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Hundreds of AC-rich junctions identified between minicircle and LINE sequences were encountered.
Based on genomic co-ordinates of LINE elements provided by the UCSC database, 899,092 LINE sequences were extracted and subjected to in silico bisulfite treatment.
Additionally, many LINE sequences were isolated simultaneously during the above process because the probe contains the common tail shared by SINE and LINE.
Amongst the 73 loci where SINEs were absent, no repeat element of any type was found at 62 loci (Additional file 5 Figure S20), while LINE sequences were found at 11 loci.
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Similarly, four line sequences are used to evaluate the performance of line scratch removal: LabL1, DanceL1, DanceL2 and DanceL3, with 25, 25, 18 and 15 frames, respectively.
The perfect alignment between the V sequences and the corresponding germ line sequences are inconsistent with the insertion of V sequence fragments, a hallmark of gene conversion.
Consequently, the LINE sequences are fused to mRNA coding sequences.
The homology of RF2-6s with dogfish shark stem cell line sequences was 88%.
In contrast, the average proportion of LINE sequences was significantly lower in CNV-type core elements than in the constant type.
Interestingly, it has been suggested that hypomethylation of L11 LINE sequences is particularly prevalent in urothelial cancers and might have diagnostic utility in these cancers (Jürgens et al, 1996).
Five microgram of genomic DNA per line sequenced was sent to Prognosys Biosciences (La Jolla, CA) for further sample preparation and sequencing.
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