Alternative Splicing and Transcript Diversity 1.1

What's new?

ASTD v1.1 build 9 Last data release: 12-February-2008 Last website update: 10-June-2009 02:33 PM

The ASTD release 1.1 build 9 (September 2008) contains the following new features:

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

Other features introduced in release 1.1 (since February 2008):

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).

See release notes for more details.

Mammalian Genomes


Homo sapiens Ensembl Human v41 NCBI 36 assembly	Mus musculus Ensembl Mouse v41 NCBI m36 mouse assembly	Rattus norvegicus Ensembl Rat v42 Assembly version 3.4

Project Description

The Alternative Splicing and Transcript Diversity (ASTD) database project is creating a database of alternative splice events and transcripts of genes from human, mouse and rat. Full length transcripts are generated with the aim of understanding the mechanism of alternative splicing on a genome-wide scale.

Acknowledgements

The ASTD project at EBI is supported by a grant from the EC: Eurasnet Network of Excellence (LSHG-CT-2005-518238). It was supported by the ASD grant from the EC (QLRT-CT-2001-02062) until November 2005 and the ATD grant from the EC (LSHG-CT-2003-503329) until May 2007.

ASTD is also grateful to all the participants of the ATD Consortium (EMBL, EBC, FIMIM, INSERM, Max-Delbrück-Center, University of Heidelberg, University of Western Cape) and the Eurasnet Network of Excellence associates.