Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription

Table 1 Evidence of intronic transcription in the human mRNA/RefSeq GenBank dataset

	mRNA clusters with overlap to exons of non-redundant RefSeq dataset*		mRNA clusters wholly intronic to non-redundant RefSeq dataset
	Antisense direction	Sense direction	Antisense direction	Sense direction	mRNA clusters not mapped to RefSeq dataset	Total
Spliced mRNA clusters^†	2,559 (1,414)^‡	14,575 (14,369^§)	1,049 (378)	780 (223)	4,181 (0)	23,144 (16,384)
Unspliced mRNA clusters^†	1,672 (26)	7,463 (87)	1,456 (56)	4,222 (87)	7,180 (927)	21,993 (1,183)
Total	4,231 (1,440)	22,038 (14,456)	2,505 (434)	5,002 (310)	11,361 (927)	45,137 (17,567)

*The non-redundant dataset comprises 15,783 spliced RefSeq units. This was defined by mapping to the human genome sequence the total of 22,458 RefSeq sequences from GenBank, excluding 1,184 unspliced RefSeq and 601 RefSeq that were wholly intronic to another RefSeq and merging the remaining 20,673 spliced RefSeq sequences that mapped to the same locus into 15,783 spliced non-redundant RefSeq units (a total of 4,890 RefSeq that represent isoforms of the same gene were thus merged into these units). ^†mRNA clusters were obtained by mapping to the human genome sequence a total of 161,993 mRNA sequences followed by merging sequences with exon overlapping coordinates (see Materials and methods for details), resulting in a non-redundant set of 45,137 mRNA clusters. This set was aligned to the non-redundant RefSeq dataset and each mRNA cluster was classified as exonic, wholly intronic or mapping outside of any spliced non-redundant RefSeq unit. Sense/antisense orientation was annotated. ^‡For each class, the number of mRNA clusters containing at least one RefSeq is shown in parentheses. ^§Excluding from the 15,783 spliced non-redundant RefSeq dataset a total of 1,414 RefSeq that map in the antisense direction with respect to another RefSeq.

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