1. Introduction to Alternative Splicing and my research report
楊佳熒
2019/5/10

2. Genome browser
2019/5/10

3. Introduce NCBI refseq (genome annotation)
2019/5/10

4. Features of a Mammalian Gene
Transcription Start 5‘ 3‘
Exon 1
Intron 1
Exon 2
Intron 2
Exon 3
Acceptor splice site
Donor splice site GT AG GT AG
Pre-mRNA
Exon 1
Intron 1
Exon 2
Intron 2
Exon 3
5‘UTR
3‘UTR
Mature mRNA
Exon 1
Exon 2
Exon 3
Translation Start Stop codon
ORF
TAA
TAG
TGA
ATG (Met)
2019/5/10
Protein

5. 2019/5/10

6. 2019/5/10

7. Homology gene of the Human and Mouse and Rat (exon<=2)
Human and Rat
2019/5/10

8. An alternative splicing example
2019/5/10

9. background knowledge What is EST ?
short cDNA sequences prepared from mRNA extracted from a cell.
ESTs are used for identification of genes and don’t cover the
entire coding sequence of a gene.
2019/5/10

10. Research about alternative splicing
Dr. Chuang and I research about alternative splicing recently
2019/5/10

11. Study the data source of Alternative splicing
cDNA (complement DNA)
EST (Expressed Sequence Tag) DB
Assembling
TIGR
(The Institute of Genomic Research)
HGI(Human Gene Index)
2019/5/10

12. Part 1 : EST comparison indicates 38% of human mRNAs contain possible alternative splice forms
Brett D, Hanke J, Lehmann G, Haase S, Delbruck S, Krueger S, Reich J, Bork P.
FEBS Letters 474(2000)
2019/5/10

13. blastn
mRNA sequences
7867 mRNAs
EST databases
2019/5/10

14. Exon insertion Cryptic exon exon skipping 5’ exon extension
5’ exon trunction
2019/5/10

15. whole intron retention
3’ exon extension
3’ exon trunction
whole intron retention
2019/5/10

16. Exon deletion
2019/5/10

17. Experimental Result
In dataset, it contains 7867 mRNAs and extract 4560 candidate alternative splicing forms in 3011 human mRNAs.
Estimated at least 38% of human genes are alternatively spliced.
3192 exon deletions(70%) and 1368 exon insertion (30%)
2019/5/10

18. Part 2 : ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome
Larry Croft ,Soeren Schandorff , Francis Clark , Kevin Burrage ,
Peter Arctander and John S. Mattick
Nature Genetics, vol. 24, pp , (April, 2000)
2019/5/10

19. gene exon intron exon intron exon blastn 2698 unique genes
Intron sequences
EST databases
mapping
genomic sequences
exon
intron
exon
2019/5/10

20. Exon insertion Cryptic exon exon skipping 5’ or 3’ exon extension
5’ or 3 ‘exon trunction
2019/5/10

21. Experimental Result
In dataset, it contain 2698 unique genes which contain at least one complete sequenced intron and two flanking exons.
We identified 582 different human genes showing unequivocal alternative splicing forms.
Estimated at least 22% of human genes are alternatively spliced.
2019/5/10

22. part1 : 22% part2 : 38% exon intron exon intron exon blastn
Intron sequences
EST databases
part2 : 38%
exon
intron
exon
intron
exon
exon
exon
exon
blastn
mRNA sequences
EST databases
2019/5/10

23. These two methods are very simple……
EST Databases
Databases
post
application
Blast Server
(localhost or NCBI)
2019/5/10

24. annotation results and visualization
Part 3 : Dr. Chuang and I research on AS recently
Human EST DB
Mouse EST DB
HGI
Reduction of EST matching results
Analysis of alternatively splicing
transcripts
MGI
alignment
alignment
Human genome
Human genome
annotation results and visualization
2019/5/10

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26. 2019/5/10

27. Test Result
2019/5/10