These programs use information in the region flanking a splice site. For analysis of other species on the web I recommend NetGene (available through the Center for Biological Sequence Analysis at the Department of Biotechnology, The Technical University of Denmark). Right now, feature browsing is only available for mammalian sites (using a classifier trained on human data), but you can carry out splice site prediction on Arabidopsis as well.ДЇor high throughput assessment of splice sites I recommend GeneSplicer. In addition to splice site prediction, the web site allows you to browse the features that contribute to the strength (or weakness) of any given site. Splice site predictors are available on the web. A survey (making the point that species with more introns have weaker splice sites) was published by Irimia et al. Consensus sequences for humans and flies are reported here. Splice site consensus sequences vary by species. 2003), and experimental work has established that splicing in vivo is possible even without the core dinucleotide GU or AG. The consensus very poorly, including cryptic splice sites which are used when a nearby natural site is inactivated by mutaiton (see, for example, Roca et al. However, there are many examples of sites that match Genomic sequence, inclusion of pseudogene sequences, or failure to accountДЇor somatic mutation. Interpretation, polymorphic differences between the sources of cDNA and Of such variant splice sites can be traced to errors in annotation or That fit into neither of the two categories mentioned above. U12 introns are found in many eukaryotes, includingДrosophila melanogaster and Arabidopsis, but notДЇinally, there are a small number of nonconsensus sites Sequences at the 5' splice site, (RTATCCTY R = A or G Y = C or T) andД«ranch site (TCCTRAY). U12 introns can be identified by highly conserved Splice site sequences that are very different from the standard consensus,Д«ut which are very similar to each other (reviewed by BurgeДЄnd Steitz 1997. Splice site consensus is U12 introns, a minor class of rare introns with It is reasonable to assume that GC sites are recognized by the standard 42 ofД¤4 sites have a consensus G residue at both position -1 and positionДҐ, and GC-AG introns have an enhanced match to the 3' splice site consensus ( Thanaraj and Clark, 2001 PubMed). GC sites conform extremely well to the standard consensus sequences at other positions. The most common class of nonconsensus splice sitesД¬onsists of 5' splice sites with a GC dinucleotide (WuДЄnd Krainer 1999). Splice site consensus sequences for U2 (major class) introns in pre-mRNA generally conform to the following consensus sequences:ДҐ' splice sites: MAG|GTRAGT where M is A or C and R is A or G The 5' end of the intron, and AG at the 3' end of the intron. Include nearly invariant dinucleotides at each end of the intron, GT at It is well-established that nearly all splice sites conform to consensus sequences ( matrices).