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Finished
Outline
" Exon-intron structure of genes
" Models of gene grammar
Example: Genscan
" Models of exon-intron sequence
" Integrating intrinsic, extrinsic information
Example: GenomeScan
" The RNA splicing code
Central Dogma
DNA 1:1
ACCGGACCGATGCGACTGCCCGAGGACTAGATAT
TGGCCTGGCTACGCTGACGGGCTCCTGATCTATA
RNA 1:1 *
GACCGAUGCGACUGCCCGAGGACUAGA
M R L P E D
Protein 3:1
MRLPED
Pre-mRNA Splicing
U2 snRNP
U1 snRNP
U1 snRNP
U2 AF6 5
intron definition exon definition
U2 AF3 5
SR proteins
...
branch signal 5 ’ splice signal
5 ’ splice signal 3 ’ splice signal
exonic repressor polyY
exonic enhancers
intronic enhancers
intronic repressor
...
Human Splice Signal Motifs
http://genes.mit.edu/pictogram.html
Semi-Markov HMM Model
Genome Scale Gene Finding Strategies
Strategy Based on Examples
Ab initio prediction Models of Genscan, GRAIL
gene GenLang,
Microarray structure/co
Hybridization hmmgene
Exon-scanning
mp array
Gene inference Homology GenomeScan
U2 snRNP
U1 snRNP
U1 snRNP
U2 AF6 5
intron definition exon definition
U2 AF3 5
SR proteins
...
branch signal 5 ’ splice signal
5 ’ splice signal 3 ’ splice signal
exonic repressor polyY
exonic enhancers
intronic enhancers
intronic repressor
...
Human Splice Signal Motifs
U2 snRNP
U1 snRNP
U1 snRNP
U2 AF6 5
intron definition exon definition
U2 AF3 5
SR proteins
...
branch signal 5 ’ splice signal
5 ’ splice signal 3 ’ splice signal
exonic repressor polyY
exonic enhancers
intronic enhancers
intronic repressor
...
Characterizing the sources of
information used for splicing
Yeast 90 43 98 86
Elegans 95 92 97 95
Fly 92 88 96 94
Arabidopsis 82 68 96 92
Human 76 65 88 85
Fivefold cross-validated
Top Ten Intronic Pentamers
Arabidopsis Drosophila Human