A. Consensus Sequence of L1H 3’ UTR
B. 3’ L1H Amplicon Structure
Structure of 3’ L1H Amplicon. (A) Consensus sequence of the L1H 3’UTR portion amplified in the protocol. Primers specific for L1 sequences are used for amplification of only the youngest families of L1 (L1H) elements from the human genome. Two primers (Gene-Specific Primers, or GSP1 and GSP2) are designed for 3’ ends of the elements. For L1H, 3’ L1H UTR-specific primers bind within the UTRs of the L1 and extend away from the element and into the chromosome insertion sites. The primers are designed in such a way that they specifically amplify only the youngest subfamilies of polymorphic transposable elements which are still active in the genome, as opposed to the ancient elements fixed in the population. (B) 3’ L1H amplicon structure. 3’ L1H fragments are amplified by 1st Round PCR followed by 2nd Round Nested PCR in Step 5. Illumina NGS P5 and P7 adapter sequences (green) are introduced during the 3rd PCR in Step 6. The library is then sequenced by Illumina NGS in Step 8 using the Read 1 Seq Primer to read the chromosome junction portion, and 3’ L1H Read 2 Seq Primer to read 13 nt (or more) of the L1H as well as the Index 1 Seq Primer to read the multiplexing index shown in red.
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