HEXEvent - a database of Human EXon splicing Events

First, specify the location of the exons you are interested in. The location can either be

• a genomic region specified by the chromosome, the strand and the start and end position,
• a whole chromosome or even the whole genome (for the whole genome, choose "all" for the chromosome), or
• a list of genes (up to 100 at a time).

Second, you select the exon types you are interested in. If you want a list of only constitutive exons, only check "constitutive". Generally, if you want a list of only a certain type of exons, only check this category. In case you are interested in a list of exons of several types, check all types you are interested in. If you check "all", you will get all exons in your specified region independent of the type of the exons.

Since exons that are only rarely alternatively spliced behave almost like constitutive exons, you can select up to which degree of alternative splicing you would like to call an exon "constitutive". This value is specified by the percentage of ESTs (of that exon) that show an alternative splicing event.

If you want to extract a dataset of cassette exons that are rarely included, you can specify an upper bound of inclusion levels of exons you want in your set.

Similarly, in case you are interested in exons with an alternative splice site that is significantly often used, you can define an upper bound of the usage level of the major splice site. This ensures a lower bound for the minor splice site(s) implicitly.

By setting the exon type definition to either "strict" or "non-strict", you can specify whether you care whether the exons in your list (that will for sure have one or more of the selected exon types) show unselected splicing events/exon types in addition. Choose "strict", if you do not allow selected exons to have unselected splicing events, and choose "non-strict" otherwise.

Finally, you can choose whether you want the resulting list of exons to be displayed in the browser or as a downloadable file.

Your output is a tab-separated list of internal human exons that fulfill all characteristics you specified at the input page. For each exon, the following features are reported:

field	example	description
chromo	chrX	reference sequence chromosome name
strand	+	+ or - for strand
start	101854639	first position of the exon (0-based)
end	101854775	last position of the exon (1-based)
count	15	number of ESTs that include the exon as given by [chromo], [strand], [start], and [end]
alt3	10	number of ESTs that include the exon with an alternative 3' splice site
alt5	0	number of ESTs that include the exon with an alternative 5' splice site
alt3+5	2	number of ESTs that include the exon with an alternative 3' and an alternative 5' splice site simultaneously
skip	0	number of ESTs in which the exon is skipped
constitLevel	0.556	constitutive level of the exon (= [count]/([count]+[alt3]+[alt5]+[alt3+5]+[skip]) )
inclLevel	1.000	inclusion level of the exon (= ([count]+[alt3]+[alt5]+[alt3+5])/([count]+[alt3]+[alt5]+[alt3+5]+[skip]) )
3usageLevel	0.556	usage level of the major 3' splice site of the exon (= ([count]+[alt5])/([count]+[alt3]+[alt5]+[alt3+5]) )
5usageLevel	0.926	usage level of the major 5' splice site of the exon (= ([count]+[alt3])/([count]+[alt3]+[alt5]+[alt3+5]) )
alt3singleCount	10	number(s) of ESTs for different alternative 3' splice site
alt3singleLoc	101854633	location(s) of alternative 3' splice sites
alt5singleCount	0	number(s) of ESTs for different alternative 5' splice site
alt5singleLoc	#	location(s) of alternative 5' splice sites
alt3and5singleCount	2	number(s) of ESTs for different alternative 3' and 5' splice site combinations
alt3and5singleLoc	101854633-101854787	location(s) of alternative 3' and 5' splice site combinations
OnlyESTexonCount	0	number of ESTs in which the exon is overlapped by an alternative version of it, that is not included in the human isoform list of the UCSC Genome Browser yet, but has at least one EST supporting it
OnlyESTexons	#	location(s) of alternative version(s) of the exon, that is/are not included in the human isoform list of the UCSC Genome Browser yet, but has/have at least one EST supporting it
genename	ARMCX5	name of the gene the exon is part of, if no gene name was assigned yet, it is indicated by "onlyEST"

A typical output looks like this:

chromo strand start end count alt3 alt5 alt3+5 skip constitLevel inclLevel 3usageLevel 5usageLevel alt3singleCount alt3singleLoc alt5singleCount alt5singleLoc alt3and5singleCount alt3and5singleLoc OnlyESTexonCount OnlyESTexons genename chr1 - 11709835 11709931 39 1 0 0 0 0.975 1.000 0.975 1.000 1 11709940 0 # 0 # 0 # FBXO2 chr1 - 11713447 11713582 2 1 0 0 52 0.036 0.055 0.667 1.000 1 11713484 0 # 0 # 0 # FBXO2 chr1 - 11741095 11741495 1 0 0 0 19 0.050 0.050 1.000 1.000 0 # 0 # 0 # 0 # MAD2L2 chr1 - 11741794 11742073 2 0 0 0 19 0.095 0.095 1.000 1.000 0 # 0 # 0 # 0 # MAD2L2 chr1 - 11854414 11854595 5 2 0 0 0 0.714 1.000 0.714 1.000 2 11854534 0 # 0 # 0 # MTHFR chr1 - 11862937 11863186 27 3 0 0 0 0.900 1.000 0.900 1.000 3 11863183 0 # 0 # 0 # MTHFR chr1 - 11907618 11907687 1 1 0 0 2 0.250 0.500 0.500 1.000 1 11907811 0 # 0 # 1 chr1-11907618-11907807 onlyEST

Input used for the example:

• genomic location: chr1,-,11700000-12000000
• cassette and alternative 3' splice site exons
• 0% of ESTs are allowed to show alternative events in order to call an exon constitutive
• cassette exons are shown up to an inclusion level of < 100%
• alternative 3' splice site exons are shown up to a major splice site usage level of < 100%
• strict exon type definition