f1a6509a2f33b00f4908de15d47f6625118b6a93
markd
  Thu Nov 3 12:46:19 2022 -0700
import of All GENCODE VM31

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 699eecb..f1bd5c3 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -7082,30 +7082,125 @@
     mm39.wgEncodeGencodeAnnotationRemarkVM30.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM30.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneVM30
 "Link together Gencode UniProt Support table with Attributes table"
     mm39.wgEncodeGencodeEntrezGeneVM30.transcriptId dupeOk
     mm39.wgEncodeGencodeEntrezGeneVM30.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportVM30
 "Link together Gencode Exon Support table with Attributes table"
     mm39.wgEncodeGencodeExonSupportVM30.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM30.transcriptId minCheck=0.80
 
 # end Gencode VM30
 
+# begin Gencode VM31
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaVM31
+# wgEncodeGencode2wayConsPseudoVM31
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsVM31
+identifier wgEncodeGencodeBasicAttrsVM31
+"Link together Gencode Basic Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM31.transcriptId
+    mm39.wgEncodeGencodeBasicVM31.name
+
+identifier wgEncodeGencodeCompAttrsVM31
+"Link together Gencode Comprehensive Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM31.transcriptId
+    mm39.wgEncodeGencodeCompVM31.name
+
+identifier wgEncodeGencodePseudoGeneAttrsVM31
+"Link together Gencode PseudoGene Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM31.transcriptId
+    mm39.wgEncodeGencodePseudoGeneVM31.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsVM31)
+identifier wgEncodeGencodeGeneSourceVM31
+"Link together Gencode Gene Source table with Attributes table"
+    mm39.wgEncodeGencodeGeneSourceVM31.geneId
+    mm39.wgEncodeGencodeAttrsVM31.geneId
+
+identifier wgEncodeGencodeGeneSymbolVM31
+"Link together Gencode gene symbol table with Attributes table"
+    mm39.wgEncodeGencodeGeneSymbolVM31.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM31.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbVM31
+"Link together Gencode Pdb table with Attributes table"
+    mm39.wgEncodeGencodePdbVM31.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM31.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedVM31
+"Link together Gencode Pubmed table with Attributes table"
+    mm39.wgEncodeGencodePubMedVM31.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM31.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqVM31
+"Link together Gencode RefSeq table with Attributes table"
+    mm39.wgEncodeGencodeRefSeqVM31.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM31.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneVM31
+"Link together Gencode RefSeq table with refGene track"
+    mm39.wgEncodeGencodeRefSeqVM31.rnaAcc dupeOk chopAfter=.
+    mm39.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagVM31
+"Link together Gencode Tag table with Attributes table"
+    mm39.wgEncodeGencodeTagVM31.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM31.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceVM31
+"Link together Gencode Transcript Source table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSourceVM31.transcriptId
+    mm39.wgEncodeGencodeAttrsVM31.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportVM31
+"Link together Gencode Transcript Support table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSupportVM31.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM31.transcriptId minCheck=0.04
+
+identifier wgEncodeGencodeTranscriptionSupportLevelVM31
+"Link together Gencode Transcription Support Level table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptionSupportLevelVM31.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM31.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtVM31
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeUniProtVM31.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM31.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkVM31
+"Link together Gencode Annotation Remark table with Attributes table"
+    mm39.wgEncodeGencodeAnnotationRemarkVM31.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM31.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneVM31
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeEntrezGeneVM31.transcriptId dupeOk
+    mm39.wgEncodeGencodeEntrezGeneVM31.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportVM31
+"Link together Gencode Exon Support table with Attributes table"
+    mm39.wgEncodeGencodeExonSupportVM31.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM31.transcriptId minCheck=0.80
+
+# end Gencode VM31
+
 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