e1b0f07ffbe7508b97259a9d3c28956152bacfa9
markd
  Sat Oct 16 16:55:27 2021 -0700
import of All gencode VM28

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 65eaf23..29d8856 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -6242,30 +6242,125 @@
     mm39.wgEncodeGencodeAnnotationRemarkVM27.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM27.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneVM27
 "Link together Gencode UniProt Support table with Attributes table"
     mm39.wgEncodeGencodeEntrezGeneVM27.transcriptId dupeOk
     mm39.wgEncodeGencodeEntrezGeneVM27.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportVM27
 "Link together Gencode Exon Support table with Attributes table"
     mm39.wgEncodeGencodeExonSupportVM27.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM27.transcriptId minCheck=0.80
 
 # end Gencode VM27
 
+# begin Gencode VM28
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaVM28
+# wgEncodeGencode2wayConsPseudoVM28
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsVM28
+identifier wgEncodeGencodeBasicAttrsVM28
+"Link together Gencode Basic Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM28.transcriptId
+    mm39.wgEncodeGencodeBasicVM28.name
+
+identifier wgEncodeGencodeCompAttrsVM28
+"Link together Gencode Comprehensive Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM28.transcriptId
+    mm39.wgEncodeGencodeCompVM28.name
+
+identifier wgEncodeGencodePseudoGeneAttrsVM28
+"Link together Gencode PseudoGene Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM28.transcriptId
+    mm39.wgEncodeGencodePseudoGeneVM28.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsVM28)
+identifier wgEncodeGencodeGeneSourceVM28
+"Link together Gencode Gene Source table with Attributes table"
+    mm39.wgEncodeGencodeGeneSourceVM28.geneId
+    mm39.wgEncodeGencodeAttrsVM28.geneId
+
+identifier wgEncodeGencodeGeneSymbolVM28
+"Link together Gencode gene symbol table with Attributes table"
+    mm39.wgEncodeGencodeGeneSymbolVM28.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM28.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbVM28
+"Link together Gencode Pdb table with Attributes table"
+    mm39.wgEncodeGencodePdbVM28.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM28.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedVM28
+"Link together Gencode Pubmed table with Attributes table"
+    mm39.wgEncodeGencodePubMedVM28.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM28.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqVM28
+"Link together Gencode RefSeq table with Attributes table"
+    mm39.wgEncodeGencodeRefSeqVM28.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM28.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneVM28
+"Link together Gencode RefSeq table with refGene track"
+    mm39.wgEncodeGencodeRefSeqVM28.rnaAcc dupeOk chopAfter=.
+    mm39.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagVM28
+"Link together Gencode Tag table with Attributes table"
+    mm39.wgEncodeGencodeTagVM28.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM28.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceVM28
+"Link together Gencode Transcript Source table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSourceVM28.transcriptId
+    mm39.wgEncodeGencodeAttrsVM28.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportVM28
+"Link together Gencode Transcript Support table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSupportVM28.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM28.transcriptId minCheck=0.04
+
+identifier wgEncodeGencodeTranscriptionSupportLevelVM28
+"Link together Gencode Transcription Support Level table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptionSupportLevelVM28.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM28.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtVM28
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeUniProtVM28.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM28.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkVM28
+"Link together Gencode Annotation Remark table with Attributes table"
+    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
+
 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