This article is part of the supplement: Tenth International Conference on Bioinformatics. First ISCB Asia Joint Conference 2011 (InCoB/ISCB-Asia 2011): Computational Biology

Open Access Proceedings

Profiling ascidian promoters as the primordial type of vertebrate promoter

Kohji Okamura12, Riu Yamashita1, Noriko Takimoto3, Koki Nishitsuji34, Yutaka Suzuki5, Takehiro G Kusakabe4 and Kenta Nakai1*

Author Affiliations

1 Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo, Japan

2 Centre for Informational Biology, Ochanomizu University, Tokyo, Japan

3 Department of Life Science, Graduate School of Life Science, University of Hyogo, Hyogo, Japan

4 Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan

5 Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan

For all author emails, please log on.

BMC Genomics 2011, 12(Suppl 3):S7  doi:10.1186/1471-2164-12-S3-S7

Published: 30 November 2011

Additional files

Additional file 1:

Ciona intestinalis embryos at mid-tailbud stage (Figure S1) A photo of two C. intestinalis embryos at mid-tailbud stage, taken 12 hours after fertilization.

Format: PDF Size: 68KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Summary of the TSS-seq experiments (Tables S1 and S2) Quantitative data for the 6312 non-trans-spliced and 8753 trans-spliced transcripts which were annotated by the nearest genes.

Format: XLSX Size: 957KB Download file

Open Data

Additional file 3:

Changes in dinucleotide scores in the vicinity of TSSs (Figure S2) The score changes are shown for ascidian promoters (A), human CpG-poor promoters (B), and human CpG-rich promoters (C).

Format: PDF Size: 671KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data