin T. Carlo et al. 2000 5' splice site-proximal enhancer binds SF1 and activates exon bridging of a microexon. Mol Cell Biol 20:3988-3995

The Drosophila melanogaster couch potato gene may have an exon of 1 nt.

The Drosophila melanogaster invected gene has an exon of 6 nt.

The Drosophila melanogaster fasciclin 1 gene has an exon of 9 nt. This microexon is flanked by an extended 3' splice site-like region devoid of AG dinucleotides (accession numbers AE003714, nt. 66,492-66,500; and M20545 nt. 1,141-1,149. This microexon also incorrectly annotated).

There is an alternatively spliced microexon of 3 nt. in the NCAM gene.

There is a conserved microexon in the troponin 1 gene that is 4 nt. in mammals and 7 nt. in birds.