SpliceAid 2: a database of human splicing factors expression data and RNA target motifs.

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   Choice 3' splice site extension being searched:  3': -8/2  3': -15/2  3': -24/2
Additionally, you can limit your search in a tissue or a cell line.
Tissue/Cell-line specific expression data are collected from:
Human Protein Atlas, HPRD, Human Proteinpedia, Transcriptome Map and CGAP.
Naturally, if you don't select any tissue or cell line your search will be performed without limitations.

Last update:
2013 February
71 splicing factors
2339 RNA binding sites
Target site length distribution
Previous versions:
2012 June
71 splicing factors
2311 RNA binding sites
2011 November
68 splicing factors
2230 RNA binding sites
2011 August
62 splicing factors
2220 RNA binding sites
2011 May
61 splicing factors
1857 RNA binding sites
2011 April
61 splicing factors
1533 RNA binding sites
2011 January
61 splicing factors
1294 RNA binding sites
2010 September
60 splicing factors
1063 RNA binding sites
2010 February
59 splicing factors
984 RNA binding sites
2009 November
57 splicing factors
851 RNA binding sites
2009 March
54 splicing factors
680 RNA binding sites

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Information for splicing process is recognized by several factors that bind pre-mRNA sequence and, by their coordinated interaction, yield mature transcripts. SpliceAid web resource was the first curated repository of experimental RNA target motifs bound by splicing proteins in humans. However, to better understand the splicing outcome, also the tissue specificity of each splicing regulatory factor has to be taken into account. To this aim the expression data related to the splicing factors extracted from the main proteomic and transcriptomic databases are collected in SpliceAid 2. In this version the maintained splicing proteins were increased from 54 to 61 and the RNA target sites from 680 to 1067, there are expression data of 178 normal tissues, 35 cancer tissues and 107 cell lines; moreover also true 5’ and 3’ splice sites, polypyrimidine tracts and branch point sequences were added.
This tool searches the exact motifs versus a database of strictly experimentally assessed target RNA sequences. It is useful for predicting the effect of the DNA mutations at the level of the target sequences of the RNA-binding proteins that determine the pattern of mRNA splicing.

Interpret the results:
It processes the sequence submitted by the user and identifies the exact correspondence with the sequences stored in the database. Such sequences are shown by an accurate graphic representation, that is by histogram in which each target RNA sequence is represented by a coloured bar. A positive score was assigned to the target sequences that facilitate exon definition that is ESE (exonic splicing enhancer) and ISS (intronic splicing silencer) motifs. According to the same criteria we assigned a negative score to the target sequences that facilitate intron definition that is ESS (exonic splicing silencer) and ISE (intronic splicing enhancer) motifs. The bars have variable width and height respectively related to the number of nucleotides of the binding site and to its score (binding affinity). Over each bar there is the label showing the name of the protein predicted to bind moreover overlapping bars are managed shifting the labels and changing the colours. Moving the mouse over the factor’s name label, a window will appear showing the references that bring to connect (support) that binding sequence with its factor.
The tool keeps the case characters of the submitted sequences so the user can used it to distinguish coding from non coding areas and he will find again it in the results.

A table showing some comparisons among different prediction tools is available here

Download data:

Splicing factor binding sites:
Splicing factor expression:
5' and 3' splice sites:
Branch point sites:
Analyzed articles to build the database:


SpliceAid 2: A database of human splicing factors expression data and RNA target motifs
Piva F, Giulietti M, Ballone Burini A, Principato G
Hum Mutat. 2012 Jan;33(1):81-85. doi:10.1002/humu.21609. Epub 2011 Oct 17.
PubMed ID: 21922594

Help us to up to date SpliceAid database by reporting new target RNA sequences or annotation slips.
Please fill the forms below not forgetting to cite the article(s):


SpliceAid-F: a database of human splicing factors and their binding sites
ESE Finder 3.0
Splicing Rainbow

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