Alternative Splicing and Transcript Diversity 1.1

ASTD features have been integrated in Ensembl and Ensembl Genomes over the course of 2009/2010. Ensembl and Ensembl Genomes provides now access to alternative splicing events not only on Human, Mouse and Rat but also on Zebrafish, Worm and FruitFly. Alternative splicing information will be expanded within the Ensembl framework.

The ASD, ATD, AEdb and ASTD resources will be phased out beginning of 2012.

From now on, you can access up-to-date alternative splicing events information through Ensembl

Alternatively, you can retrieve all the archived data from ASD/ATD/ASTD/AEdb projects on the EBI ftp site at ftp.ebi.ac.uk/pub/databases/astd

Please check out Ensembl to see if it can meet your needs already; if you have any questions, please send an e-mail to helpdesk AT ensembl.org.

• Human splicing event experimental validations with RT-PCR (ATD Consortium). Example.

• Improved TSS predictions covering 80% of human genes and 68% of mouse genes.
• Rat transcripts associated with developmental stages and pathology states information (like human and mouse).
• Rat development stages terms are mapped to the Witschi' embryology classification.
• In Silico expression values, known as TPM (transcript per million), are derived for each transcript from each tissue/development/pathology related evidences.
• Mouse PolyA sites experimental validations from the work of Moucadel and colleagues (Beyond the 3' end: experimental validation of extended transcript isoforms, Nucleic Acids Research, 2007, Vol. 35, No. 6 1947-1957) are displayed in the gene view.
• Human and mouse miRNA targets prediction from EIMMo incorporated. Gaidatzis and colleagues describe the methodology of prediction in the following paper, Inference of miRNA targets using evolutionary conservation and pathway analysis (BMC Bioinformatics 2007, 8:69 doi:10.1186/1471-2105-8-69).
• Fast and efficient advanced search with selection criteria on splicing events.
• Improved display of the splicing events for each gene. Example: GAPDH
• BED and GFF3 export for splicing events.
• Splicing Junction Array expression data for Mus Musculus from a study on the functional coordination of alternative splicing in the central nervous system by Fagnani and colleagues (Genome Biology 2007, 8:R108 doi:10.1186/gb-2007-8-6-r108).