Characterization and potential functional significance of human-chimpanzee large INDEL variation

Table 1 Number of INDELs associated with different categories of sequences

Categories of gaps	Human gaps	Chimpanzee gaps	Total INDELs (HGs + CGs)
Total gaps	11,365	15,144	26,509
Interspersed repeats (all)	7,176	11,398	18,574
Interspersed sequences (retrotransposons)	7,121	11,355	18,476
Retrotransposons (SINEs)	3,494	7,021	10,515
Retrotransposons (LINEs)	1,847	2,052	3,899
Retrotransposons (ERVs)	519	356	875
Retrotransposons (SVAs)	114	681	795
Retrotransposons (MEs)	1,147	1,245	2,392
Interspersed sequences (DNA elements)	55	43	98
Noninterspersed sequences (all)	4,189	3,746	7,935
Noninterspersed sequences/tandem repeats (NIS/TR)	1,266	1,334	2,600
Noninterspersed sequences/unique sequences (NIS/US)	2,923	2,412	5,335

CG = chimpanzee gap; ERV = endogenous retrovirus; HG = human gap; INDEL = insertion and deletion; LINE = long interspersed nuclear element; ME = mosaic element; NIS = noninterspersed sequence; SINE = short interspersed nuclear element; SVA = biologically active composite elements consisting of fragments of SINE, VNTRs and Alu elements; TR = tandem repeat; US = unique sequence; VNTR = variable number of tandem repeats. Interspersed repeats are transposable element sequences that are present multiple times throughout the genome. The majority of interspersed repeats are retrotransposon sequences (subcategories: SINEs, LINEs, ERVs, SVAs, and MEs). DNA family transposable elements constitute less than 1% of interspersed repeats. Noninterspersed sequences are TRs or USs that map to specific INDEL sites in the genome.

ISSN: 1759-8753