Alternative Splicing and Transcript Diversity Databases

ASD/ATD/ASTD/AEdb projects are closed and the databases have been phased out beginning of 2012.

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.

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 contact Ensembl helpdesk.

FTP Archive

ASTD Feb 2008 Release 1.1 (current release)

Go to the FTP site
README - read these first!

Species	Feb 2008 Release 1.1
Homo Sapiens	data in EMBL format Genome coordinates (GFF3) Genome coordinates (GTF2.2) Fasta format sequences of all transcripts Fasta format sequences of all exons Fasta format sequences of all peptides Splice events (GFF3) Splice events (UCSC BED) transcripts per million (TPM) expression dbSNP mapping analysis
Mus Musculus	data in EMBL format Genome coordinates (GFF3) Genome coordinates (GTF2.2) Fasta format sequences of all transcripts Fasta format sequences of all exons Fasta format sequences of all peptides Splice events (GFF3) Splice events (UCSC BED) transcripts per million (TPM) expression Experimentally validated poly(A)s dbSNP mapping analysis
Rattus Norvegicus	data in EMBL format Genome coordinates (GFF3) Genome coordinates (GTF2.2) Fasta format sequences of all transcripts Fasta format sequences of all exons Fasta format sequences of all peptides Splice events (GFF3) Splice events (UCSC BED) transcripts per million (TPM) expression dbSNP mapping analysis

ASTD Jun 2007 Release 1.0 (previous release)

Go to the FTP site

Species	Jun 2007 Release 1.0
Homo Sapiens	data in EMBL format Genome coordinates (GFF3) Genome coordinates (GTF2.2) Fasta format sequences of all transcripts Fasta format sequences of all exons Fasta format sequences of all peptides
Mus Musculus	data in EMBL format Genome coordinates (GFF3) Genome coordinates (GTF2.2) Fasta format sequences of all transcripts Fasta format sequences of all exons Fasta format sequences of all peptides
Rattus Norvegicus	data in EMBL format Genome coordinates (GFF3) Genome coordinates (GTF2.2) Fasta format sequences of all transcripts Fasta format sequences of all exons Fasta format sequences of all peptides

ATD Data Download

Species	Oct 2006 Release 2	May 2005 Release 1
Homo Sapiens	Ensembl 36.35i (Dec 2005): AT classes, Merged PolyA	Ensembl 27.35a.1 (Dec 2004): AT classes, Merged PolyA
Mus Musculus	Ensembl 37.34e (Feb 2006): AT classes, Merged PolyA	Ensembl 27.33c.1 (Dec 2004): AT classes, Merged PolyA

ASD Data Download

Species	Oct 2006 Release 3	May 2005 Release 2	Nov 2004 Release 1
Homo Sapiens	Ensembl 36.35i (Dec 2005): Genes Reference transcripts Transcripts Introns Exons Splice Patterns Splice Pattern Sequences Peptide Sequences Splicing Events	Ensembl 27.35a.1 (Dec 2004): Genes Reference transcripts Transcripts Introns Exons Splice Patterns Splice Pattern Sequences Peptide Sequences Splicing Events	Ensembl 19.34b2 (Jul 2003): Genes Reference transcripts Transcripts Introns Exons Splice Patterns Splice Pattern Sequences Peptide Sequences Splicing Events
Mus Musculus	Ensembl 37.34e (Feb 2006): Genes Reference transcripts Transcripts Introns Exons Splice Patterns Splice Pattern Sequences Peptide Sequences Splicing Events	Ensembl 27.33c.1 (Dec 2004): Genes Reference transcripts Transcripts Introns Exons Splice Patterns Splice Pattern Sequences Peptide Sequences Splicing Events	Ensembl 24.33.1 (Sept 2004): Genes Reference transcripts Transcripts Introns Exons Splice Patterns Splice Pattern Sequences Peptide Sequences Splicing Events

AltExtron Data Download

Species	July 2003
Arabidopsis thaliana	Flat files
Bos taurus	Flat files
Caenorhabditis elegans	Flat files
Danio rerio (zebrafish)	Flat files
Drosophila melanogaster	Flat files
Gallus gallus	Flat files
Homo sapiens	Flat files
Mus musculus	Flat files
Rattus norvegicus	Flat files

Publications

Koscielny G., Le Texier V., Gopalakrishnan C., Kumanduri V., Riethoven J.J., Nardone F., Stanley E., Fallsehr C., Hofmann O., Kull M., Harrington E., BouÃ© S., Eyras E., Plass M., Lopez F., Ritchie W., Moucadel V., Ara T., Pospisil H., Herrmann A., G Reich J., GuigÃ³ R., Bork P., Doeberitz M.K., Vilo J., Hide W., Apweiler R., Thanaraj T.A., Gautheret D. (2009)

ASTD: The Alternative Splicing and Transcript Diversity database.

Genomics. 2009 Mar;93(3): 213-220. [Epub 2008 Dec 24]

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Le Texier V., Riethoven J.J., Kumanduri1 V., Gopalakrishnan C., Lopez F., Gautheret D. and Thanaraj T.A. (2006)

AltTrans: Transcript pattern variants annotated for both alternative splicing and alternative polyadenylation.

