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Kim JM, et al.  (1998) Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res 8(5):464-78

Abstract: We conducted a genome-wide survey of Saccharomyces cerevisiae retrotransposons and identified a total of 331 insertions, including 217 Ty1, 34 Ty2, 41 Ty3, 32 Ty4, and 7 Ty5 elements. Eighty-five percent of insertions were solo long terminal repeats (LTRs) or LTR fragments. Overall, retrotransposon sequences constitute >377 kb or 3.1% of the genome. Independent evolution of retrotransposon sequences was evidenced by the identification of a single-base pair insertion/deletion that distinguishes the highly similar Ty1 and Ty2 LTRs and the identification of a distinct Ty1 subfamily (Ty1'). Whereas Ty1, Ty2, and Ty5 LTRs displayed a broad range of sequence diversity (typically ranging from 70%-99% identity), Ty3 and Ty4 LTRs were highly similar within each element family (most sharing >96% nucleotide identity). Therefore, Ty3 and Ty4 may be more recent additions to the S. cerevisiae genome and perhaps entered through horizontal transfer or past polyploidization events. Distribution of Ty elements is distinctly nonrandom: 90% of Ty1, 82% of Ty2, 95% of Ty3, and 88% of Ty4 insertions were found within 750 bases of tRNA genes or other genes transcribed by RNA polymerase III. tRNA genes are the principle determinant of retrotransposon distribution, and there is, on average, 1.2 insertions per tRNA gene. Evidence for recombination was found near many Ty elements, particularly those not associated with tRNA gene targets. For these insertions, 5'- and 3'-flanking sequences were often duplicated and rearranged among multiple chromosomes, indicating that recombination between retrotransposons can influence genome organization. S. cerevisiae offers the first opportunity to view organizational and evolutionary trends among retrotransposons at the genome level, and we hope our compiled data will serve as a starting point for further investigation and for comparison to other, more complex genomes.

Status: Published Type: Journal Article PubMed ID: 9582191

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YALCdelta2 YALWdelta1 YAR009C YAR010C YARCdelta3 YARCdelta4 YARCdelta5 YARCdelta8 YARCTy1-1 YARWdelta6
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YARWdelta7 YARWsigma1 YBL005W-A YBL005W-B YBL100W-A YBL100W-B YBLCdelta7 YBLCtau1 YBLWdelta1 YBLWdelta10
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Topics Genes linked to topics (#21 - 30 )
YBLWdelta2 YBLWdelta3 YBLWdelta4 YBLWdelta5 YBLWdelta6 YBLWdelta8 YBLWdelta9 YBLWsigma1 YBLWTy1-1 YBLWTy2-1
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Topics Genes linked to topics (#31 - 40 )
YBR012W-A YBR012W-B YBRCdelta11 YBRCdelta14 YBRCdelta19 YBRCtau2 YBRWdelta12 YBRWdelta13 YBRWdelta15 YBRWdelta16
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Topics Genes linked to topics (#41 - 50 )
YBRWdelta17 YBRWdelta18 YBRWTy1-2 YCL019W YCL020W YCL074W YCL075W YCLCdelta1 YCLWdelta2a YCLWdelta2b
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YCLWdelta3 YCLWdelta4 YCLWdelta5 YCLWomega1 YCLWomega2 YCLWTy2-1 YCLWTy5-1 YCRCdelta14 YCRCdelta6 YCRCdelta7
