Identification of HPRT1 PGs for primer design.
Top panel: Blat search using HPRT1 mRNA sequence (1405-bp long after deletion of the poly-A tail) as the bait pulls out three putative PGs, besides the authentic HPRT1 genomic sequence that spans 40514 nt on the plus strand of X chromosome. The three putative PGs match the 193–1383rd, the 269–1413th, and the 213–1143rd nt regions of the HPRT1 mRNA as illustrated. There are three additional very short fragments, spanning only 28, 35 and 35 bp, respectively, that also match parts of HPRT1 mRNA but are not considered as PGs. Bottom panel: We pulled out the sequence of each PG (by clicking “details”) and assembled those homologous parts to construct the “cDNA” of the PGs on chromosomes 11 and 4. Alignment of the three sequences with the HPRT1 mRNA reveals that the HPRT1 mRNA has some unique regions. The forward and reverse primers (table 2) we designed are underlined.