Table 1 |
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Useful databases for identifying alternatively spliced RNAs and regulatory elementsof alternative splicing data |
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| Name |
Description |
URL |
Published reference |
|
|
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| Alternative Splicing database |
Alternative exon database compiled from the literature |
http://cgsigma.cshl.org/new_alt_exon_db2/ webcite |
[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/ webcite |
|
| AltExtron |
Transcript-confirmed human introns and exons; includes alternatively spliced data
subsets |
http://www.bit.uq.edu.au/altExtron/ webcite or http://www.ebi.ac.uk/~thanaraj/altExtron/ webcite |
[6] |
| ASAP |
Human alternative splicing database; part of the Alternative Splicing Annotation Project |
http://www.bioinformatics.ucla.edu/HASDB webcite |
[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 webcite |
[41] |
| AsMamDB |
Alternatively spliced mammalian genes; includes human, mouse, and rat |
http://166.111.30.65/ASMAMDB.html webcite |
[42] |
| Gene Resource Locator |
Gene map database; includes information on alternatively spliced transcripts |
http://grl.gi.k.u-tokyo.ac.jp webcite |
[44] |
| Intronerator |
Introns in C. elegans; includes a catalog of alternatively spliced transcripts |
http://www.cse.ucsc.edu/~kent/intronerator/ webcite |
[45] |
| ISIS |
All introns identified in GenBank |
http://isis.bit.uq.edu.au/ webcite |
[46] |
| PALS db |
Putative alternative splicing predicted by EST alignments for mouse and human |
http://palsdb.ym.edu.tw/ webcite |
[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/ webcite |
[48] |
| SpliceDB |
Mammalian splice sites |
http://genomic.sanger.ac.uk/spldb/SpliceDB.html webcite or http://www.softberry.com/spldb/SpliceDB.html webcite |
[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/ webcite |
[50] |
| STACK |
Putative human transcripts reconstructed from ESTs; includes the context of different
tissues or pathological states |
http://www.sanbi.ac.za/Dbases.html webcite |
[51] |
| Yeast Intron Database |
Introns in Saccharomyces cerevisiae |
http://www.cse.ucsc.edu/research/compbio/yeast_introns.html webcite |
[52] |
|
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Ladd and Cooper Genome Biology 2002 3:reviews0008.1 doi:10.1186/gb-2002-3-11-reviews0008 |
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