ba39846fb30a64ba6df41c0aae781915ddf61c80
markd
  Mon Mar 4 22:15:06 2024 -0800
import of GENCODE VM35

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 48dbc2d..f1af006 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -8189,30 +8189,124 @@
     mm39.wgEncodeGencodeAnnotationRemarkVM34.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM34.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneVM34
 "Link together Gencode UniProt Support table with Attributes table"
     mm39.wgEncodeGencodeEntrezGeneVM34.transcriptId dupeOk
     mm39.wgEncodeGencodeEntrezGeneVM34.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportVM34
 "Link together Gencode Exon Support table with Attributes table"
     mm39.wgEncodeGencodeExonSupportVM34.transcriptId dupeOk
     mm39.wgEncodeGencodeAttrsVM34.transcriptId minCheck=0.50
 
 # end Gencode VM34
 
+# begin Gencode VM35
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaVM35
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsVM35
+identifier wgEncodeGencodeBasicAttrsVM35
+"Link together Gencode Basic Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM35.transcriptId
+    mm39.wgEncodeGencodeBasicVM35.name
+
+identifier wgEncodeGencodeCompAttrsVM35
+"Link together Gencode Comprehensive Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM35.transcriptId
+    mm39.wgEncodeGencodeCompVM35.name
+
+identifier wgEncodeGencodePseudoGeneAttrsVM35
+"Link together Gencode PseudoGene Table with Attributes table"
+    mm39.wgEncodeGencodeAttrsVM35.transcriptId
+    mm39.wgEncodeGencodePseudoGeneVM35.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsVM35)
+identifier wgEncodeGencodeGeneSourceVM35
+"Link together Gencode Gene Source table with Attributes table"
+    mm39.wgEncodeGencodeGeneSourceVM35.geneId
+    mm39.wgEncodeGencodeAttrsVM35.geneId
+
+identifier wgEncodeGencodeGeneSymbolVM35
+"Link together Gencode gene symbol table with Attributes table"
+    mm39.wgEncodeGencodeGeneSymbolVM35.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM35.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbVM35
+"Link together Gencode Pdb table with Attributes table"
+    mm39.wgEncodeGencodePdbVM35.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM35.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedVM35
+"Link together Gencode Pubmed table with Attributes table"
+    mm39.wgEncodeGencodePubMedVM35.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM35.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqVM35
+"Link together Gencode RefSeq table with Attributes table"
+    mm39.wgEncodeGencodeRefSeqVM35.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM35.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneVM35
+"Link together Gencode RefSeq table with refGene track"
+    mm39.wgEncodeGencodeRefSeqVM35.rnaAcc dupeOk chopAfter=.
+    mm39.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagVM35
+"Link together Gencode Tag table with Attributes table"
+    mm39.wgEncodeGencodeTagVM35.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM35.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceVM35
+"Link together Gencode Transcript Source table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSourceVM35.transcriptId
+    mm39.wgEncodeGencodeAttrsVM35.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportVM35
+"Link together Gencode Transcript Support table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptSupportVM35.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM35.transcriptId minCheck=0.02
+
+identifier wgEncodeGencodeTranscriptionSupportLevelVM35
+"Link together Gencode Transcription Support Level table with Attributes table"
+    mm39.wgEncodeGencodeTranscriptionSupportLevelVM35.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM35.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtVM35
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeUniProtVM35.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM35.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkVM35
+"Link together Gencode Annotation Remark table with Attributes table"
+    mm39.wgEncodeGencodeAnnotationRemarkVM35.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM35.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneVM35
+"Link together Gencode UniProt Support table with Attributes table"
+    mm39.wgEncodeGencodeEntrezGeneVM35.transcriptId dupeOk
+    mm39.wgEncodeGencodeEntrezGeneVM35.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportVM35
+"Link together Gencode Exon Support table with Attributes table"
+    mm39.wgEncodeGencodeExonSupportVM35.transcriptId dupeOk
+    mm39.wgEncodeGencodeAttrsVM35.transcriptId minCheck=0.50
+
+# end Gencode VM35
+
 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