The current knowledge on the functions of lincRNAs is scarce because very few of the lincRNAs have been assigned a function experimentally, but their functional range is believed to be broad on the basis of indirect evidence (Bertone et al. 2004; Ponjavic et al. 2007; Mercer et al. 2009; Ponting and Belgard 2010).
Based on relevant literature and functional information in databanks, we assigned a function and a possible type(s) of cell(s) responsible for expression for most of the genes on our list (Fig. 3).
Prior to the release of the sequence, only a few genes were assigned a function each year.
Of the 2,122 CDS, 1,387 (65%) were assigned a function through sequence analysis.
Again, a huge proportion of proteins (10 out of 26) has not been assigned a function yet.
Of those, 4,518 CDS were assigned a function using one of five evidence classes, while 1,274 and 611 CDS remained, respectively, 'conserved hypothetical' or 'hypothetical'hypothetical
This is potentially important because it is usually assumed that when genes are assigned a function, it is due to either a valid prediction or a false positive due to "promiscuity" or other issues with the data.
Genes annotated to encode a transcriptional regulator (HMPREF0421_20023), a toxin-antitoxin (TA) system toxin (HMPREF0421_20022) and two permeases map within the transposon; the remaining genes were unable to be assigned a function.
Comparative analyses of Plasmodium genomes and genomes of other organisms have greatly improved the identification and assignation of putative functions to Plasmodium genes, and these analyses have revealed that about 50% of malaria parasites genes cannot be assigned a function by homology and it is therefore likely that many of these genes perform functions that are unique to Plasmodium.
Assembling increased the number reads that were assigned a function.
These genes have been assigned a function related to resistance in many pathosystems.
