Table 4

Repetitive elements within the bovine Type I IFN sub-loci.

Sub-locus 1

Sub-locus 2


    SINEs:

    15.29%

    15.68%

Alu/B1

0.00%

0.00%

MIRs

0.51%

0.81%

    LINEs:

    17.74%

    11.23%

LINE1

10.33%

2.20%

LINE2

0.44%

0.29%

L3/CR1

0.04%

0.00%

RTE

6.93%

8.73%

    LTR elements:

    4.01%

    2.75%

MaLRs

0.89%

0.98%

ERVL

0.12%

0.03%

ERV classI

0.79%

0.22%

ERV classII

0.00%

0.00%

    DNA elements:

    2.36%

    2.68%

MER1_type

1.72%

2.45%

MER2_type

0.45%

0.00%

Unclassified:

0.00%

0.00%

Total interspersed repeats:

39.40%

32.35%

Small RNA:

0.24%

0.40%


The percentage of repetitive elements for the Type I IFN sub-loci was calculated in RepeatMasker 3.1.9. The length of nucleotide sequence encompassing the repetitive element divided by the length of the total nucleotide sequence for either sub-locus 1 or sub-locus 2 was used to calculate the percentage shown in each column. Sub-locus 1 has a higher proportion of LINE1 and LTR elements than sub-locus 2 resulting in a higher total number of interspersed repeats within sub-locus.

Walker and Roberts BMC Genomics 2009 10:187   doi:10.1186/1471-2164-10-187

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