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Table 2 Annotation of known repeats in core elements with large CNV and without CNV

From: Identification of both copy number variation-type and constant-type core elements in a large segmental duplication region of the mouse genome

   Expected copy numberc  
Core element Type Length (bp) Known repeats and RefSeq genes a Ratiob B6 BLG2 MSM Probe (N) Total length in
  B6 (bp)
Core element 042 Constant 3000 LINE, Vmn2r , LTR 0.610 9 10 9 252 27000
Core element 108 Constant 3000 Cbx3 , LTR, SINE 0.250 3 3 3 154 9000
Core element 127 Constant 2700 Vmn2r , LINE 0.158 12 13 13 196 32400
Core element 244 Constant 3247 LINE, Vmn2r , SINE 0.563 8 8 8 68 25976
Core element 352 Constant 3900 LINE,LTR, Simple, SINE 0.911 8 8 8 264 31200
Core element 454 Constant 3372 Vmn2r, LINE 0.123 11 10 11 348 37092
Core element 462 Constant 2700 LINE, SINE, 0.910 6 7 6 40 16200
Core element 484 Constant 3000 LINE, Simple, SINE 0.839 4 4 4 54 12000
AVERAGE (Constant)   3115   0.545 8 8 8 172 23859
Core element 103.1 CNV 1802 LTR, SINE 0.959 14 20 19 127 25228
Core element 103.2 CNV 1686 Zfp , LINE, LTR 0.225 8 15 12 129 13488
Core element 146 CNV 2877 LINE, SINE 0.979 19 33 26 103 54663
Core element 154 CNV 2691 LTR, SINE 0.749 24 30 28 236 64584
Core element 177.1 CNV 3900 Simple, Zfp 0.110 23 28 27 112 89700
Core element 182 CNV 2629 LINE, LTR, MurSatRep1 0.622 20 27 25 305 52580
Core element 364 CNV 1468 SINE, LTR 0.343 13 16 18 190 19084
Core element 447 CNV 2248 LTR, SINE, Simple/Sat 0.768 24 35 30 108 53952
Core element 510 CNV 2735 LINE, Simple/Sat 0.094 13 19 16 348 35555
Core element 541 CNV 3195 Simple/Sat, Zfp 0.076 14 21 20 413 44730
AVERAGE (CNV)   2523   0.492 17 24 22 207 45356
  1. a Detailed information on the known repeats and RefSeq genes that were detected in each core element is provided in Additional file 5. LTR retrotransposons are underlined. Core elements with large CNV were selected by two criteria: 1) a P value lower than the significance value; 2) the 10 core elements that showed the greatest variation among strains. b Proportion of each core element that comprised the known repeat. The proportion was calculated by dividing the total length of the known repeat in the core element by the total length of the core element. c Expected copy numbers in B6 were calculated from the number of homologous sequences in each of the 60 groups (Additional file 5). Expected copy numbers in BLG2 and MSM were calculated from the average of the aCGH values and the copy number in B6 (Additional file 7).