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First, specify the location of the exons you are interested in. The location can either be
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" |
Input used for the example: