ACEScan

Identification and Analysis of Alternative Splicing Events Conserved in Human and Mouse

Supplementary Online Webtool

Gene Yeo^1,2, Eric Van Nostrand¹, Dirk Holste¹, Tomaso Poggio², Christopher B. Burge¹,

¹ Department of Biology, Massachusetts Institute of Technology
² Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology

Display ACEScan scores for Ensembl exons

Description
This website provides ACEScan scores for orthologous human-mouse exons filtered by our automated process
(described in Supplementary Online Text).

Available options once a human Ensembl ID is provided:

Display: provides a graphical representation of all ACEScan scored exons in that human Ensembl gene
Properties: provides extended data for all ACEScan scored exons in the provided human Ensembl gene, in tab delimited form:

Exon Number: the human exon number, as annotated in Ensembl Version XX (may have changed in newer Ensembl versions)
EST: Whether our automated process identified EST evidence for skipping (SE) or no evidence (CE)
Human_exnum|Mouse_exnum: The human and orthologous mouse Ensembl ids, and the exon number of exons identified as an orthologous exon pair in the longest transcript for these Ensembl genes. (e.g., ENSG00000176884_2|ENSMUSG00000026959_2 refers to the orthologous pair of exon 2 in the longest Ensembl transcript associated to human Ensembl id ENSG00000176884, and exon 2 in the longest transcript associated to mouse Ensembl id ENSMUSG00000026959)
ACEScan: The ACEScan score for this orthologous exon pair
Human_exlen: The length of the human exon (bp)
Mouse_exlen: The length of the mouse exon (bp)

Ensembl link: Direct link to the provided Ensembl ID

Download: ACEScan training data set in FASTA format
Positive samples are labeled SHM, and negative samples are labeled S_hm.
Each sample consists of human upstream intron, human exon, human downstream intron (separated by 'X').
This is followed by a space, and the orthologous mouse upstream intron, mouse exon, and mouse downstream intron (separated by 'X').

Limitation with Ensembl genome annotation: we had to rely on orthologous exons being present in the longest transcripts of the human and mouse gene. In consequence, exons have definitely not been scanned. As an mportant update, ACEScan scores for exons from known Genes with a multiz alignment in mouse (increasing the number of ACEScan[+] exons by two-fold) are also available as a custom track at the UCSC Genome Browser.