Supplementary Online Webtool
|Identification and Analysis of Alternative Splicing Events Conserved in Human and Mouse|
Eric Van Nostrand1,
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
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:
Ensembl link: Direct link to the provided Ensembl ID
- 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)
Download: ACEScan training data set in FASTA format
Positive samples are labeled SHM, and negative samples are labeled Shm.
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.
Please address comments/questions/suggestions regarding this webpage to
Copyright © 2004
Last modified: Sun Jul 10 13:18:10 EDT 2005