Index: src/hg/makeDb/trackDb/trackDb.chainNet.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/trackDb.chainNet.ra,v
retrieving revision 1.11
retrieving revision 1.12
diff -b -B -U 4 -r1.11 -r1.12
--- src/hg/makeDb/trackDb/trackDb.chainNet.ra	22 Dec 2009 19:19:19 -0000	1.11
+++ src/hg/makeDb/trackDb/trackDb.chainNet.ra	22 Dec 2009 20:16:29 -0000	1.12
@@ -658,8 +658,50 @@
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign rn4 chainRn4
 
+# release alpha until rn3 individual chain/net tracks phased out
+track chainNetRn3
+release alpha
+compositeTrack on
+shortLabel $o_db Chain/Net
+longLabel Rat (Jun. 2003/rn3), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 209
+color 100,50,0
+altColor 255,240,200
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
+matrixHeader A, C, G, T
+otherDb rn3
+chainMinScore 3000
+chainLinearGap medium
+spectrum on
+html chainNet
+
+    track chainRn3
+    release alpha
+    subTrack chainNetRn3
+    subGroups view=chain
+    shortLabel $o_Organism Chain
+    longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+    type chain rn3
+
+    track netRn3
+    release alpha
+    subTrack chainNetRn3
+    subGroups view=net
+    shortLabel $o_Organism Net
+    longLabel $o_Organism ($o_date/$o_db) Alignment Net
+    type netAlign rn3 chainRn3
+
 track chainNetEquCab2
 compositeTrack on
 shortLabel Horse Chain/Net
 longLabel Horse (Sep. 2007/equCab2), Chain and Net Alignments