BMC Bioinformatics 7: 169.

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Stamm S., Riethoven J.J., Le Texier V., Gopalakrishnan C., Kumanduri V., Tang Y., Barbosa-Morais N.L., Thanaraj T.A. (2006)

ASD: a bioinformatics resource on alternative splicing.

Nucleic Acids Research 34: D46-D55.

abstract full-text HTML full-text PDF

Thanaraj T. A., Stamm S., Clark F., Riethoven J.J., Le Texier V. and Muilu J. (2004)

ASD: the Alternative Splicing Database.

Nucleic Acids Research 32: D64-D69.

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Thanaraj T.A., Clark F. and Muilu J. (2003)

Conservation of Human Alternative splice Events in Mouse.

Nucleic Acids Research 31(10): 2544-2552.

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Thanaraj T.A. and Stamm S. (2003)

Prediction and statistical analysis of alternatively spliced exons.

Progress in Molecular and Subcellular Biology 31: 1-31.

abstract

Clark F. and Thanaraj T.A. (2002)

Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human.

Human Molecular Genetics 11: 451-464.

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Thanaraj T.A. and Clark F. (2001)

GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions.

Nucleic Acids Research 29: 2581-2593.

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Thanaraj T.A. and Robinson A.J. (2000)

Prediction of Exact Boundaries of Exons.

Briefings in Bioinformatics 1(4): 343-356.

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Thanaraj T.A., Robinson A.J., Muilu J. and Riethoven J.J.M. (2000)

Paradigm Shifts in the Approaches for Gene Annotation.
Editorial article for special issue on our Gene Prediction symposium.

Briefings in Bioinformatics 1(4): 324-329.

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Thanaraj T.A. (2000)

Positional Characterisation of False Positives from Computational Predictions of Human Splice Sites.

Nucleic Acids Research 28(3): 744-754.

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Thanaraj T.A. (1999)

A Clean Data Set of EST-confirmed Splice Sites From Homo Sapiens and Standards for Clean-up Procedures.

Nucleic Acids Research 27(13): 2627-2637.

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¹Reproduced with permission from NAR Online http://www.oup.co.uk/nar/

Past Members & External collaborators

EBI team

The team was made up of the following people:

Daniel Lawson	Project Coordinator (headed from July 2008 until February 2011)
Gautier Koscielny	Technical Leader of the project (headed from July 2006 until February 2011)
Eleanor Stanley	Project Coordinator (headed from 01 September 2005 until 30 June 2008)
Vincent Le Texier	Software Engineer
Chellappa Gopalakrishnan	Software Engineer
Vasudev Kumanduri	Software Engineer
Francesco Nardone	Technical Leader of the project (headed from 01 September 2005 until 30 June 2006)
Alphonse Thangavel Thanaraj	Founding Leader of the project (headed until 31 Aug 2005)
Jean-Jack M. Riethoven	Senior Software Engineer

ASD Consortium Members

The ASD Project was supported by the ASD grant from the EC (QLRT-CT-2001-02062).

The ASD Team at the consortium level is made up of the following members:

Stefan Stamm	Institute of Biochemistry, University Erlangen Nurenberg, 91054 Erlangen, GERMANY. Work web pages: www.stamms-lab.net (Coordinator of the Consortium)
Peer Bork	Structural and Comp. Biology Dept., European Molecular Biological Laboratory, 69177 Heidelberg, GERMANY.
Roderic Guigo	Genomics Laboratory Group, IMIM/Research on Biomedical Informatics, 08003, Barcelona, SPAIN.
Laurent Bracco	Exonhit Therapeutics, 75013 Paris, FRANCE.
Hermona Soreq	Department of Biological Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, ISRAEL.
Eleanor Stanley and Gautier Koscielny	EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UNITED KINGDOM
Juan Valcárcel	Centre de RegulaciÃ³ GenÃ²mica, Passeig MarÃtim 37-49, 08003 Barcelona, Spain

ATD Consortium Members

The ATD Project was supported by the ATD grant from the EC (LSHG-CT-2003-503329) until May 2007.

Daniel Gautheret	Institut de GÃ©nÃ©tique et Microbiologie - UMR CNRS 8621 - UniversitÃ© Paris-Sud - BÃ¢timent 400 - 91405 Orsay Cedex - France (Coordinator of the Consortium)
Peer Bork	EMBL, Germany
Christiane Dascher-Nadel	INSERM Transfert, France
Roderic Guigo	IMIM, Spain
Winston Hide	SANBI, South Africa
Magnus von Knebel	University of Heidelberg, Germany
Jans Reich	Max-Delbruck-Centrum fur Molecular Medizin, Germany
Eleanor Stanley and Gautier Koscielny	EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UNITED KINGDOM
Jaak Vilo	Estonian Biocenter, Estonia

EURASNET Members

The ASTD project at EBI was supported by a grant from the EC: Eurasnet Network of Excellence (LSHG-CT-2005-518238).

More information: http://www.eurasnet.info/members