Schema for UCSC Alt Events - Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes
Database: hg19 Primary Table: knownAlt Row Count: 94,820   Data last updated: 2013-06-14|
Format description: Browser extensible data
|field||example||SQL type ||info ||description |
|bin ||585||smallint(5) unsigned ||range ||Indexing field to speed chromosome range queries.|
|chrom ||chr1||varchar(255) ||values ||Reference sequence chromosome or scaffold|
|chromStart ||12594||int(10) unsigned ||range ||Start position in chromosome|
|chromEnd ||12612||int(10) unsigned ||range ||End position in chromosome|
|name ||altThreePrime||varchar(255) ||values ||Name of item|
|score ||0||int(10) unsigned ||range ||Optional score, nominal range 0-1000|
|strand ||+||char(1) ||values ||+ or -|
Note: all start coordinates in our database are 0-based, not
1-based. See explanation
UCSC Alt Events (knownAlt) Track Description
This track shows various types of alternative splicing and other
events that result in more than a single transcript from the same
gene. The label by an item describes the type of event. The events are:
- Alternate Promoter (altPromoter) - Transcription starts at multiple places. The altPromoter extends from 100 bases before to 50 bases after transcription start.
- Alternate Finish Site (altFinish) - Transcription ends at multiple places.
- Cassette Exon (cassetteExon) - Exon is present in some transcripts but
not others. These are found by looking for exons that overlap an intron in the
- Retained Intron (retainedIntron) - Introns are spliced out in some
transcripts but not others. In some cases, particularly when the intron is near
the 3' end, this can reflect an incompletely processed transcript rather than
a true alt-splicing event.
- Overlapping Exon (bleedingExon) - Initial or terminal exons overlap
in an intron in another transcript. These often are associated with incompletely
- Alternate 3' End (altThreePrime) - Variations on the 3' end of an intron.
- Alternate 5' End (altFivePrime) - Variations on the 5' end of an intron.
- Intron Ends have AT/AC (atacIntron) - An intron with AT/AC ends rather than
the usual GT/AG. These are associated with the minor spliceosome.
- Strange Intron Ends (strangeSplice) - An intron with ends that are not
GT/AG, GC/AG, or AT/AC. These are usually artifacts of some sort due to
sequencing error or polymorphism.
This track is based on an analysis by the txgAnalyse program of splicing graphs
produced by the txGraph program. Both of these programs were written by Jim
Kent at UCSC.