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YCRCtau1 YCRWdelta10 YCRWdelta11 YCRWdelta12 YCRWdelta13 YCRWdelta8 YCRWdelta9 YCRWomega3 YDLCdelta1 YDLWtau1
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YDR034C-C YDR034C-D YDR098C-A YDR098C-B YDR170W-A YDR210C-C YDR210C-D YDR210W-A YDR210W-B YDR261C-C
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YDR261C-D YDR261W-A YDR261W-B YDR316W-A YDR316W-B YDR365W-A YDR365W-B YDRCdelta2 YDRCdelta21 YDRCdelta22
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Topics Genes linked to topics (#91 - 100 )
YDRCdelta3 YDRCdelta4 YDRCdelta5 YDRCdelta6a YDRCdelta6b YDRCdelta7 YDRCdelta8 YDRCdelta9 YDRCsigma1 YDRCsigma3
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YDRCsigma4 YDRCsigma6 YDRCTy1-1 YDRCTy1-2 YDRCTy1-3 YDRCTy2-1 YDRWdelta10 YDRWdelta11 YDRWdelta12 YDRWdelta13
DNA/RNA Sequence Features blue ball blue ball blue ball blue ball
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Topics Genes linked to topics (#111 - 120 )
YDRWdelta14 YDRWdelta19 YDRWdelta20 YDRWdelta23 YDRWdelta24 YDRWdelta25 YDRWdelta26 YDRWdelta27 YDRWdelta28 YDRWdelta29
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Topics Genes linked to topics (#121 - 130 )
YDRWdelta30 YDRWdelta31 YDRWdelta7 YDRWsigma2 YDRWsigma5 YDRWTy1-4 YDRWTy1-5 YDRWTy2-2 YDRWTy2-3 YELCdelta3
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Topics Genes linked to topics (#131 - 140 )
YELCdelta4 YELCtau1 YELWdelta1 YELWdelta2 YELWdelta5 YELWdelta6 YER137C-A YER138C YER159C-A YER160C
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Topics Genes linked to topics (#141 - 150 )
YERCdelta10 YERCdelta14 YERCdelta15 YERCdelta16 YERCdelta19 YERCdelta20 YERCdelta23 YERCdelta24 YERCdelta26 YERCdelta8
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YERComega1 YERCsigma1 YERCsigma2 YERCsigma3 YERCsigma4 YERCtau2 YERCtau3 YERCTy1-1 YERCTy1-2 YERWdelta11
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YERWdelta12 YERWdelta13 YERWdelta17 YERWdelta21 YERWdelta22 YERWdelta25 YERWdelta7 YERWdelta9 YERWomega2 YFL002W-A
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YFL002W-B YFLCdelta6 YFLWdelta1 YFLWdelta2 YFLWdelta3 YFLWdelta4 YFLWdelta5 YFLWtau1 YFLWTy2-1 YFRCdelta8
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Topics Genes linked to topics (#181 - 190 )
YFRCdelta9 YFRWdelta10 YFRWdelta7 YGLCdelta1 YGLCdelta5 YGLCsigma1 YGLCsigma3 YGLCtau3 YGLWdelta10 YGLWdelta2
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Topics Genes linked to topics (#191 - 200 )
YGLWdelta3 YGLWdelta4 YGLWdelta6 YGLWdelta7 YGLWdelta8 YGLWdelta9 YGLWomega1 YGLWsigma2 YGLWtau1 YGLWtau2
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YGR027W-A YGR027W-B YGR038C-A YGR038C-B YGR109W-A YGR109W-B YGR161C-C YGR161C-D YGR161W-A YGR161W-B
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YGRCdelta12 YGRCdelta15 YGRCdelta16 YGRCdelta17 YGRCdelta18 YGRCdelta20 YGRCdelta25 YGRCdelta29 YGRCdelta30 YGRCtau3
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Topics Genes linked to topics (#221 - 230 )
YGRCTy1-2 YGRCTy1-3 YGRCTy2-1 YGRWdelta11 YGRWdelta13 YGRWdelta14 YGRWdelta19 YGRWdelta21 YGRWdelta22 YGRWdelta23
DNA/RNA Sequence Features blue ball blue ball blue ball
