Table 2

Novel transcriptional active regions (TARs) and exons discovered in placental tissues

Amnion

Chorion

Decidua


Transcripts


Total transcripts

92,265

107,371

105,158


Multi-exon# transcripts

69,721

69,858

75,958


Perfect match with annotated transcripts (ignoring transcript start and end)

21,288

22,724

25,077


Total TARs*

13,469

16,987

15,158


Novel TARs (not overlapping with the combined annotation of Ensembl, UCSC, RefSeq and Vega genes)

604

1,007

896


Internal exons in TARs overlapping annotated transcripts


Total exons

93,506

103,356

100,003


Annotated exons

75,154

81,591

83,283


Novel exons with one end (5' or 3') shared with an annotated exon

16,907

20,121

15,246


Novel exons overlapping with an annotated exon but with no shared 5' or 3' end

950

1,093

876


Novel exons not overlapping with any annotated exons

494

537

585


Analysis was performed using software Scripture for ab initio reconstruction of transcripts for each placental tissue after sequence mapping with Tophat.

*TAR: Transcriptional Active Region after merging overlapping transcripts

# Single exon transcripts were not included in all the downstream analysis

Kim et al. BMC Genomics 2012 13:115   doi:10.1186/1471-2164-13-115

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