ASTD: The Alternative Splicing and Transcript Diversity database

Gautier Koscielny, Vincent Le Texier, Chellappa Gopalakrishnan, Vasudev Kumanduri, Jean Jack Riethoven, Francesco Nardone, Eleanor Stanley, Christine Fallsehr, Oliver Hofmann, Meelis Kull, Eoghan Harrington, Stéphanie Boué, Eduardo Eyras, Mireya Plass, Fabrice Lopez, William Ritchie, Virginie Moucadel, Takeshi Ara, Heike Pospisil, Alexander HerrmannJens G. Reich, Roderic Guigó, Peer Bork, Magnus von Knebel Doeberitz, Jaak Vilo, Winston Hide, Rolf Apweiler, Thangavel Alphonse Thanaraj, Daniel Gautheret

Research output: Contribution to journalArticle

75 Scopus citations

Abstract

The Alternative Splicing and Transcript Diversity database (ASTD) gives access to a vast collection of alternative transcripts that integrate transcription initiation, polyadenylation and splicing variant data. Alternative transcripts are derived from the mapping of transcribed sequences to the complete human, mouse and rat genomes using an extension of the computational pipeline developed for the ASD (Alternative Splicing Database) and ATD (Alternative Transcript Diversity) databases, which are now superseded by ASTD. For the human genome, ASTD identifies splicing variants, transcription initiation variants and polyadenylation variants in 68%, 68% and 62% of the gene set, respectively, consistent with current estimates for transcription variation. Users can access ASTD through a variety of browsing and query tools, including expression state-based queries for the identification of tissue-specific isoforms. Participating laboratories have experimentally validated a subset of ASTD-predicted alternative splice forms and alternative polyadenylation forms that were not previously reported. The ASTD database can be accessed at http://www.ebi.ac.uk/astd.

Original languageEnglish (US)
Pages (from-to)213-220
Number of pages8
JournalGenomics
Volume93
Issue number3
DOIs
StatePublished - Mar 1 2009

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Keywords

  • Alternative initiation
  • Alternative polyadenylation
  • Alternative splicing
  • Alternative transcription

ASJC Scopus subject areas

  • Genetics

Cite this

Koscielny, G., Texier, V. L., Gopalakrishnan, C., Kumanduri, V., Riethoven, J. J., Nardone, F., Stanley, E., Fallsehr, C., Hofmann, O., Kull, M., Harrington, E., Boué, S., Eyras, E., Plass, M., Lopez, F., Ritchie, W., Moucadel, V., Ara, T., Pospisil, H., ... Gautheret, D. (2009). ASTD: The Alternative Splicing and Transcript Diversity database. Genomics, 93(3), 213-220. https://doi.org/10.1016/j.ygeno.2008.11.003