Figure 2.
L1 subfamily enrichment for chromosomes X and 7. L1 elements were grouped into 75 different subclasses based on the original ORF2 and 3′ untranslated region classification (29). In a, an enrichment factor for the X chromosome was determined for each element (bp fraction of X chromosome sequence/bp fraction of sequence not from the X chromosome) and is depicted (y axis). The various L1 elements are grouped into 10 major subfamilies (x axis) and are arranged from the evolutionarily most ancient [L1M4 (mammalian group 4)] to the currently active element in the human lineage (L1Hs). Within each of the 10 major L1 classes, individual subclasses were arranged on the basis of increasing average similarity to the consensus. L1 subclasses that differed significantly from random (P < 0.006 after a Bonferroni correction for 75 subclasses) are colored red (n = 10,000 replicates; 56 Mb). The alignment number, total bp, and fraction of bp for each element were calculated for both the X and non-X groups (see Table 2 in supplemental material at www.pnas.org). In b, a similar analysis was performed for chromosome 7. Two subclasses (red) were significantly depleted.