Table 1.

Computationally derived intersections of all pseudogene, lncRNA, cDNA, and EST databases.

File 1 GID	File 2 GID	Exon-exon gene IDs	Sense Overlaps	Antisense Overlaps	Complex Loci
GENCODE 17 Pseudogenes	GENCODE 17 lncRNA	163	87	56	20
GENCODE 17 Pseudogenes vs. GENCODE 17 lncRNA	cDNA	64	33	4	27
GENCODE 17 Pseudogenes vs. GENCODE 17 lncRNA	EST	68	4	2	62
GENCODE 17 Pseudogenes vs. GENCODE 17 lncRNA	cDNA and EST	48	23	3	22
GENCODE 17 Pseudogenes	Human lincRNA	870	725	45	100
GENCODE 17 Pseudogenes vs. Human lincRNA	cDNA	371	216	15	140
GENCODE 17 Pseudogenes vs. Human lincRNA	EST	646	53	18	575
GENCODE 17 Pseudogenes vs. Human lincRNA	cDNA and EST	325	186	12	127
Retro Ali5	GENCODE 17 lncRNA	211	79	120	12
Retro Ali5 vs. GENCODE 17 lncRNA	cDNA	78	35	17	26
Retro Ali5 vs. GENCODE 17 lncRNA	EST	162	30	16	116
Retro Ali5 vs. GENCODE 17 lncRNA	cDNA and EST	69	32	15	22
Retro Ali5	Human lincRNA	557	405	108	44
Retro Ali5 vs. Human lincRNA	cDNA	129	61	26	42
Retro Ali5 vs. Human lincRNA	EST	381	64	34	283
Retro Ali5 vs. Human lincRNA	cDNA and EST	113	53	23	37
Yale 60	GENCODE 17 lncRNA	105	66	25	14
Yale 60 vs. GENCODE 17 lncRNA	cDNA	40	25	2	13
Yale 60 vs. GENCODE 17 lncRNA	EST	46	2	1	43
Yale 60 vs. GENCODE 17 lncRNA	cDNA and EST	31	18	1	12
Yale 60	Human lincRNA	547	468	24	55
Yale 60 vs. Human lincRNA	cDNA	192	123	6	63
Yale 60 vs. Human lincRNA	EST	372	38	12	322
Yale 60 vs. Human lincRNA	cDNA and EST	157	96	5	56

Directionality is relative to pseudogene locus, and complex loci refer to intersects which contain both sense and antisense overlaps.