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Table 1 Transposon loci that show large difference after correcting for pre-mRNA/retained introns. a. Transposon loci embedded within introns or exons of genes that frequently result in the largest correction in each sample. Locus id, genomic location, surrounding gene and structure the TE is embedded in, and the maximum number of reads removed in a sample

From: Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements

locus chr start end surrounding gene TE embedded in # of samples Max correction
MIRc_dup47590 8 22021288 22021431 SFTPC Intron 4, Exon 5 105 428021
AluY_dup80589 12 69747275 69747567 LYZ Exon 4 62 313317
MIRb_dup137684 10 81315669 81315913 SFTPA2 Exon 5 106 266566
MIRb_dup137689 10 81374907 81375150 SFTPA1 Exon 5 106 230394
MIR3_dup57107 10 81316603 81316678 SFTPA2 Exon 5 103 90241
AluSz6_dup3320 1 207102295 207102608 PIGR Exon 11 124 59130
MIRc_dup74805 12 50351953 50352157 AQP2 Exon 4 109 57581
LTR39_dup404 6 160102172 160102969 SOD2 Exon 4, Intron 7 119 34545
AluSx1_dup59209 Y 21153222 21153521 TTTY14 Exon 1 305 25867
AluJb_dup119100 17 16344881 16345132 C17orf76-AS1 Intron 4, Exon 5 253 21915
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Mobile DNA

ISSN: 1759-8753