07942970a19230fee2cbb6bf8ae1c15427533c66
markd
  Wed Jan 26 08:53:49 2022 -0800
loaded GENCODE VM29 pre-release

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 9234b9d..6e1b136 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -6522,30 +6522,125 @@
     mm39.wgEncodeGencodeAnnotationRemarkVM28.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM28.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneVM28
 "Link together Gencode UniProt Support table with Attributes table"
     mm39.wgEncodeGencodeEntrezGeneVM28.transcriptId dupeOk
     mm39.wgEncodeGencodeEntrezGeneVM28.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportVM28
 "Link together Gencode Exon Support table with Attributes table"
     mm39.wgEncodeGencodeExonSupportVM28.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM28.transcriptId minCheck=0.80
 
 # end Gencode VM28
 
+# begin Gencode VM29
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaVM29
+# wgEncodeGencode2wayConsPseudoVM29
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsVM29
+identifier wgEncodeGencodeBasicAttrsVM29
+"Link together Gencode Basic Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM29.transcriptId
+    mm39.wgEncodeGencodeBasicVM29.name
+
+identifier wgEncodeGencodeCompAttrsVM29
+"Link together Gencode Comprehensive Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM29.transcriptId
+    mm39.wgEncodeGencodeCompVM29.name
+
+identifier wgEncodeGencodePseudoGeneAttrsVM29
+"Link together Gencode PseudoGene Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM29.transcriptId
+    mm39.wgEncodeGencodePseudoGeneVM29.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsVM29)
+identifier wgEncodeGencodeGeneSourceVM29
+"Link together Gencode Gene Source table with Attributes table"
+    mm39.wgEncodeGencodeGeneSourceVM29.geneId
+    mm39.wgEncodeGencodeAttrsVM29.geneId
+
+identifier wgEncodeGencodeGeneSymbolVM29
+"Link together Gencode gene symbol table with Attributes table"
+    mm39.wgEncodeGencodeGeneSymbolVM29.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM29.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbVM29
+"Link together Gencode Pdb table with Attributes table"
+    mm39.wgEncodeGencodePdbVM29.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM29.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedVM29
+"Link together Gencode Pubmed table with Attributes table"
+    mm39.wgEncodeGencodePubMedVM29.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM29.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqVM29
+"Link together Gencode RefSeq table with Attributes table"
+    mm39.wgEncodeGencodeRefSeqVM29.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM29.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneVM29
+"Link together Gencode RefSeq table with refGene track"
+    mm39.wgEncodeGencodeRefSeqVM29.rnaAcc dupeOk chopAfter=.
+    mm39.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagVM29
+"Link together Gencode Tag table with Attributes table"
+    mm39.wgEncodeGencodeTagVM29.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM29.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceVM29
+"Link together Gencode Transcript Source table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSourceVM29.transcriptId
+    mm39.wgEncodeGencodeAttrsVM29.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportVM29
+"Link together Gencode Transcript Support table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSupportVM29.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM29.transcriptId minCheck=0.04
+
+identifier wgEncodeGencodeTranscriptionSupportLevelVM29
+"Link together Gencode Transcription Support Level table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptionSupportLevelVM29.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM29.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtVM29
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeUniProtVM29.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM29.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkVM29
+"Link together Gencode Annotation Remark table with Attributes table"
+    mm39.wgEncodeGencodeAnnotationRemarkVM29.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM29.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneVM29
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeEntrezGeneVM29.transcriptId dupeOk
+    mm39.wgEncodeGencodeEntrezGeneVM29.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportVM29
+"Link together Gencode Exon Support table with Attributes table"
+    mm39.wgEncodeGencodeExonSupportVM29.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM29.transcriptId minCheck=0.80
+
+# end Gencode VM29
+
 identifier wgEncodeGencodeClassesV3Hg19
 "Link together Gencode gene model (Known) and class for July 2009 Data Version"
     hg19.wgEncodeGencodeClassesV3.name
     hg19.wgEncodeGencodeAutoV3.name unique
     hg19.wgEncodeGencodeManualV3.name unique
     hg19.wgEncodeGencodePolyaV3.name unique
 
 identifier acemblyName dependency
 "Link together Acembly gene model structure and peptide."
     $hg,$mm.acembly.name
     $hg,!hg17,$mm.acemblyPep.name unique minCheck=0.90
     hg17.acemblyPep.name unique minCheck=0.63
     $hg,$mm.acemblyClass.name full unique
 
 identifier ECgeneName dependency