Table 3

RP pseudogenes expression identified in Human Body Map 2.0 RNA-seq data
pg-id Parent gene Location Tissue with Max RPKM Max RPKM Total RPKM Tissue specificity Reads coverage
249508 RPL21 chr8:134084035-134084502 Thyroid 170.3 170.6 0.977 0.976
237215 RPL7A chr17:6984988-6985635 White Blood Cells 17.3 18.0 0.881 0.913
249146 RPS24 chr16:55497947-55498335 Kidney 16.5 17.6 0.855 0.693
239833 RPS11 chr12:63076580-63077044 Testes 11.3 12.5 0.813 0.970
236635 RPL24 chr9:72021934-72022269 Colon 9.7 9.7 1.000 0.358
248697 RPL26 chr16:1953719-1954097 Lymph 9.0 37.9 0.376 0.854
242376 RPS20 chr11:77202016-77202370 Colon 8.6 41.6 0.355 1.00
251340 RPLP1 chr5:151125656-151125993 Testes 7.4 40.1 0.339 0.567
237777 RPL7 chr3:133445060-133445787 Prostate 7.3 8.0 0.819 0.371
234492 RPL10 chr19:9791817-9792131 Brain 7.2 10.8 0.635 0.121
248932 RPL21 chr16:72904438-72904782 Ovary 6.5 34.3 0.343 1.00
234407 RPL39 chr19:58143205-58143330 Colon 6.3 21.3 0.414 1.00
239633 RPL13 chr12:6863424-6864038 Kidney 6.0 27.0 0.365 0.923
245936 RPL6 chr4:66121772-66122638 Colon 5.9 7.2 0.746 0.109
243590 RPL32 chr6:33155206-33155612 Adrenal 5.8 9.2 0.617 1.00
241074 RPL13A chr2:203093361-203093957 Lung 5.4 9.7 0.571 0.995
238877 RPL11 chr10:89695235-89695766 Adipose 5.2 20.4 0.387 0.847

Expression levels of pseudogenes with their pseudogene ID (pg-id, prefix ‘PGOHUM00000’ omitted) are measured in terms of RPKM. Only pseudogenes with maximum RPKM > 5 are shown. Tissue specificities are measured by the JS divergence [20]. Read coverage is the ratio of pseudogene exon length covered by uniquely mapped reads to the total pseudogene exon length.

Tonner et al.

Tonner et al. BMC Genomics 2012 13:412   doi:10.1186/1471-2164-13-412

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