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

Genome browser 2019/5/10

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

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

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

An alternative splicing example 2019/5/10

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

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

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

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

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

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

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

Exon deletion 2019/5/10

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

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. 340-341, (April, 2000) 2019/5/10

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

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

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

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

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

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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Test Result 2019/5/10