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letter
. 2003 Mar 1;13(3):358–368. doi: 10.1101/gr.923303

Table 2.

Primate Retrotransposition Events

Human–Chimpanzee
Repeats Chimpanzee Human
Insertions Rate (/Mb/My) Insertions Rate (/Mb/My)
Events Length (bp) Mean length (bp) Count Base Events Length (bp) Mean length (bp) Count Base
LINE/L1 5 4404 881 0.18 162 9 32393 3599 0.33 1195
SINE/Alu 11 3311 301 0.41 122 23 7036 306 0.85 259
Other 0 0 — 0.00 0 2 2040 1020 0.07 75
Subtotal 16 7715 482 0.59 69 34 41469 1220 1.25 369
Human–Baboon
Repeats Baboon Human
Insertions Rate (/Mb/My) Insertions Rate (/Mb/My)
Events Length (bp) Mean length (bp) Count Base Events Length (bp) Mean length (bp) Count Base
LINE/L1 26 48882 1880 0.23 435 36 58670 1630 0.32 523
LTR 2 1407 704 0.02 13 11 31297 2845 0.08 279
SINE/Alu 153 45538 298 1.36 406 96 29000 302 0.86 258
Other 1 130 130 0.01 1 2 2836 1418 0.02 25
Subtotal 182 95957 527 1.62 855 145 121803 840 1.29 1085
Human–Lemur
Lemur Human
Insertions Rate (/Mb/My) Insertions Rate (/Mb/My)
Events Length (bp) Mean length (bp) Count Base Events Length (bp) Mean length (bp) Count Base
DNA 8 4903 613 0.19 119 5 1223 245 0.10 24
LINE/L1*** 3 3223 1074 0.07 78 53 40635 767 1.04 799
LTR*** 5 2131 426 0.12 52 16 8416 526 0.31 165
SINE/Alu*** 40 10659 266 0.97 259 234 64991 278 4.60 1278
Other 2 281 141 0.05 7 2 750 375 0.04 15
Subtotal*** 50 16294 326 1.21 395 305 114792 376 6.00 2257

We examined all insertion deletion events in excess of 100 bp from global alignments. An indel was classified as a retrotransposition event if at least 80% of the indel contained one predominant repeat. We considered the known interspersed repeat phylogeny based on the established repeat subclasses as reported previously (Smit 1999). All insertions were considered including the ancient repeat subclasses that passed our test. Further, in the case of L1 and Alu repeats, insertion sequences were examined for the presence of target-site duplications and a polyadenylation signal at the site of integration. The rate calculation assumed divergence times of the human lineage from chimpanzee, baboon, and lemur of 5.5, 25, and 55 Mya. Pairwise alignment lengths were 5.0, 5.0, and 0.62 Mb for human–chimpanzee, human–baboon, and human–lemur sequence alignment, respectively.

*

P < 0.05; ***P < 0.001 by χ2 test.