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Analysis of Alternate Splicing in Human Genes

Analysis of Alternate Splicing in Human Genes. Name : Bingding Huang 　(黄炳顶) Email : markero@263.net Address : Bioinformation center of Shanghai Instutes for Biological Sciences Date : 08/31/01.

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Analysis of Alternate Splicing in Human Genes

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  1. Analysis of Alternate Splicing in Human Genes • Name: Bingding Huang　(黄炳顶) • Email: markero@263.net • Address:Bioinformation center of Shanghai Instutes for Biological Sciences • Date: 08/31/01

  2. The human genome sequence can be thought of as a picture of the human organism. However,like an impressionist painting,the genome is a very large canvas whose details becomes fuzzy when you look closely. • ---by Douglas L.Black

  3. Index • Definition:What is the alternative splice gene?Especially in human genes. • Mechanism:How the alternative splice genes work? • Type:How many types the alternative splice genes are? • Database:current databases and how to establish the corresponding database?Materials and method? • Future work:

  4. Definition

  5. Alternative Splicing is a major cellular process by which functionally diverse proteins can be generated from the transcript of a single gene,often in tissue-specific,patterns. As many as 30% of human genes utilize this mechanism to generate mature mRNA with difference in exon composition at the 5’-end,within internal coding regions or at the 3’-end.

  6. Mechanism

  7. How to predict the donor and acceptor sites? • GT---AG Rule:The donor site of introns in most eukaryotes usually contains GT(GU in pre-mRNA)while the acceptor site contains AG;a pyrimidine-rich region at 3’;a shorter consensus sequence at 5’;a very weak sequence at the branch point; • algorithm and Software: GeneSplicer, NetGene2,HSPL,NNSplice,HMMGene, Spliceview,and so on. • False or True: how to determine the false sites from true sites?

  8. Current Database • Intron Sequence Information System (ISIS) :ISIS contains phylogenetic and protein homology categories, information about individual sequences and various bioinformatics analyses of taxonomical groupings of sequences • Exon-Intron Database :An exhaustive database of protein-coding intron-containing genes. • Intron Sequence and Evolution DatabasesThis includes a non-redundant database of nuclear, protein-encoding, genomic DNA sequences highlighting nuclear pre-mRNA introns

  9. Types of alternate splicing gene

  10. Method 1,Data collection 2,Construction intron-EST homology dataset 3,Analysis of type and frequency of alternative splicing using intron-EST homolies 4,Construction of an exon-EST homology dataset 5,Analysis of exon skipping,exon extensions or shortening using exon-EST homologies

  11. Data Collection • GenBank and UniGene:entries contaiing alternative splice are picked out and recorded in a list. • EST: Download ESTs database from NCBI • Swiss-port :

  12. Intron-EST homologies • Contigs overlaping two flanking exons: a,cryptic exon; b, 5’exon extension; c, 3’exon extension; d,whole intron retention • Contigs overlaping one flanking exon:a,cryptic exon or exon extention; b,whole intron retention

  13. Contigs overlaping two flanking exons

  14. Contigs overlaping two flanking exons • cryptic exon: a1<b1 and a2<b2 The intron fragment was less than the size of the whole intron,from middle of the intron • 5’exon extension: a1<b1 and a2=b2 3’end of the intron was contained within in the EST contig • 3’exon extention: a1=b1 and a2<b2 5’end of the intron was contained within the EST conting • Whole intron retention: |CG—GG|<10 where the whole intron was contained in the contig

  15. Contigs overlaping one flanking exon

  16. Contigs overlaping one flanking exon • Cryptic exon or exon extension: CG<GG—10 • Whole intron retention: CG>=GG--10 ,

  17. Exon—EST homologies • EST contigs with matches to non-consecutive exons(eg.exon1-exon3) 1,perfect exon skipping 2,exon skipping with exon truncation • EST contigs with matches to consecutive exons (eg.exon1-exon2) 1,exon trucation 2,cryptic exon or 3’or 5’ exon extension 3,whole intron retention 4.normal splicing

  18. EST contigs with matches to non-consecutive exons(eg.exon1-exon3) • perfect exon skipping 　　　　 CG<1 and GG=<0 • exon skipping with exon truncation CG<1 and GG>0

  19. EST contigs with matches to consecutive exons(eg.exon1-exon2)

  20. EST contigs with matches to consecutive exons(eg.exon1-exon2) • exon trucation 　　 CG<(GG—IN) 　　 • cryptic exon or 3’or 5’ exon extension CG>(GG—IN)but (CG—(GG—IN))<(IN—10) • whole intron retention CG>(GG—IN)but (CG—(GG—IN))>=(IN—10) • Normal splicing CG=(GG-IN)

  21. Thank you

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