584d70ac259b9b2f818e40a2f838ac114e4b234d
markd
  Tue Apr 25 19:58:18 2023 -0700
import of gencode V44 pre-release

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index b232655..561946f 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -3656,30 +3656,124 @@
     hg38.wgEncodeGencodeAnnotationRemarkV43.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV43.transcriptId minCheck=0.10
 
 identifier wgEncodeGencodeEntrezGeneV43
 "Link together Gencode UniProt Support table with Attributes table"
     hg38.wgEncodeGencodeEntrezGeneV43.transcriptId dupeOk
     hg38.wgEncodeGencodeEntrezGeneV43.transcriptId minCheck=0.35
 
 identifier wgEncodeGencodeExonSupportV43
 "Link together Gencode Exon Support table with Attributes table"
     hg38.wgEncodeGencodeExonSupportV43.transcriptId dupeOk
     hg38.wgEncodeGencodeAttrsV43.transcriptId minCheck=0.80
 
 # end Gencode V43
 
+# begin Gencode V44
+
+# gencode genePred tables with no associations
+# wgEncodeGencodePolyaV44
+
+# gencode genePred tables with joining through wgEncodeGencodeAttrsV44
+identifier wgEncodeGencodeBasicAttrsV44
+"Link together Gencode Basic Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV44.transcriptId
+    hg38.wgEncodeGencodeBasicV44.name
+
+identifier wgEncodeGencodeCompAttrsV44
+"Link together Gencode Comprehensive Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV44.transcriptId
+    hg38.wgEncodeGencodeCompV44.name
+
+identifier wgEncodeGencodePseudoGeneAttrsV44
+"Link together Gencode PseudoGene Table with Attributes table"
+    hg38.wgEncodeGencodeAttrsV44.transcriptId
+    hg38.wgEncodeGencodePseudoGeneV44.name
+
+# gencode association tables (joined through wgEncodeGencodeAttrsV44)
+identifier wgEncodeGencodeGeneSourceV44
+"Link together Gencode Gene Source table with Attributes table"
+    hg38.wgEncodeGencodeGeneSourceV44.geneId
+    hg38.wgEncodeGencodeAttrsV44.geneId
+
+identifier wgEncodeGencodeGeneSymbolV44
+"Link together Gencode gene symbol table with Attributes table"
+    hg38.wgEncodeGencodeGeneSymbolV44.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV44.transcriptId minCheck=0.20
+
+identifier wgEncodeGencodePdbV44
+"Link together Gencode Pdb table with Attributes table"
+    hg38.wgEncodeGencodePdbV44.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV44.transcriptId minCheck=0.015
+
+identifier wgEncodeGencodePubMedV44
+"Link together Gencode Pubmed table with Attributes table"
+    hg38.wgEncodeGencodePubMedV44.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV44.transcriptId  minCheck=0.63
+
+identifier wgEncodeGencodeRefSeqV44
+"Link together Gencode RefSeq table with Attributes table"
+    hg38.wgEncodeGencodeRefSeqV44.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV44.transcriptId minCheck=0.05
+
+identifier wgEncodeGencodeRefSeqToRefGeneV44
+"Link together Gencode RefSeq table with refGene track"
+    hg38.wgEncodeGencodeRefSeqV44.rnaAcc dupeOk chopAfter=.
+    hg38.refGene.name minCheck=0.77
+
+identifier wgEncodeGencodeTagV44
+"Link together Gencode Tag table with Attributes table"
+    hg38.wgEncodeGencodeTagV44.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV44.transcriptId minCheck=0.36
+
+identifier wgEncodeGencodeTranscriptSourceV44
+"Link together Gencode Transcript Source table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSourceV44.transcriptId
+    hg38.wgEncodeGencodeAttrsV44.transcriptId
+
+identifier wgEncodeGencodeTranscriptSupportV44
+"Link together Gencode Transcript Support table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptSupportV44.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV44.transcriptId minCheck=0.02
+
+identifier wgEncodeGencodeTranscriptionSupportLevelV44
+"Link together Gencode Transcription Support Level table with Attributes table"
+    hg38.wgEncodeGencodeTranscriptionSupportLevelV44.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV44.transcriptId minCheck=0.30
+
+identifier wgEncodeGencodeUniProtV44
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeUniProtV44.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV44.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeAnnotationRemarkV44
+"Link together Gencode Annotation Remark table with Attributes table"
+    hg38.wgEncodeGencodeAnnotationRemarkV44.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV44.transcriptId minCheck=0.10
+
+identifier wgEncodeGencodeEntrezGeneV44
+"Link together Gencode UniProt Support table with Attributes table"
+    hg38.wgEncodeGencodeEntrezGeneV44.transcriptId dupeOk
+    hg38.wgEncodeGencodeEntrezGeneV44.transcriptId minCheck=0.35
+
+identifier wgEncodeGencodeExonSupportV44
+"Link together Gencode Exon Support table with Attributes table"
+    hg38.wgEncodeGencodeExonSupportV44.transcriptId dupeOk
+    hg38.wgEncodeGencodeAttrsV44.transcriptId minCheck=0.50
+
+# end Gencode V44
+
 # begin Gencode V24lift37
 
 # gencode genepreds with no associations
 # wgEncodeGencodePolyaV24lift37
 # wgEncodeGencode2wayConsPseudoV24lift37
 
 # gencode genepreds with joining through wgEncodeGencodeAttrsV24lift37
 identifier wgEncodeGencodeBasicAttrsV24lift37
 "Link together Gencode Basic Table with Attributes table"
     hg19.wgEncodeGencodeAttrsV24lift37.transcriptId
     hg19.wgEncodeGencodeBasicV24lift37.name
 
 identifier wgEncodeGencodeCompAttrsV24lift37
 "Link together Gencode Comprehensive Table with Attributes table"
     hg19.wgEncodeGencodeAttrsV24lift37.transcriptId