The intergenic transcripts most probably represent genes by themselves, either encoding small proteins or being a non-coding RNA.
Most probably, these genes are less conserved and, therefore, remain undetected in model genomes, however, a few of them could be novel wheat/Triticeae-specific genes.
The recurrent DNA sequence changes detected in this study suggest that the corresponding chromosomal areas most probably contain genes important for the initiation and progression of mesothelioma.
Consequently, our approach is to pairwise-align the first intergenic region from the "+" cluster (containing all the structural - most probably late genes) both with itself and the remaining intergenic regions.
This is supported by the fact that increasing the number of 454 sequencing runs shows a significant increase on the number of novel genomic sequences matched with expressed sequence tags, providing expression evidence for such genome regions, which most probably represent genes or transcriptionally active non-coding regions with low levels of expression.
It has to be taken into account, however, that the cucumber gene density was calculated based on as much as 70% of the complete genomic sequence, which most probably included gene-poor regions, while the melon gene density has been estimated using BAC clones that have gene- or EST- based genetic markers and thus probably represent gene-rich regions.
The structures of the genes for Hdac1 and Hdac2 are nearly identical indicating that the two genes most probably arose from gene duplication of a common ancestor (Khier et al. 1999; Zeng et al. 1998).
Most probably each gene copy was present only on one chromosome.
These results most probably represent gene sequences that are still not annotated or assembled into the bovine genome, and hence were completely missed by the Ensembl orthology prediction.
It appears that this region of chromosome 19, most probably the gene RAI, often contains a genetic variant, which increases the risk of several cancers among fairly young humans.
