Schema for Alt Events - Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes

Database: hg19 Primary Table: knownAlt Row Count: 92,222
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	Score from 0-1000
`strand`	+	`char(1)`	values	+ or -

bin	chrom	chromStart	chromEnd	name	strand
585	chr1	12594	12612	altThreePrime	+
585	chr1	13220	13402	altThreePrime	+
585	chr1	14406	16606	bleedingExon	-
585	chr1	14829	15795	retainedIntron	-
585	chr1	14829	14969	retainedIntron	-
585	chr1	14969	15038	cassetteExon	-
585	chr1	15038	15795	retainedIntron	-
585	chr1	15602	15795	bleedingExon	-
585	chr1	15942	16606	retainedIntron	-
585	chr1	15942	15947	altThreePrime	-

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

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 same transcript.
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 processed transcripts.
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.

Credits

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.