MATRICES USED IN RP PREDICTION

Lopez Lab - Carnegie Mellon

Fly RP Matrix

This matrix is based on the paper by Steve Mount, et al., (1992). The matrix is numbered so that the exon/intron boundary is between -1 and 1.

 -14-13-12-11-10-9-8-7-6-5-4-3-2-112345678
A2121222021192419101128510000060719113927
C2123162422372836282023680000192141321
G810999611654230010010003598261920
T4945534748393740576425270001004116682932

Mammalian RP Matrix

This matrix is based on Senapathy et al (1990) and Burge et al (1999). The matrix is numbered so that the exon/intron boundary is between -1 and 1.

 -14-13-12-11-10-9-8-7-6-5-4-3-2-1123456
A108669989662321000005474516
C313634343738444144402879000028618
G141412891098662610100100042118521
T44434852454440414548231800010028445

References

Burge, C.B., Tuschl, T. and Sharp, P. (1999) Splicing of precursors to mRNAs by the spliceosome, pp. 525-560 in The RNA World, edited by R. F. Gesteland, T.R. Cech, and J.F. Atkins. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

Mount SM, Burks C, Hertz G, Stormo GD, White O, Fields C (1992). Splicing signals in Drosophila: intron size, information content, and consensus sequences. Nucleic Acids Res. 20(16):4255-62.

Senapathy, P., Shapiro, M.B., and Harris, N.L. (1990) Splice junctions, branch point sites, and exons: Sequence stastics, identification, and applications to genome projects, pp 252-278 in Methods in Enzymology Academic Press.

Sequence Logos generated using enoLogos.