Table 1. Top pseudogene candidates of three different types of predicted functional potentials (ND, not determined). The full lists can be found in Table S1.

Pseudogene	Genomic Location	Parental gene	Transcribed strand	ρpg:g	Note
A. miRNA decoy
PTENP1	chr9:33673502-33677497 (−)	PTEN	sense	0.87	Compete with PTEN for miRNA binding [28].
FAM92A1P1	chr15:41455322-41456695 (+)	FAM92A1	sense	0.80
MYLKP1	chr3:75377700-75388222 (−)	MYLK	sense	0.94	Promote cell proliferation [100], but miRNA involvement unknown.
CROCCP3	chr1:16802411-16817802 (−)	CROCC	sense	0.70
ABCC6P2	chr16:14914649-14918526 (−)	ABCC6	NA	0.50
RP11-321E8	chr7:63929563-63931031 (+)	ZNF680	sense	0.39
B. siRNA repressing coding gene
ψPPM1K	chr4:89179936-89180414 (−)	PPM1K	antisense	ND	Target both NEK8 and PPM1K gene and suppress cell growth [30]. Not annotated by GENCODE.
ATP8A2P1	chr10:37537046-37604729 (+)	ATP8A2	antisense	−0.22	KD inhibited cell proliferation [12]
HMGA1P7	chr6:134435733-134436628 (−)	HMGA1	antisense	−0.25
CNN2P1	chr22:30442265-30443182 (−)	CNN2	antisense	−0.32
RP11-553K8.3	chr1:198648263-198649162 (−)	PEBP1	NA	−0.56
MSNP1	chr5:25909612-25911343 (+)	MSN	sense	−0.5	Antisense ncRNA was reported [19]
RP11-159C21.4	chr1:53237865 -53238320(−)	RPS13	sense	0.52
C. siRNA mediating H3K9me3 enrichment
MTND4P12	chr5:134262350-134263726(−)	MTND4	both	ND
RP5-857K21.6	chr1:566454-567996(+)	MT-CO1	sense	ND
SDHAP2	chr3:195384967-195412775(+)	SDHA	ND	0.54
FTLP3	chr20:4004564-4005091(+)	FTL	sense	ND
RP11-7G23.4	chr9:45729709-45730417(+)	FAM27A	ND	ND