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Table 1 Chimeric TE insertions supported by EST evidence in the D. melanogaster Release 3 genome sequence. The leftmost column gives the gene(s) that generate(s) the chimeric transcript. FlyBase ID refers to the TE accession number in the Release 3.2 annotation. Rec. rate refers to the estimated recombination rate in the vicinity of the gene. Rightmost column gives the number of wild strain pools (out of six) where the TE insertion is present. An asterisk in the last column indicates that independent population frequency estimates are available for these TE insertions in [12, 17, 27-29].

From: Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome

Gene TE class TE family Chimera# FlyBase ID TE length (bp) Chrom. Arm Rec. rate Pool frequency
CG1098(Madm) TIR pogo 1 FBti0019306 185 3R 0 0
CG9766 LTR Burdock 2 FBti0019283 6412 3R 0 0
CG32306 LTR roo 3 FBti0020022 9097 3L 3.25 0
CG7110 LINE Doc 4 FBti0019166 4725 2L 2.83 0
CG3318(Dat) LTR 412 5 FBti0018872 7520 2R 3.16 0
CG4821(Tequila) LTR 412 6 FBti0020072 7502 3L 3.17 0
CG8166(unc-5) LTR Tirant 7 FBti0018948 8532 2R 3.44 0
CG6214 TIR pogo 8 FBti0019155 185 2L 3.07 0
CG1915(sls) LTR copia 9 FBti0020021 5145 3L 3.21 0
CG17632(bw) LTR 412 10 FBti0018870 7518 2R 3.31 0
CG2162 TIR S-element 11 FBti0020026 1733 3L 3.3 0
CG9181(Ptp61F) LINE Rt1a 12 FBti0020016 5192 3L 3.13 0
CG17274 LINE Doc 13 FBti0019412 4719 3R 3.09 0
CG32850 LTR Stalker2 14 FBti0020416 8118 4 0 0
CG7231 LTR 297 15 FBti0019135 6916 2L 4.02 0
CG7356 LTR copia 16 FBti0019136 5145 2L 4.01 0
CG7314(Bmcp) LINE Doc 17 FBti0020095 4709 3L 2.73 0*
CG11406 LTR 412 18 FBti0018873 7427 2R 3.15 0
CG3894 LINE G2 19 FBti0018918 1917 2R 2.99 0
CG5055(baz) LTR blastopia 20 FBti0019073 5031 X 2.88 0*
CG31692(fbp) TIR pogo 21 FBti0019206 186 2L 0 0
CG31177 LTR mdg1 22 FBti0019414 7338 3R 3.16 0
CG8776 LTR roo 23 FBti0019021 8313 2R 2.75 0
CG12885 LTR roo 24 FBti0020389 1051 3R 3.21 0*
CG32030 LINE I-element 25 FBti0020071 5348 3L 3.21 0
CG32594 LTR rover 26 FBti0019061 7469 X 3.61 0
CG17642(mRpL48) LTR mdg3 27a FBti0019107 267 2L 3.11 0*
CG17657 LTR mdg3 27b FBti0019107 267 2L 3.11 0*
CG7213 LINE Rt1a 28 FBti0020068 5177 3L 3.27 1
CG32684(alpha-Man-I) LTR roo 29 FBti0019615 9091 X 4.24 1
CG12094 LTR 412 30 FBti0019614 7441 X 4.23 1
CG18316 LTR 297 31 FBti0019977 6522 2R 0.68 1*
CG17697(fz) LINE X-element 32 FBti0020107 4728 3L 2.06 1*
CG18754 LTR roo 33 FBti0019420 427 3R 3.26 2
CG5130 LTR springer 34a FBti0020178 7542 3L 0 2
CG5976 LTR springer 34b FBti0020178 7542 3L 0 2
CG5656 TIR Tc1 35 FBti0020191 462 3L 0 4
CG31146 LTR invader3 36 FBti0020315 717 3R 0 4
CG14693 LTR 17.6 37 FBti0019354 7474 3R 1.03 4
CG11081(plexA) TIR Tc1 38 FBti0019510 530 4 0 5
CG32021 LTR invader4 39 FBti0019504 3082 4 0 5
CG18026(Caps) LINE F-element 40 FBti0020453 346 4 0 5
CG3812 TIR 1360 41 FBti0019634 376 X 4.07 5
CG32021 TIR 1360 42 FBti0019502 1075 4 0 6
CG18446 LTR roo 43 FBti0019985 427 2R 1.6 6*
CG10618 LINE Doc 44 FBti0019430 4512 3R 3.28 6
CG3136 LINE X-element 45 FBti0018950 1399 2R 0 6
CG32021 TIR transib3 46 FBti0019501 935 4 0 6
CG15347 TIR HB 47 FBti0019605 358 X 4.13 6
CG5541 TIR HB 48 FBti0019636 413 X 3.61 6
CG6191 LINE jockey 49 FBti0018988 265 2R 3.02 N.D.
CG10987 LTR roo 50 FBti0019665 427 X 0.94 N.D.
CG9527 LTR roo 51 FBti0019753 9098 2L 4.02 N.D.*
CG17521(Qm) TIR S2 52 FBti0020228 988 3L 0 N.D.
CR32865 LTR DM88 53 FBti0020348 168 3R 1.53 N.D.
CR32865 LTR invader1 54 FBti0020349 419 3R 1.53 N.D.
CG1090 LTR roo 55 FBti0019285 8325 3R 0 N.D.
CG1558(l(1)G0237) TIR pogo 56 FBti0019627 186 X 4.2 N.D.
CG1710 (Hcf) TIR 1360 57 FBti0020419 499 4 0 N.D.
CG1548(cathD) LTR Burdock 58 FBti0018882 6412 2R 0.52 N.D.*
CG3857 LTR opus 59 FBti0019540 7515 X 2.14 N.D.
CG32000 TIR 1360 60 N.A. 963 4 - N.D.
CG4494 (smt3) LTR mdg1 61 N.A. 51 2L - N.D.
CG6998 (ctp) LTR HMS-Beagle 62 N.A. 261 X - N.D.
CG3164 LTR McClintock 63 N.A. 80 2L - N.D.
CG7187(Ssdp) LTR HMS-Beagle 64 N.A. 212 3R - N.D.
CG9075(eIF-4a) LTR blood 65 N.A. 47 2L - N.D.