Alternative splicing analysis tools through the UCSC genome browser

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Alternative splicing analysis tools through the
UCSC genome browser

• Part I

Splicing fundamentals Splicing regulatory
sequences tools
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Gene structure
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Exon recognition elements
5 splice site
branch site
3 splice site
U1
XXCAUUCA
AGGUAAGU----------------A------(Py)nNCAGG
Exon 1
Exon 2
Intron
Polypyrimidine tract
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The mechanism of pre-mRNA splicing
branch-point adenosine
5 splice site
3 splice site
Exon 1
Intron
Exon 2
5-
-3
pre-mRNA
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trans-esterification
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trans-esterification
ligated exons
lariat intron
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Splicing is carried out by the spliceosome

• Several steps in the splicing reaction require ATP

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(No Transcript)
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Gene structure
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Exon recognition elements
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Alternative Splicing
pre-mRNA
Intron 20
Intron 19
Normal splicing
Alternative-splicing
mRNA
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Types of Alternative Splicing
Exon Skipping
Alternative 3ss
Alternative 5ss
Intron Retention
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Finding ESEs ESSs

• Experimentally (SELEX)
• Computationally
• Exons VS Introns
• Exons VS pseudo-exons (pseudo-genes)
• Exons with strong VS weak splice signals
• Overabundant and/or over-conserved k-mers

Finding ISEs ISSs
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(No Transcript)
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gtEXON ATTGGAGATCTCACTGGGTATTGCACCAATCCGAACCGTCATCA
GATGGGGTGGGCTAAACGCAATGTGGACCACCGCCCTAAGAGCAACAGTA
TGGTGGATGTCTGCTCAGTGGACCGCCGCTCAGTGCTGCAGAGGATCATG
GAGACGGACCCCCTGCAACAGGGCCAGGCTCTGGCATCTGCCCTGAAAAA
T AAGAAGAAGATGCAGAAACGTGCAG
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(No Transcript)