Alternative Splicing PALS Putative Alternative Splicing database. Searchable, limited to mouse and human ASDB Alternative Splicing Database --based on GenBank entries HASDB Human Alternative Splicing Database. Chris Lee. UCLA. 6201 alternative splice relationships in human genes identified through a genome-wide analysis of expressed sequence tags(ESTs) Splicing anomalies in Arabidopsis put into categories that include alternative splicing, based on l-length cDNA sequences Splice Site Consensus It is well-established that nearly all splice sites conform to consensus sequences. These consensus sequences include nearly invariant dinucleotides at each end of the intron, gt at the 5 end of the intron, and AG at the 3 end of the intron, and generally resemble MAGgtRagt at the 5 splice ite and Cagg at the 3 splice site The most common class of nonconsensus splice sites consists of 5' splice sites with a GC dinucleotide (Wu and Krainer 1999) GC sites conform extremely well to the standard consensus positions.42of 44 sites have a consensus G residue at both position-1and position 5. It is reasonable to assume that GC sites are recognized by the standard(U2-dependent) spliceosome The second class of exception to splice site consensus is U12 introns, a minor class of rare introns with splice site sequences that are very different from the standard consensus, but which are very milar to each other(reviewed by Burge et al 1999 and Tarn and Steitz 1997. U12 introns can be identified by highly conserved sequences at the 5 splice site, (RTATCCTY; R=A or G;Y=Cor T); and branch site (TCCTRAY). U12 introns are found in many eukaryotes, including Drosophila melanogaster and Arabidopsis, but not C. elegans Finally, there are a small number of nonconsensus sites that fit into neither of the two categories mentioned above. Many reports of such variant splice sites can be traced to errors in annotation or interpretation, polymorphic differences between the sources of cDNA and genomic sequence. inclusion of pseudogene sequences, or failure to account for somatic mutation However, there are many examples of sites that match the consensus very poorly, and experimental work has established that 5 splice sites do not absolutely require gt, and 3 splice sites do not absolutely require AG, to be recognized in vivoAlternative Splicing PALS Putative Alternative Splicing database. Searchable, limited to mouse and human. ASDB Alternative Splicing Database -- based on GenBank entries. HASDB Human Alternative Splicing Database. Chris Lee. UCLA. 6201 alternative splice relationships in human genes identified through a genome-wide analysis of expressed sequence tags (ESTs). Splicing anomalies in Arabidopsis put into categories that include alternative splicing, based on full-length cDNA sequences. Splice Site Consensus It is well-established that nearly all splice sites conform to consensus sequences . These consensus sequences include nearly invariant dinucleotides at each end of the intron, GT at the 5' end of the intron, and AG at the 3' end of the intron, and generally resemble MAG|GTRAGT at the 5' splice site and CAG|G at the 3' splice site. The most common class of nonconsensus splice sites consists of 5' splice sites with a GC dinucleotide (Wu and Krainer 1999). GC sites conform extremely well to the standard consensus sequences at other positions. 42 of 44 sites have a consensus G residue at both position -1 and position 5. It is reasonable to assume that GC sites are recognized by the standard (U2-dependent) spliceosome. The second class of exception to splice site consensus is U12 introns, a minor class of rare introns with splice site sequences that are very different from the standard consensus, but which are very similar to each other (reviewed by Burge et al 1999 and Tarn and Steitz 1997. U12 introns can be identified by highly conserved sequences at the 5' splice site, (RTATCCTY; R = A or G; Y = C or T); and branch site (TCCTRAY). U12 introns are found in many eukaryotes, including Drosophila melanogaster and Arabidopsis, but not C. elegans. Finally, there are a small number of nonconsensus sites that fit into neither of the two categories mentioned above. Many reports of such variant splice sites can be traced to errors in annotation or interpretation, polymorphic differences between the sources of cDNA and genomic sequence, inclusion of pseudogene sequences, or failure to account for somatic mutation. However, there are many examples of sites that match the consensus very poorly, and experimental work has established that 5' splice sites do not absolutely require GT, and 3' splice sites do not absolutely require AG, to be recognized in vivo