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This article is part of the supplement: Ninth International Conference on Bioinformatics (InCoB2010): Computational Biology

Open Access Proceedings

RNA editing of nuclear transcripts in Arabidopsis thaliana

Yijun Meng123, Dijun Chen12, YongFeng Jin3, Chuanzao Mao2, Ping Wu2 and Ming Chen12*

Author Affiliations

1 Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China

2 State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China

3 Institute of Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, P. R. China

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BMC Genomics 2010, 11(Suppl 4):S12  doi:10.1186/1471-2164-11-S4-S12

Published: 2 December 2010

Additional files

Additional file 1 - Data S1 Edited sites in protein-coding genes in Arabidopsis (only the editing sites resided in mRNAs were considered):

Prediction criteria: more than two candidate editing sites should be present in one transcript and each editing site must be supported by more than five distinct short-read sequences.

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Open Data

Additional file 2 - Data S2 Editing sites in pre-miRNAs in Arabidopsis:

Prediction criteria: each editing site in one pre-miRNA should be supported by more than two distinct short-read sequences.

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Open Data

Additional file 9:

Data S7 Detailed information of the MPSS and PARE data utilized in this study.

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Additional file 3:

Data S3 100-nt sequences surrounding the editing sites in protein-coding genes, which were utilized for conserved element detection. The random sequences for control analysis are included.

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Additional file 4:

Data S4 Results of searching for conserved elements surrounding the editing sites in protein-coding genes. The results of three replicates of control analysis are included.

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Additional file 5:

Data S5 Result of GO term enrichment analysis of edited protein-coding genes in Arabidopsis.

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Additional file 6:

Figure S1 Clustering analysis of RNA editing sites.

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Additional file 7:

Data S6 Codon variation by RNA editing in nuclear protein-coding genes (only the edited codons resided in CDSs were considered).

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Additional file 8:

Figure S2 Secondary structure transformation of edited ath-MIR854a, ath-MIR854b, and ath-MIR854d.

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Open Data