The second copy of Trp53rk appears to have arisen from local tandem duplication on chromosome 2. Both copies are supported by expressed sequence tag and capped analysis of gene expression evidence and have intact ORFs. Although the syn tenic copy of Trp53rk lies within a region of selleck screening library chromosome 2 that shares the same gene order as a region of human chromosome 20 between the Sl2a10 and Slc13a3 loci, the new locus is adjacent to Arfgef2 locus and is not conserved in human. Identifying the transcripts of the phosphoregulator transcriptome As part of the FANTOM3 project, a transcript clustering algo rithm was developed that grouped sequences with shared splice sites, transcription start sites, or transcription termina tion sites into transcriptional frameworks.
These frame works effectively Inhibitors,Modulators,Libraries define the Inhibitors,Modulators,Libraries set of cDNA sequences observed for each locus. Using a representative cDNA sequence for each phosphoregulator, we Inhibitors,Modulators,Libraries extracted the corresponding framework cluster, the set of all observed cDNA Inhibitors,Modulators,Libraries sequences, and the genomic mappings for each cDNA. Additionally, high throughput 5 end sequences from CAGE and 5 3 DiTag sequences were also mapped to these framework clusters and used to provide additional sup port for alternative 5 and 3 ends. The cDNA resources are summarized in Tables 1 and 2. By combining these cDNA and tag resources, we reviewed the level of support for each transcript. The ORF of each full length transcript was also assessed to determine whether it encoded a variant peptide and whether the variant had an altered domain structure. These results were compiled into a database and can be viewed online.
This web based interface permits visualization of each locus in its genomic context and provides an annotated view of each transcript with access to peptide and domain predictions. Alternatively spliced transcripts of the phosphoregulator transcriptome Inhibitors,Modulators,Libraries With all alternative transcripts for the mouse phosphoregula tors identified, we then searched for the level of support for each alternative transcription start site, termination site, and splice junction event. For the analysis of splice junctions we clustered pairs of splice donors and acceptors based on their genomic coordinates. When a given donor mapped to multiple acceptors, or acceptor to multiple donors, the junction was considered alternative. For an alter native junction to be considered reliable we required there to be two independent cDNA sequences for each alternative and a class of loci with a reported high level of alternative splice forms, namely the zinc finger pro teins. For these sets, 39% of all multi exon selleck chem Nutlin-3a frameworks and 80% of zinc finger protein encoding frameworks have at least two cDNAs supporting an alternative splice form.