LINE1 OFR2 Primer Design - (Jun/22/2010 )
I'm trying to design a primer that will detect ORF2 in LINE1 in humans. I know that basically what I"m supposed to do is find the sequence, and design a primer complementary to it, but I have no idea where or how to start. Any help would be much appreciated!
Thank you all in advance
What do you want the primers for exactly?
There is no easy way to design primers for transposons. As you know there are placed all over human genome, so any primer specific for L1 sequence will detect all of them. If you want to detect a transposon in one specific location (which I assume is what you want) you must design primers partialy for the L1 sequence any partialy for the gene where it's inserted (so you must know the exact site of insertion). You can search NCBI Nucleotide database for L1 retroelement in your specific sequence, if it was published. Also there is L1base with sequences of L1 elements.