title: A study of alternative splicing in the pig.
abstract: BACKGROUND
  Since at least half of the genes in mammalian genomes are subjected to alternative splicing, alternative pre-mRNA splicing plays an important contribution to the complexity of the mammalian proteome. Expressed sequence tags (ESTs) provide evidence of a great number of possible alternative isoforms. With the EST resource for the domestic pig now containing more than one million porcine ESTs, it is possible to identify alternative splice forms of the individual transcripts in this species from the EST data with some confidence.
  
  
  RESULTS
  The pig EST data generated by the Sino-Danish Pig Genome project has been assembled with publicly available ESTs and made available in the PigEST database. Using the Distiller package 2,515 EST clusters with candidate alternative isoforms were identified in the EST data with high confidence. In agreement with general observations in human and mouse, we find putative splice variants in about 30% of the contigs with more than 50 ESTs. Based on the criteria that a minimum of two EST sequences confirmed each splice event, a list of 100 genes with the most distinct tissue-specific alternative splice events was generated from the list of candidates. To confirm the tissue specificity of the splice events, 10 genes with functional annotation were randomly selected from which 16 individual splice events were chosen for experimental verification by quantitative PCR (qPCR). Six genes were shown to have tissue specific alternatively spliced transcripts with expression patterns matching those of the EST data. The remaining four genes had tissue-restricted expression of alternative spliced transcripts. Five out of the 16 splice events that were experimentally verified were found to be putative pig specific.
  
  
  CONCLUSIONS
  In accordance with human and rodent studies we estimate that approximately 30% of the porcine genes undergo alternative splicing. We found a good correlation between EST predicted tissue-specificity and experimentally validated splice events in different porcine tissue. This study indicates that a cluster size of around 50 ESTs is optimal for in silico detection of alternative splicing. Although based on a limited number of splice events, the study supports the notion that alternative splicing could have an important impact on species differentiation since 31% of the splice events studied appears to be species specific.
authors.affiliation: University of Copenhagen, Faculty of Life Sciences, Department of Basic Animal and Veterinary Sciences, Division of Genetics and Bioinformatics, Groennegaardsvej 3, 1870 Frederiksberg C, Denmark. mf@life.ku.dk.
authors.forename: Ann-Britt
authors.initials: AB
authors.lastname: Nygard
authors.forename: Susanna
authors.initials: S
authors.lastname: Cirera
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Gilchrist
authors.forename: Jan
authors.initials: J
authors.lastname: Gorodkin
authors.forename: Claus B
authors.initials: CB
authors.lastname: Jørgensen
authors.forename: Merete
authors.initials: M
authors.lastname: Fredholm
references.citation: Methods Mol Biol. 2000;132:365-86
references.pmid: 10547847
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):296-7
references.pmid: 10592252
references.citation: Genome Biol. 2007;8(4):R45
references.pmid: 17407547
references.citation: Nucleic Acids Res. 2003 May 15;31(10):2544-52
references.pmid: 12736303
references.citation: Genome Res. 2001 May;11(5):889-900
references.pmid: 11337482
references.citation: BMC Genomics. 2006 Feb 27;7:36
references.pmid: 16504160
references.citation: Dev Biol. 2004 Jul 15;271(2):498-516
references.pmid: 15223350
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D46-55
references.pmid: 16381912
references.citation: Science. 2003 Dec 19;302(5653):2141-4
references.pmid: 14684825
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D484-8
references.pmid: 14681463
references.citation: Methods. 2005 Dec;37(4):360-7
references.pmid: 16314265
references.citation: Nature. 2001 Feb 15;409(6822):860-921
references.pmid: 11237011
references.citation: Nat Genet. 2003 Jun;34(2):177-80
references.pmid: 12730695
references.citation: Nucleic Acids Res. 2003 Oct 1;31(19):5635-43
references.pmid: 14500827
references.citation: Genes Dev. 2007 Nov 15;21(22):2963-75
references.pmid: 17978102
references.citation: RNA. 2007 May;13(5):661-70
references.pmid: 17369312
references.citation: BMC Genomics. 2004 Sep 28;5:72
references.pmid: 15453915
references.citation: Genome Biol. 2002 Jun 18;3(7):RESEARCH0034
references.pmid: 12184808
references.citation: Nucleic Acids Res. 2002 Sep 1;30(17):3754-66
references.pmid: 12202761
references.citation: Nat Genet. 2002 Jan;30(1):29-30
references.pmid: 11743582
references.citation: Nucleic Acids Res. 2007;35(1):125-31
references.pmid: 17158149
references.citation: DNA Cell Biol. 2000 Dec;19(12):739-56
references.pmid: 11177572
references.citation: Genome Res. 2002 Dec;12(12):1837-45
references.pmid: 12466287
references.citation: Nucleic Acids Res. 2002 Jan 1;30(1):186-90
references.pmid: 11752289
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D262-6
references.pmid: 14681408
references.citation: Hum Mol Genet. 2003 Jun 1;12(11):1313-20
references.pmid: 12761046
references.citation: Trends Genet. 2004 Feb;20(2):68-71
references.pmid: 14746986
references.citation: Nat Genet. 2000 Apr;24(4):340-1
references.pmid: 10742092
references.citation: BMC Mol Biol. 2007 Aug 15;8:67
references.pmid: 17697375
references.citation: Nucleic Acids Res. 2003 Jan 1;31(1):101-5
references.pmid: 12519958
references.citation: Nucleic Acids Res. 2007 Jan;35(Database issue):D93-8
references.pmid: 17108355
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
references.pmid: 12824337
references.citation: Genome Biol. 2002;3(12):RESEARCH0074
references.pmid: 12537563
references.citation: Biol Proced Online. 2006;8:87-152
references.pmid: 17033699
references.citation: Oncogene. 2004 Apr 15;23(17):3013-23
references.pmid: 15048092
references.citation: Nat Genet. 2002 Jan;30(1):13-9
references.pmid: 11753382
references.citation: Genome Res. 1999 Dec;9(12):1288-93
references.pmid: 10613851
references.citation: FEBS Lett. 2000 May 26;474(1):83-6
references.pmid: 10828456
references.citation: Mamm Genome. 1996 Jul;7(7):509-17
references.pmid: 8672129
references.citation: Physiol Genomics. 2003 Dec 16;16(1):153-9
references.pmid: 14559975
references.citation: Nucleic Acids Res. 2001 Jul 1;29(13):2850-9
references.pmid: 11433032
references.citation: Nature. 2002 Dec 5;420(6915):520-62
references.pmid: 12466850