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Predominantly, potential lncRNAs mapped in intergenic chromosome regions (4,365) and therefore, were classified as potential intergenic lncRNA.
The alignment of the 10,884 UTs on the bovine reference genome assembly indicated that the transcripts not yet annotated were predominantly mapped in intergenic chromosomal regions.
As noticed in previous RNA seq studies, the background was very low, with no or few reads mapped in intergenic regions.
Nevertheless, the current gene annotation still needs to be improved in order to determine the function of approximately 20% of reads, which mapped in intergenic regions.
A total of 4,130 putative unannotated protein-coding sequences were identified in the 20% of reads which mapped in intergenic regions.
Similar(55)
These pre-miRNA and mature miRNA were mapped in the intergenic region of the mitochondrial genome.
If there are new miRNAs in our small RNA sequence reads, they are likely to be mapped in the gene or intergenic region (Table 1).
We have selected and examined the EST loci that are highly conserved across species (E-values lower than 1 × 10-4), and have at least five or more EST reads mapped in the middle of large intergenic regions (more than 10 kb) away from neighboring genes (Table 2).
With the exception of ORE-13, that lies more than 14 kb from the closest annotated gene, the other ORESTES mapping in intergenic regions (ORE-2, -3, -4, -10, -11, -12, -17) are located less than 1 kb of the last exon of the nearest gene, and could represent a novel alternate 3'UTR of these genes.
In total, we found that only ~2.5% of informative reads mapped into genic lincs and only ~0.7% mapped into intergenic lincs (Table 6).
In cases in which open reading frames mapped in very close proximity to each other (<700 bp), the query sequence spanned both genes and the intergenic region.
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