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Table 1 TE effect on the human transcriptome

From: Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome

RE

Total

Intronic

TE in introns of UCSC annotated genesa

TE in introns of non-annotated genesa

TE exonization in UCSC annotated genesa

TE exonization in non-annotated genesa

Alu

1,094,409

718,460 (66%)

480,052

238,408

1060 (0.2%)

584 (0.2%)

MIR

537,730

351,366 (65%)

231,893

119,473

181 (0.08%)

134 (0.1%)

L1

830,062

486,901 (58%)

282,146

204,755

219 (0.08%)

250 (0.1%)

L2

375,116

240,350 (64%)

154,309

86,041

103 (0.07%)

72 (0.08%)

CR1

50,156

33,365 (66%)

22,087

11,278

12 (0.04%)

6 (0.05%)

LTR

654,897

292,456 (44%)

136,461

155,995

155 (0.1%)

150 (0.09%)

DNA

389,688

226489 (58%)

145,968

80,521

93 (0.06%)

142 (0.17%)

Total

3,932,058

2,349,387 (60%)

1,452,916

896,471

1824 (0.12%)

1653 (0.18%)

  1. Insertions of transposed elements (TEs) within the human genome. The different classes of the examined TEs are shown in the left column. 'Total' (second column) indicates the overall amount of each TE within the human and mouse genomes. 'Intronic' (third column) indicates the number of TEs within intronic regions, and the percentage of TEs within introns relative to the total amount of TEs is shown in parentheses brackets. The fourth and fifth columns show the number of TEs within introns of the University of California, Santa Cruz (UCSC) knownGene list (version hg17) and those inserted within genes not listed within UCSC knownGene list. The sixth and seventh columns show the number of exonized TEs within the UCSC knownGene list and those exonized within genes not listed within UCSC knownGene list. In parentheses are indicated the percentage of exonized TEs is indicated. The lower row shows the total number of all TEs. aGene annotation is based on the annotations of the known gene list in the UCSC genome browser (version hg17). LTR, long terminal repeat; MIR, mammalian interspersed repeat; RE, retroelement.