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Topics Genes linked to topics (#231 - 240 )
YGRWdelta24 YGRWdelta26 YGRWdelta27 YGRWdelta28 YGRWdelta31 YGRWdelta32 YGRWsigma4 YGRWsigma5 YGRWsigma6 YGRWsigma7
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Topics Genes linked to topics (#241 - 250 )
YGRWTy1-1 YGRWTy2-2 YGRWTy3-1 YHL009W-A YHL009W-B YHLCdelta1 YHLComega1 YHLCsigma1 YHLWdelta2 YHLWtau1
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Topics Genes linked to topics (#251 - 260 )
YHLWtau2 YHLWTy4-1 YHR214C-B YHR214C-C YHRCdelta10 YHRCdelta11 YHRCdelta12 YHRCdelta14 YHRCdelta15 YHRCdelta16
DNA/RNA Sequence Features blue ball
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Topics Genes linked to topics (#261 - 270 )
YHRCdelta3 YHRCdelta4 YHRCdelta5 YHRCdelta6 YHRCdelta8 YHRCsigma2 YHRCsigma3 YHRCtau4 YHRCTy1-1 YHRWdelta13
DNA/RNA Sequence Features blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#271 - 280 )
YHRWdelta7 YHRWdelta9 YHRWtau3 YIL080W YIL082W YIL082W-A YILCdelta1 YILCdelta3 YILCdelta5 YILCtau1
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Topics Genes linked to topics (#281 - 290 )
YILWdelta2 YILWdelta4 YILWsigma1 YILWsigma2 YILWsigma3 YILWTy3-1 YIRCdelta6 YJL113W YJL114W YJLCdelta3
DNA/RNA Sequence Features blue ball
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Topics Genes linked to topics (#291 - 300 )
YJLCdelta4 YJLCdelta5 YJLCdelta6 YJLCdelta7 YJLWdelta1 YJLWdelta10 YJLWdelta8 YJLWdelta9 YJLWsigma1 YJLWtau1
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Topics Genes linked to topics (#301 - 310 )
YJLWtau2 YJLWtau3 YJLWtau4 YJLWTy4-1 YJR026W YJR027W YJR028W YJR029W YJRCdelta15 YJRCdelta16
DNA/RNA Sequence Features blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#311 - 320 )
YJRCdelta19 YJRWdelta11 YJRWdelta12 YJRWdelta13 YJRWdelta14 YJRWdelta17 YJRWdelta18 YJRWdelta20 YJRWTy1-1 YJRWTy1-2
DNA/RNA Sequence Features blue ball blue ball
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Topics Genes linked to topics (#321 - 330 )
YKLCdelta2 YKLCdelta4 YKLCdelta5 YKLCdelta6 YKLCsigma1 YKLWdelta1 YKLWdelta3 YKLWdelta7 YKRCdelta11 YKRCdelta12
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Topics Genes linked to topics (#331 - 340 )
YKRCdelta8 YKRCdelta9 YKRWdelta10 YKRWomega1 YLLCdelta1 YLR035C-A YLR157C-A YLR157C-B YLR227W-A YLR227W-B
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#341 - 350 )
YLR256W-A YLR410W-A YLR410W-B YLRCdelta16 YLRCdelta18 YLRCdelta19 YLRCdelta2 YLRCdelta21 YLRCdelta25 YLRCdelta26
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Topics Genes linked to topics (#351 - 360 )
YLRCdelta27 YLRCdelta3 YLRCdelta5 YLRCdelta7 YLRCdelta8 YLRCdelta9 YLRCsigma1 YLRCtau1 YLRCTy1-1 YLRCTy2-2
DNA/RNA Sequence Features blue ball blue ball
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Topics Genes linked to topics (#361 - 370 )
YLRWdelta10 YLRWdelta11 YLRWdelta12 YLRWdelta13 YLRWdelta14 YLRWdelta15 YLRWdelta17 YLRWdelta20 YLRWdelta22 YLRWdelta23
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YLRWdelta24 YLRWdelta4 YLRWdelta6 YLRWsigma2 YLRWsigma3 YLRWsigma4 YLRWTy1-2 YLRWTy1-3 YLRWTy2-1 YML039W
DNA/RNA Sequence Features blue ball blue ball blue ball
