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Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells

Georges St Laurent12*, Dmitry Shtokalo23, Michael R Tackett2, Zhaoqing Yang2, Tatyana Eremina2, Claes Wahlestedt4, Silvio Urcuqui-Inchima1, Bernd Seilheimer5, Timothy A McCaffrey6 and Philipp Kapranov2*

Author Affiliations

1 Immunovirology – Biogenisis Group, University of Antioquia, Medellin, A.A. 1226, Colombia

2 St. Laurent Institute, One Kendall Square, Cambridge, MA, USA

3 A.P.Ershov Institute of Informatics Systems SB RAS, 6, Acad. Lavrentjev pr, Novosibirsk, 630090, Russia

4 University of Miami Miller School of Medicine, 1501 NW 10th Ave, Miami, FL, 33136, USA

5 Biologische Heilmittel Heel GmbH, Dr.-Reckeweg-Str. 2-4, Baden-Baden, 76532, Germany

6 Department of Medicine, Division of Genomic Medicine, The George Washington University Medical Center, 2300 I St. NW, Washington, DC, USA

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BMC Genomics 2012, 13:504  doi:10.1186/1471-2164-13-504

Published: 24 September 2012

Additional files

Additional file 1:

Figure S1. A scheme of the strategy to partition intronic coordinates in the cases of overlapping transcripts. Boxes –exons, lines – introns. Regions 1–4 were used to calculate the average read density of the corresponding introns.

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Additional file 2:

Table S1. Correlation of specified introns of Prkca and Slc24a3 with their corresponding exons.

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Additional file 3:

Table S2. Properties of individual mouse introns.

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Additional file 4:

Table S3. Details of RT-PCR analysis in selected mouse introns.

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Additional file 5:

Figure S2. An example of DE bins specifically detecting a specific up-regulated isoform of Adora3 locus.

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Additional file 6:

Figure S3. Examples of DE bins detecting regions around annotated miRNAs, found both in an intron (mir-135b, A) and an interegenic region (mir-146a, B).

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