Public sources of alternative splicing data, descriptions and references obtained from the individual web sites.

• UniGene UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.

• AceView AceView shows the alignment of mRNAs and ESTs to the genome sequence, and the genes and (alternative) transcripts reconstructed from these alignments, using the Acembly program inspired by Yuji Kohara and Tsodas Shin'I, and developped by Michel Potdevin, Danielle and Jean Thierry-Mieg on top of the Acedb object oriented database manager. The genes can be viewed aligned on the genome, and as spliced mRNA variants, decorated with BLASTp homologies, PFAM and PSORT motifs Stops and Met in the 3 frames, and all supporting mRNAs and ESTs. Text descriptions of the gene and its mRNAs (with useful links) are also shown. This work is in continuous development, please send us wishes, comments and bug reports. Please quote us as Danielle, Jean and Yann Thierry-Mieg, Michel Potdevin, Mark Sienkiewicz, Vahan Simonyan, www.humangenes.org: Identification and functional annotation of cDNA-supported genes in higher organisms using Acembly, unpublished . We just released our new Acembly genes, built over the human genome sequence from November 2002 (build 31 / golden path hg13).

• ISIS Intron Sequence and Information database The database contains phylogenetic and protein homology categories, information on alternative splicing, repetitive elements, small RNA genes and splice sites. There are also bioinformatic analyses such as fourier periodicities, Shannon entropies, base composition and other bioinformatic and biological properties.
  Nature Genetics 2000 Apr;24(4):340-1

• ProSplicer A Putative Alternative Splicing Database Based on Proteins, mRNAs and EST Clusters Release 1.0 Aug. 1st 2002

• PALS db (Updated on April 21, 2003) Putative AL ternative Splicing Data base ( PALS db ) is a database designed to provide biologists a wide coverage of putative alternative splicing (AS) sites to all known human genes. We used the unique sequences of UniGene clusters as reference sequences to construct PALS db.

• splice Nest: Visualizing Splicing of Genes from EST Data SpliceNest [1] is a web based graphical tool to explore gene structure, including alternative splicing, based on a mapping on the EST consensus sequences (contigs) from GeneNest [2] to the complete human genome. SpliceNest is integrated with GeneNest and the SYSTERS [3] protein sequence cluster set in one framework, permitting an overall exploration of the whole sequence space covering protein, mRNA and EST sequences, as well as genomic DNA.
  E. Coward, S.A. Haas, and M. Vingron (2002). SpliceNest: visualization of gene structure and alternative splicing based on EST clusters. Trends Genet. ,18 (1), 53-55.

• TIGR Human Gene Index The TIGR Human Gene Index (HGI) integrates research results from international human gene research projects, including research at TIGR. The Index is an outgrowth of our Human cDNA Database (HCD) and Expressed Gene Anatomy Database (EGAD) projects. All data in the Index are freely available and do not require a user account for access. The goal of this project is ultimately to represent a non-redundant view of all human genes and data on their expression patterns, cellular roles, functions, and evolutionary relationships. The database will also include links to genomic sequences, mapping data, 3D structures, and literature references Current Release - Version 12.0, Release Date - June 3, 2003

• ASAP the Alternative Splicing Annotation Project Molecular Biology Institute, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA also http://www.bioinformatics.ucla.edu/HASDB
  Christopher Lee Nucleic Acids Research, Vol. 31, No. 1, pp. 101-105 (January, 2003)

• ASDB database of alternatively spliced genes
  I Dralyuk, M.Brudno, M. S. Gelfand, M. Zorn, and I. Dubchak (2000) Nucleic Acids Research 28(1), 296- 297.

• DoTS (Database Of Transcribed Sequences) DoTS is a human and mouse transcript index created from all publicly available transcript sequences. The input sequences are clustered and assembled to form the DoTS Consensus Transcripts that comprise the index. These transcripts are assigned stable identifiers of the form DT.123456 (and are often referred to as "dots"). The transcripts are in turn clustered to form putative DoTS Genes . These are assigned stable identifiers of the form DG.1234356. The DoTS Transcripts and DoTS Genes are extensively annotated and a significant number have been manually curated. As of June 19, 2003, the DoTS annotation team has manually annotated 29,703 human and 39,283 mouse DoTS Transcripts (DTs/RNAs), corresponding to 3,126 human and 6,255 mouse DoTS Genes (DGs). Use the manually annotated gene query to see the DoTS Transcripts that have been manually annotated.

• HTM Human Transcriptome Map
  H. Caron, B. van Schaik, M. van der Mee, F. Baas, G. Riggins, P. van Sluis, M.-C. Hermus, R. van Asperen, K. Boon, P.A. Vote, S. Heisterkamp, A. van Kampen and R. Versteeg (2001). The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains. Science 291, 1289- 1292

• Query Alternative Splicing Datbase at Dr. Lee's lab/LPG/NCI/NIH
  Cancer Research 63, 655-657, February 1, 2003 Computational Analysis and Experimental Validation of Tumor-associated Alternative RNA Splicing in Human Cancer Zhining Wang ,H. Shuen Lo ,Howard Yang ,Sheryl Gere ,Ying Hu ,Kenneth H. Buetow and Maxwell P. Lee

• Human Transcriptome Server (Version 1.0) This server allows you to view and query the NCI/Affymetrix Transcriptome Maps alongside Affymetrix chip designs, public genomic annotations from Ensembl , reference genomic sequence (version: NCBI 30) from NCBI , and clones from the Mammalian Gene Collection.

• EASED Extended Alternatively Spliced EST Database We developed a computational method which allows to detect large numbers of alternative splice forms by comparison with ESTs. Using this method we created a database of 34.340 novel candidate alternative splice forms for nine organisms: Arabidopsis thaliana, Bos taurus, Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Mus musculus, Rattus norvegicus, Xenopus laevis and Homo sapiens . You may use either a GenBank accession number or keywords to request the database. Pospisil H, Herrmann A, Pankow H, Reich J: A database on alternative splice forms on the Integrated Genetic Map Service (IGMS) In silico biology (accepted) online version
  Brett D, Pospisil H, Valcarcel J, Reich J, Bork P: Alternative splicing and genome complexity ,Nat Genet 2002 Jan 1;30(1):29-30