Table 3.

Summary of classification of lncRNA transcripts with respect to their localization, overlap and orientation relative to transcription of proximal protein-coding RNA transcripts.

	1aOverlapping	1GENIC	1cNested	Total
		1bContaining
Antisense Exonic	9,326	1,816	3,552	14,694
Antisense Intronic	1,302	1,284	8,330	10,916
Sense Exonic	29,942	42,160	29,087	101,189
Sense Intronic	327	994	13,274	14,595
Total	40,897	46,254	54,243	141,394
		2INTERGENIC
	2aConvergent	2bDivergent	2cSame_Strand	Total
Upstream	—	14,930	13,408	26,470
Downstream	11,540	—	10,662	24,070
Total	11,540	14,930	24,070	50,540

The legend below explains the categories in detail:

¹GENIC: when the lncRNA gene overlaps an RNA gene from the reference annotation file

²INTERGENIC (lincRNA): otherwise.

GENIC type:

Then exonic or intronic locations:

^1aOverlapping subtype: the lncRNA partially overlaps the RNA partner transcript.

^1bContaining subtype: the lncRNA contains the RNA partner transcript.

^1cNested subtype: the lncRNA is contained in the RNA partner transcript.

INTERGENIC type:

^2aDivergent subtype: the lncRNA is transcribed in head to head orientation with RNA partner transcript: upstream or downstream.

^2bConvergent subtype: the lncRNA is oriented in tail to tail with orientation with RNA partner transcript: upstream or downstream.

^2cSame_strand subtype: the lncRNA is transcribed in the same orientation with RNA partner transcript: upstream or downstream.