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AltExtron Database - Flat filesAltExtron is a computer generated high quality dataset of human transcript-confirmed constitutive and alternative exons and introns, and the delineated events. On this page links to the various data files are given - documentation of the file format can be found within the individual file links. As part of the general documentation illustrative diagrams of splice signals and alternative events are available. It is important to note that although there are three sections on this page, all data is an integral part of the AltExtron database as it can be queried through web interfaces (as mentioned in the access pages). Release 1 of the AltExtron database is available for nine species - all based on the gene data from the February 2003 release of EMBL. The tar files below unpack into the same files as listed in the next section in this page - also the documentation remains the same.
Prototype Human DataThe data files in this section point to the prototype human AltExtron database. The tar files (from the latest build) hyper-linked above for multiple organisms contain a similar organisation as that of below. The sequence and alignment data: The intron and exon flat and table files: The alternatively spliced introns and exons:
Other Data:
The data given above is the subject of the paper "Categorisation and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human". Clark, F. and T.A. Thanaraj. (Human Molecular Genetics 2002 11: 451-464). [abstract] Human-mouse comparisonThe data given here are human introns and alternative splicing events that are conserved in mouse. Notes on the data files - read this first I. Results of matching human splice junctions with mouse transcript sequences. I.1.1 Conserved Human Constitutive Introns I.1.2 Sequences of human and mouse exon constructs for the Conserved Constit Introns I.2.1 Conserved Human Alternative Introns I.2.2 Sequences of human and mouse exon constructs for the Conserved Alt Introns II. Results of the analysis of mapping the matching mouse transcript sequences onto mouse draft genome sequence. II.1 Summary of the analysis of matching the mouse exon constructs with mouse genome sequence. II.2.1 Human splice junctions that are unambiguously seen in mouse genes also III. Delineating the conserved alternative splicing events. III.1.1 Conserved Human Alternatively spliced EventsIII.1.2 Effects on protein sequences due to conserved Human Alternatively spliced Events III.1.3 Protein product names of the genes in which conserved alternative splice events were observed The data given in this section is the subject of the paper "Conservation of Human Alternative splice Events in Mouse". Thanaraj, T.A., F. Clark and J. Muilu. Communicated Human GC-AG intronsA specialised dataset on GC-AG introns isoforms. This data is subject of paper "GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions". Thanaraj, T.A. and F. Clark. Nucleic Acids Research 29:2581-2593 (2001). [abstract, full text pdf, full text html] MIrror siteAll data on this page is mirrored at the University of Queenlands at the following url: http://bit.uq.edu.au/altExtron/ |
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