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
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 |