src/hg/makeDb/trackDb/knownAlt.html 1.5

Index: src/hg/makeDb/trackDb/knownAlt.html
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/knownAlt.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -b -B -U 1000000 -r1.4 -r1.5
--- src/hg/makeDb/trackDb/knownAlt.html	3 Apr 2007 17:51:23 -0000	1.4
+++ src/hg/makeDb/trackDb/knownAlt.html	2 Apr 2010 02:42:54 -0000	1.5
@@ -1,30 +1,30 @@
 <H2>Description</H2>
 <P>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:</P>
 <UL>
-<LI>Alternate Promoter (<B>altPromoter</B>) - Transcription starts at multiple places.
+<LI>Alternate Promoter (<B>altPromoter</B>) - Transcription starts at multiple places.  The altPromoter extends from 100 bases before to 50 bases after transcription start.
 <LI>Alternate Finish Site (<B>altFinish</B>) - Transcription ends at multiple places.
 <LI>Cassette Exon (<B>cassetteExon</B>) - Exon is present in some transcripts but 
 not others. These are found by looking for exons that overlap an intron in the 
 same transcript.
 <LI>Retained Intron (<B>retainedIntron</B>) - 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.
 <LI>Overlapping Exon (<B>bleedingExon</B>) - Initial or terminal exons overlap 
 in an intron in another transcript. These often are associated with incompletely 
 processed transcripts.
 <LI>Alternate 3' End (<B>altThreePrime</B>) - Variations on the 3' end of an intron.
 <LI>Alternate 5' End (<B>altFivePrime</B>) - Variations on the 5' end of an intron.
 <LI>Intron Ends have AT/AC (<B>atacIntron</B>) - An intron with AT/AC ends rather than 
 the usual GT/AG. These are associated with the minor spliceosome.
 <LI>Strange Intron Ends (<B>strangeSplice</B>) - 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.
 </UL>
 
 <H2>Credits</H2>
 <P>This track is based on an analysis by the <TT>txgAnalyse</TT> program of splicing graphs
 produced by the <TT>txGraph</TT> program. Both of these programs were written by Jim
 Kent at UCSC.</P>