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The majority of sRNAs is 25 to 30 nt-long and maps to repetitive and silenced Transposable Elements marked by DNA methylation.
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Surprisingly, some unannotated TARs were connected to read ends that mapped to multiple chromosomes, possibly due to mapping to repetitive sequences, erroneous mapping or possible cross-chromosome splicing (trans-splicing), a rare phenomenon that was previously observed [ 41].
Thirteen of 107 (12%) of the high confidence class mapped to repetitive elements including SINEs, LINEs, LTRs, and DNA transposons.
Since 17 of the 52 (32%) that met fewer criteria - "potential miRNAs" - were also mapped to repetitive elements, this provides some validation for the cut site criteria.
Many miRNA genes derived from repetitive elements have been identified, but the current methods used to identify miRNAs always discard the segments that map to repetitive elements annotated in the genomes.
In a large number of the cases where detected genes have long reads aligned to them, false positives were attributable to these long reads mapping to repetitive elements or low complexity regions within the transcripts.
Does the probe map to repetitive sequence elements?
We can determine the number of reads mapping to repetitive element subfamilies, repetitive element families, or repetitive element classes.
Nearly 40% of the reads were mapped to repetitive sequence regions, which contained 53 types of repetitive elements.
A major fraction of transcripts with increased enrichment in tdp-1 mutant J2-IP also mapped to repetitive elements.
In cells, the majority of small RNA reads mapped to microRNAs (miRNAs) (miRbase 19), whereas in exosomes, the majority of small RNA reads mapped to repetitive elements.
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