Table 1.

Useful databases for identifying alternatively spliced RNAs and regulatory elementsof alternative splicing data

Name	Description	URL	Published reference
Alternative Splicing database	Alternative exon database compiled from the literature	http://cgsigma.cshl.org/new_alt_exon_db2/	[40]
Alternative splicing databases	Several alternative splicing databases, including a database of splice variants of disease genes, a complete splice-site database, and a database of alternative splice forms for seven organisms	http://www.bioinf.mdc-berlin.de/splice/
AltExtron	Transcript-confirmed human introns and exons; includes alternatively spliced data subsets	http://www.bit.uq.edu.au/altExtron/ or http://www.ebi.ac.uk/~thanaraj/altExtron/	[6]
ASAP	Human alternative splicing database; part of the Alternative Splicing Annotation Project	http://www.bioinformatics.ucla.edu/HASDB	[43]
ASDB	Alternatively spliced gene database; includes protein and nucleotide sequences for human, mouse, rat, Drosophila, Caenorhabditis elegans, chicken, cow and rabbit and viruses	http://cbcg.nersc.gov/asdb	[41]
AsMamDB	Alternatively spliced mammalian genes; includes human, mouse, and rat	http://166.111.30.65/ASMAMDB.html	[42]
Gene Resource Locator	Gene map database; includes information on alternatively spliced transcripts	http://grl.gi.k.u-tokyo.ac.jp	[44]
Intronerator	Introns in C. elegans; includes a catalog of alternatively spliced transcripts	http://www.cse.ucsc.edu/~kent/intronerator/	[45]
ISIS	All introns identified in GenBank	http://isis.bit.uq.edu.au/	[46]
PALS db	Putative alternative splicing predicted by EST alignments for mouse and human	http://palsdb.ym.edu.tw/	[47]
SELEX-DB	In vitro selected oligomers; includes SELEX sequences for splicing factors and is supplemented by SYSTEM (experimental design) and CROSS_TEST (cross-validation test) databases	http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/	[48]
SpliceDB	Mammalian splice sites	http://genomic.sanger.ac.uk/spldb/SpliceDB.html or http://www.softberry.com/spldb/SpliceDB.html	[49]
SpliceNest	A database that maps GeneNest onto human genomic sequence and is integrated with GeneNest (EST clusters for human, mouse, zebrafish and Arabidopsis thaliana) and SYSTERS (protein sequence clusters) databases	http://splicenest.molgen.mpg.de/	[50]
STACK	Putative human transcripts reconstructed from ESTs; includes the context of different tissues or pathological states	http://www.sanbi.ac.za/Dbases.html	[51]
Yeast Intron Database	Introns in Saccharomyces cerevisiae	http://www.cse.ucsc.edu/research/compbio/yeast_introns.html	[52]