The number of cis-element sequences and trans-acting factors implicated in the alternative splicing of H-Ras pre-mRNA, as well as RNA secondary structures, indicates how complex and fine-tuned the regulation of this gene is.
These results confirm that exon 3 is not properly spliced in 01640 mutants, the mRNA contains P-element sequences, and this likely produces a truncated form of the CF2 protein.
This enhanced understanding will better enable us to define cis-element sequences and trans-acting factors as well as to determine their interactions in generating future models for other exon splicing processes.
The presence and the position of P-elements was verified by inverse PCR using primers complementary to P-element sequences and the effect of the P-element insertion on specific gene transcript was verified by using semi-quantitative RT-PCR with specific primers of the target gene (Table S3).
Line 2.1 retains no P-element sequences and has repaired roX1 without incorporating MS2 loops.
Results indicated that there was no correlation between shared element sequences and tight clustering of the genes.
The mouse data, based on mouse genome build mm10, including SNPs, expressed sequence tag (EST) sequences, repetitive element sequences and CpG islands, were downloaded from the UCSC Table Browser.
In addition, many of the genes share element sequences and simple repeats, and, on a larger scale, the genes themselves can be viewed as imperfect repeats.
Clearly, the microarrays utilised by the two studies were of independent design and construction so the gene representation, reporter element sequences and PCR product amplicons will differ.
The TIGR plant repeat database is composed largely of transposable element sequences and noncoding RNA genes, and as with any database using incompletely sequenced genome data, it is incomplete.
