Sequence Walkers with RNA Structures

A Y shaped RNA with two arms and a stem ont the bottom.

RNA structures can now be displayed with the lister program along with sequence walkers.

This page gives an example of mutations affecting the tau gene in humans, which cause inherited dementia FTDP-17 (M. Hutton et al Association of missense and 5'-splice-site mutations in tau with the inherited dementia FTDP-17 Nature 393 702-705: 1998). the mutations are interesting because they affect an RNA structure poised exactly over a donor site.


Sequence walker for a 6.6 bit human donor splice site at
the end of an exon shown overlapping a -9.9 kcal per mole
RNA structure.  Below this a mutated sequence in the
structure reduces its energy to -8.1 kcal per mole.
These results are inconsistant with the Hutton et al paper, since that paper gives a delta G of -5.2 kcal/mole based on the 1986 Freier data.


Sequence walker for a 6.6 bit human donor splice site at
the end of an exon shown overlapping a -9.9 kcal per mole
RNA structure.  Below this a mutated sequence in the
structure reduces its energy to -7.6 kcal per mole.


Sequence walker for a 6.6 bit human donor splice site at
the end of an exon shown overlapping a -9.9 kcal per mole
RNA structure.  Below this a mutated sequence in the
structure reduces its energy to -9.1 kcal per mole.


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The Mfold program was used to generate the foldings. It was written by Michael Zuker (zukerm@rpi.edu, http://www.rpi.edu/~zukerm/).

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Schneider Lab

origin: 1999 August 11
updated: 2000 Nov 7
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