Open Access Research article

Alternative splicing at NAGNAG acceptors in Arabidopsis thaliana SR and SR-related protein-coding genes

Stefanie Schindler1*, Karol Szafranski1, Michael Hiller2, Gul Shad Ali3, Saiprasad G Palusa3, Rolf Backofen2, Matthias Platzer1 and Anireddy SN Reddy3

Author Affiliations

1 Genome Analysis, Leibniz Institute for Age Research – Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany

2 Institute of Computer Science, Bioinformatics Group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany

3 Department of Biology and Program in Molecular Plant Biology, Colorado State University, Fort Collins, CO, USA

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BMC Genomics 2008, 9:159  doi:10.1186/1471-2164-9-159

Published: 10 April 2008

Additional files

Additional file 1:

All NAGNAG acceptor cases identified within the Arabidopsis genome. The absolute numbers of ESTs supporting the E- or the I-acceptor ("ESTs_E" and "ESTs_I", respectively) and the sequence-based prediction of E-transcript frequency ("expected_E") are given.

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Additional file 2:

Counts of Arabidopsis NAGNAG cases depending on local EST coverage. The number of cases at least reaching a given coverage is presented.

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Additional file 3:

Heptamer motif classification. Heptameric motif classes are presented with corresponding maximum-likelihood estimators for E-to-I-transcript ratios, used for sequence-based prediction.

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Additional file 4:

Comprehensive list of experimental values from all analyzed SR and SR-related protein-coding genes. Column 'avg' lists the averaged E-transcript proportions derived from three independent experiments per probe with corresponding standard deviation in column 'sd'. The values derived from the 3d, 5d, 10d, 15d old seedlings, callus and organs were averaged (column 'avg organs-seedlings') as well as the corresponding standard deviations ('avg error') to gain appropriate values for a comparison with the sequence-based predictions (see column 'predicted'). Grey shaded values mark the cases where NAGNAG alternative splicing was validated [(avg error × 2) < (avg organs-seedlings)].

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