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ASIP Selection



       


Data set for Wang et al, BMC plant biology 2008

  Medicago Lotus Arabidopsis Rice
cDNA/EST
150,855 691,516 1,009,754
Genome Mt1.0 GenBank records TAIR 6 & 7 TIGR 4 & 5
Raw alignments
ASgenes 1,107 92 4,497 6,313
Introns 32,860 4,357 97,095 107,162
Internal exons 24,600 2,717 78,911 83,668
MySQL dump

Data set for Wang and Brendel, PNAS 2006 (AtTAG1/RiceTAG1)

1. List and annotation of alternatively spliced genes

  • Arabidopsis: text, html
  • Rice: text, html

    Note:The total numbers here are slightly different than the numbers in our PNAS paper, due to the ambiguity of assinging gene models to EST/cDNA contigs covering multiple annotated genes. We will update these lists again using newer version of gene annotation.

    2. Intron, exon, and junction* sequences

  • Arabidopsis: introns, exons, junctions*
  • Rice: introns, exons, junctions*

    * Note: Junction sequences are 30bp upstream and downstream exon sequences surrounding each intron.

    3. Raw GeneSeqer alignment, MySQL database dump.

  • Arabidopsisaee mysql database, Raw GeneSeqer alignment.
  • Rice: mysql database.
  • Both: Table and columns description.

    ASIP tools

    The tool we developped for identification of AS events from EST alignments (ASpipe) is available through Sourceforge.
    The visualization tool ASviewer is available upone request.

    Note

    Other types of data are available upon request.