7fb2f3f334694376f7bec47237552ddf8eb186dc
markd
  Wed Apr 26 10:13:42 2023 -0700
import of gencode VM33 prerelease

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 561946f..5a905a8 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -7635,30 +7635,124 @@
     mm39.wgEncodeGencodeAnnotationRemarkVM32.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM32.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneVM32
 "Link together Gencode UniProt Support table with Attributes table"
     mm39.wgEncodeGencodeEntrezGeneVM32.transcriptId dupeOk
     mm39.wgEncodeGencodeEntrezGeneVM32.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportVM32
 "Link together Gencode Exon Support table with Attributes table"
     mm39.wgEncodeGencodeExonSupportVM32.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM32.transcriptId minCheck=0.80
 
 # end Gencode VM32
 
+# begin Gencode VM33
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaVM33
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsVM33
+identifier wgEncodeGencodeBasicAttrsVM33
+"Link together Gencode Basic Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM33.transcriptId
+    mm39.wgEncodeGencodeBasicVM33.name
+
+identifier wgEncodeGencodeCompAttrsVM33
+"Link together Gencode Comprehensive Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM33.transcriptId
+    mm39.wgEncodeGencodeCompVM33.name
+
+identifier wgEncodeGencodePseudoGeneAttrsVM33
+"Link together Gencode PseudoGene Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM33.transcriptId
+    mm39.wgEncodeGencodePseudoGeneVM33.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsVM33)
+identifier wgEncodeGencodeGeneSourceVM33
+"Link together Gencode Gene Source table with Attributes table"
+    mm39.wgEncodeGencodeGeneSourceVM33.geneId
+    mm39.wgEncodeGencodeAttrsVM33.geneId
+
+identifier wgEncodeGencodeGeneSymbolVM33
+"Link together Gencode gene symbol table with Attributes table"
+    mm39.wgEncodeGencodeGeneSymbolVM33.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM33.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbVM33
+"Link together Gencode Pdb table with Attributes table"
+    mm39.wgEncodeGencodePdbVM33.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM33.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedVM33
+"Link together Gencode Pubmed table with Attributes table"
+    mm39.wgEncodeGencodePubMedVM33.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM33.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqVM33
+"Link together Gencode RefSeq table with Attributes table"
+    mm39.wgEncodeGencodeRefSeqVM33.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM33.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneVM33
+"Link together Gencode RefSeq table with refGene track"
+    mm39.wgEncodeGencodeRefSeqVM33.rnaAcc dupeOk chopAfter=.
+    mm39.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagVM33
+"Link together Gencode Tag table with Attributes table"
+    mm39.wgEncodeGencodeTagVM33.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM33.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceVM33
+"Link together Gencode Transcript Source table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSourceVM33.transcriptId
+    mm39.wgEncodeGencodeAttrsVM33.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportVM33
+"Link together Gencode Transcript Support table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSupportVM33.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM33.transcriptId minCheck=0.02
+
+identifier wgEncodeGencodeTranscriptionSupportLevelVM33
+"Link together Gencode Transcription Support Level table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptionSupportLevelVM33.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM33.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtVM33
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeUniProtVM33.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM33.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkVM33
+"Link together Gencode Annotation Remark table with Attributes table"
+    mm39.wgEncodeGencodeAnnotationRemarkVM33.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM33.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneVM33
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeEntrezGeneVM33.transcriptId dupeOk
+    mm39.wgEncodeGencodeEntrezGeneVM33.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportVM33
+"Link together Gencode Exon Support table with Attributes table"
+    mm39.wgEncodeGencodeExonSupportVM33.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM33.transcriptId minCheck=0.50
+
+# end Gencode VM33
+
 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