Table 5

L1 insertions into annotated genes

L1 genome location compared to genes^*

mRNA

CDS

Fully contained in genes

17%

13%

Same orientation

38%

38%

Average L1 length within gene annotation (nucleotides)

1,470

1,490

Opposite orientation

62%

62%

Average L1 length within gene annotation (nucleotides)

1,815

1,780

Average distance from an L1 to a gene (kb)

282

283

Minimum distance 9 nucleotides

Maximum distance 3,840 kb

Same orientation as nearest gene

49%

49%

Opposite orientation as nearest gene

51%

51%

Annotated genes with L1s within boundaries

Total number of genes with L1s

2,864

2,352

Average genome extent (kb)

161

141

Minimum genome extent (kb)

1.9

2.5

Maximum genome extent (kb)

1,971

1,281

Average AT composition

55%

55%

Minimum AT composition

31%

31%

Maximum AT composition

69%

69%

^*The location of all L1 insertions with TSDs was compared to the genomic location of genes. The start-end coordinates of genes were determined from the headers of the GenBank contig (NT_*) files.

Szak et al. Genome Biology 2002 3:research0052.1   doi:10.1186/gb-2002-3-10-research0052