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Topics Genes linked to topics (#381 - 390 )
YML040W YML045W YML045W-A YMLCdelta1 YMLCdelta2 YMLWdelta3 YMLWdelta4 YMLWdelta5 YMLWdelta6 YMLWTy1-1
DNA/RNA Sequence Features blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#391 - 400 )
YMLWTy1-2 YMR045C YMR046C YMR050C YMR051C YMRCdelta10 YMRCdelta11 YMRCdelta13 YMRCdelta14 YMRCdelta18
DNA/RNA Sequence Features blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#401 - 410 )
YMRCdelta7 YMRCdelta8 YMRCdelta9 YMRCtau1 YMRCtau3 YMRCTy1-3 YMRCTy1-4 YMRWdelta12 YMRWdelta15 YMRWdelta16
DNA/RNA Sequence Features blue ball blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#411 - 420 )
YMRWdelta17 YMRWdelta19 YMRWdelta20 YMRWdelta21 YMRWtau2 YNL054W-A YNL054W-B YNL284C-A YNL284C-B YNLCdelta1
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Topics Genes linked to topics (#421 - 430 )
YNLCdelta2 YNLCdelta5 YNLCdelta6 YNLCsigma1 YNLCTy1-1 YNLCTy2-1 YNLWdelta3 YNLWdelta4 YNLWsigma2 YNLWsigma3
DNA/RNA Sequence Features blue ball blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#431 - 440 )
YNLWtau1 YNLWtau2 YNLWTy1-2 YNRCdelta7 YNRCdelta8 YNRCdelta9 YNRCtau3 YNRWsigma4 YOL103W-A YOL103W-B
DNA/RNA Sequence Features blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#441 - 450 )
YOLCdelta1 YOLCdelta2 YOLCdelta3 YOLCdelta7 YOLCdelta8 YOLWdelta4 YOLWdelta5 YOLWdelta6 YOLWsigma1 YOLWtau1
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#451 - 460 )
YOLWTy1-1 YOR142W-A YOR142W-B YOR192C-A YOR192C-B YOR343W-A YOR343W-B YORCdelta11 YORCdelta15 YORCdelta18
DNA/RNA Sequence Features blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#461 - 470 )
YORCdelta20 YORCdelta21 YORCdelta25 YORCdelta9 YORCTy2-1 YORWdelta10 YORWdelta12 YORWdelta13 YORWdelta14 YORWdelta16
DNA/RNA Sequence Features blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#471 - 480 )
YORWdelta17 YORWdelta19 YORWdelta22 YORWdelta23 YORWdelta24 YORWsigma2 YORWsigma3 YORWsigma4 YORWtau2 YORWtau3
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Topics Genes linked to topics (#481 - 490 )
YORWTy1-2 YORWTy2-2 YPL060C-A YPL257W-A YPL257W-B YPLCdelta1 YPLCdelta10 YPLCtau1 YPLCtau2 YPLCTy4-1
DNA/RNA Sequence Features blue ball blue ball blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#491 - 500 )
YPLWdelta11 YPLWdelta2 YPLWdelta3 YPLWdelta4 YPLWdelta5 YPLWdelta6 YPLWdelta7 YPLWdelta8 YPLWdelta9 YPLWsigma1
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Topics Genes linked to topics (#501 - 510 )
YPLWTy1-1 YPR137C-A YPR137C-B YPR158C-C YPR158C-D YPR158W-A YPR158W-B YPRCdelta13 YPRCdelta15 YPRCdelta18
DNA/RNA Sequence Features blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#511 - 520 )
YPRCdelta19 YPRCdelta22 YPRCdelta23 YPRCdelta24 YPRCtau3 YPRCTy1-2 YPRCTy1-4 YPRWdelta12 YPRWdelta14 YPRWdelta16
DNA/RNA Sequence Features blue ball blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

Topics Genes linked to topics (#521 - 528 )
YPRWdelta17 YPRWdelta20 YPRWdelta21 YPRWsigma2 YPRWsigma3 YPRWsigma4 YPRWtau4 YPRWTy1-3
DNA/RNA Sequence Features blue ball
Primary Literature blue ball blue ball blue ball blue ball blue ball blue ball blue ball blue ball

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