Characterization of L1 at 4p15.32. (a) Diagram of L1 at 4p15.32 and the surrounding region. The arrow designates the L1 transcript. Blue boxes indicate exons of the CD38 gene, with exon number designated. Oligonucleotides CD38-a and CD38-b are indicated. Unmarked triangles indicate the positions of oligonucleotides used in L1 TaqMan qPCR assay. (b) Alignments of L1 at 4p15.32 3' end and related sequences. 'chr 4 short tag' - the major 3' expression tag cloned from this site. 'chr4 long tag' - longer 3' expression tag and 3' RACE sequence cloned from this site. 'chr6 transduction' - paralogous, transduced sequence downstream of L1 on chromosome 6. 'U35' - similar distinct 3' expression tag that cannot be mapped to the human reference genome. 3' end target site duplications are highlighted in blue. Single nucleotide differences in the chromosome 6 sequence are highlighted in dark red. (c) Diagram of the pedigree of the CEPH/UTAH individuals used in this study. (d) Relative expression of the L1 at 4p15.32 in lymphoblastoid cell lines from CEPH individuals. Expression is in arbitrary units normalized to HPRT1. Error bars indicate ± standard deviation from three replicates. (e) Expression of CEPH individuals of the L1 at 4p15.32 compared to flanking exons of CD38, normalized to HPRT1. Expression is plotted on a logarithmic scale so that levels for both amplicons can be clearly visualized. Error bars represent ± standard deviations from three replicates. All data are representative of at least two biological replicates.
Rangwala et al. Genome Biology 2009 10:R100 doi:10.1186/gb-2009-10-9-r100