Skip to main content

Table 1 Useful databases for identifying alternatively spliced RNAs and regulatory elementsof alternative splicing data

From: Finding signals that regulate alternative splicing in the post-genomic era

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]