Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data

BMC Genomics

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.

ISSN: 1471-2164