Splicy graphical report for Probeset 200826 at (GeneChipHuman Genome U133A) and mapping on the two transcript variants for Gene SNRPD2

<p><b>Copyright information:</b></p><p>Taken from "Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S17</p><p>BMC Bioinformatics 2007;8(Suppl 1):S17-S17.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885846.</p><p></p> The probe at position X = 587 and Y = 389 corresponds to the probe pair with low signal intensity at Figure 2. This probe matches only with the variant of SNRPD2 that skips an exon, while the other variant doesn't maintain the same exon junctions

Projection of coordinates relatives to the transcript structure over the genome

<p><b>Copyright information:</b></p><p>Taken from "Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S17</p><p>BMC Bioinformatics 2007;8(Suppl 1):S17-S17.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885846.</p><p></p> Once the intron and exon positions on the chromosome are collected, Splicy first finds in which exon the single probe matches, then projects this information on the chromosome coordinates

Bioconductor plot of Perfect Match signal for normal Breast tissue samples (black lines) and Breast cancer samples (red lines)

<p><b>Copyright information:</b></p><p>Taken from "Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S17</p><p>BMC Bioinformatics 2007;8(Suppl 1):S17-S17.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885846.</p><p></p

Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates-1

<p><b>Copyright information:</b></p><p>Taken from "Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates"</p><p>http://www.biomedcentral.com/1471-2148/7/187</p><p>BMC Evolutionary Biology 2007;7():187-187.</p><p>Published online 4 Oct 2007</p><p>PMCID:PMC2082429.</p><p></p>yan. and are represented as grey blocks. The chromosome number in the corresponding genome is provided. Dashed lines correspond to regions of break of synteny. Abbreviations: , Homo sapiens; , Pan troglodytes; , Macaca mulatta; , Mus musculus; , Rattus norvegicus; , Gallus gallus. . Since for chimp and macaque no mRNA sequences are available, the human and were used as templates for gene predictions. In chimp, the intron putatively gained by is composed of eight repeats. In the genomic regions corresponding to chimp , there are four additional Zn-Fingers, which are reported in black because there is no evidence for their transcription. The dashed lines represent regions of gaps in the genome assembly. In rodents, the last intron is longer and not in scale; the corresponding length is reported in brackets. . The grey lines represent the genomic regions of segmental duplication. The corresponding chromosome number, chromosomal coordinates and direction of transcription are given. For , the splicing variants present in the database are shown. For , both the database transcripts and the isoforms detected in this study are reported together with an in-silico gene prediction obtained by using the PRDM9 long isoform as template

Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates-0

<p><b>Copyright information:</b></p><p>Taken from "Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates"</p><p>http://www.biomedcentral.com/1471-2148/7/187</p><p>BMC Evolutionary Biology 2007;7():187-187.</p><p>Published online 4 Oct 2007</p><p>PMCID:PMC2082429.</p><p></p>are shown in grey. On main bifurcations, the corresponding posterior probability from Bayesian inference is reported (see Methods). Different colours associated to tree branches correspond to the main subfamilies. For each subfamily, the gene structure of human PRDM ortholog is depicted. The scale refers to exons only. The tree image was produced using iTOL [44]. . PRDM genes are ordered by increasing evolutionary divergence, calculated as cumulative branch lengths from the tip to the root of the phylogenetic tree. The expression data were measured as the mean values of different assays for each gene (see Methods). The upper limit of the 2values was set to 10. For original values see Additional file