RScan: fast searching structural similarities for structured RNAs in large databases-0

<p><b>Copyright information:</b></p><p>Taken from "RScan: fast searching structural similarities for structured RNAs in large databases"</p><p>http://www.biomedcentral.com/1471-2164/8/257</p><p>BMC Genomics 2007;8():257-257.</p><p>Published online 31 Jul 2007</p><p>PMCID:PMC1949409.</p><p></p>hadowed symbol sequences is defined as the "structural database"

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse-1

, based on the alignment between human and mouse (human-referenced, see methods). The x-axis indicates the positions of nucleotides and the y-axis is the average percent identity in a 9-base sliding window. The range of x is 50 nt into the exon and 150 nt into the intron. Subfigure (A) and (B) are for upstream and downstream exons, respectively. Exons in LNK are most conserved, and ME exons are more conserved than IND. The flanking introns in the strongly-correlated groups (ME and LNK), especially the intermediate intron (the intron between upstream and downstream exons), are more conserved than in IND. Of the ME and LNK groups, the intermediate introns in ME show even more conservation. This observation indicates the strongly-correlated groups may be under more delicate regulatory control. Another observation is that the downstream exons are more conserved than upstream ones, especially in the ME group. This reflects the different age of upstream and downstream alternative exons (See text).<p><b>Copyright information:</b></p><p>Taken from "Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse"</p><p>http://www.biomedcentral.com/1471-2164/9/191</p><p>BMC Genomics 2008;9():191-191.</p><p>Published online 26 Apr 2008</p><p>PMCID:PMC2432081.</p><p></p

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse-4

multiple genome alignment (See text and method). The figures show the distributions of age in different groups. Most LNK pairs are old: the younger the age, the fewer pairs. IND shows the opposite trend: The older, the fewer. ME group is a mixture of LNK and IND. The numbers of young and old pairs in ME are roughly equal. These distributions indicate possible different evolutionary courses of the three groups. All the distributions are consistent in human and mouse. However, the label assignment procedures are different in human and mouse, so the amount of the data of each label can not be compared directly.<p><b>Copyright information:</b></p><p>Taken from "Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse"</p><p>http://www.biomedcentral.com/1471-2164/9/191</p><p>BMC Genomics 2008;9():191-191.</p><p>Published online 26 Apr 2008</p><p>PMCID:PMC2432081.</p><p></p

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse-3

Lated the inclusion level as /(+). The left column is for human and the right is for mouse. The frequencies of inclusion levels in ME, IND and LNK are quite different. Exons in LNK tend to be included often, which indicates that LNK transcripts with exon are the dominating form. Exons in IND are included at either a very high or very low level. Inclusion levels in ME are similar to IND, but there are more cases in which the transcripts with or without the cassette exon are express at similar levels. These results are observed in both mouse and human.<p><b>Copyright information:</b></p><p>Taken from "Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse"</p><p>http://www.biomedcentral.com/1471-2164/9/191</p><p>BMC Genomics 2008;9():191-191.</p><p>Published online 26 Apr 2008</p><p>PMCID:PMC2432081.</p><p></p

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse-2

, based on the alignment between mouse and human (mouse-referenced, see methods). The x- and y-axis are the same as Figure 3. Results in the mouse are consistent with what was seen in the human: the strongly-correlated groups are more conserved than the weakly-correlated group, in both exon and flanking introns; the intermediate introns in the strongly-correlated groups are even more conserved. The conservation difference is also observed between the upstream and downstream exons. Compared with Figure 3, the difference between the upstream and downstream exons is less pronounces for the ME group, but it's more clear in the IND group.<p><b>Copyright information:</b></p><p>Taken from "Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse"</p><p>http://www.biomedcentral.com/1471-2164/9/191</p><p>BMC Genomics 2008;9():191-191.</p><p>Published online 26 Apr 2008</p><p>PMCID:PMC2432081.</p><p></p