Schema for UCSC Alt Events - Alternative Splicing, Alternative Promoter and Similar Events in UCSC Genes
  Database: hg38    Primary Table: knownAlt    Row Count: 245,964
Format description: Browser extensible data
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 29453int(10) unsigned range Start position in chromosome
chromEnd 29603int(10) unsigned range End position in chromosome
name altPromotervarchar(255) values Name of item
score 0int(10) unsigned range Score from 0-1000
strand +char(1) values + or -

Sample Rows

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

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 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.


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.