This confirms that the two copies of CYP6P9 are transcribed and functional as seen also in other strains of An. funestus such as FUMOZ-R (C. Wondji, unpublished data).
The primary mechanisms by which a retrocopy can be transcribed and become functional are fusion (or insertion) with an existing gene or acquisition of new gene elements from a de novo sequence [ 4, 15, 20].
These sequences have often been claimed to be transcribed and fulfill a functional role.
More recent work has demonstrated that they play a critical role in human development, tissue differentiation, and gene expression, as these elements can be transcribed and translated into functional proteins (Belancio et al. 2009; Han and Boeke 2005).
Interestingly, three RP pseudogenes, with 89%-95 89%-95nce identity to their parent (progenitor) RP genes, were found to be transcribed and seem to be functional, by a bioinformatics scan of cDNA and expression sequence tag (EST) databases and confirmation by PCR and Northern blot [ 8].
As we have established, all share common features (for example, DNase I hypersensitivity, active chromatin marks and interaction with transcription factors and RNAPII); therefore, we propose that canonical regulatory elements are primarily transcription units (Table 1) and that, in order for them to be functional, they need to be transcribed (and so associated with a transcription factory).
The paralogs that were studied are still being transcribed and are presumably functional (with the possible exception of some rarely transcribed pseudogenes) and have not been subject to non-functionalization.
Entries genuinely without SP and TMD could be secreted or anchored to the cell surface through unknown mechanisms or could represent non-functional proteins, perhaps corresponding to pseudogenes, although EST suggest that all types of TvBspA proteins are transcribed and could be functional.
No redundant tRNAs with the same anticodon have been found in the N. equitans genome, and experimental data suggest that these split tRNAs are transcribed and processed into functional tRNA molecules [9].
In addition to these cases, ORFs conserved across plant species have been reported in a number of cases, some of which are transcribed and might be functional.
