a35f450f1d4f1f128460141ab8e8faea28980fe6
hiram
  Mon Jun 15 10:35:08 2020 -0700
adding rules for panPan3 refs #25720

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index 49b1b6b..e955e52 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -97,31 +97,31 @@
 set nanGal nanGal1
 set nanPar nanPar1
 set nasLar nasLar1
 set neoSch neoSch1
 set nomLeu nomLeu1,nomLeu2,nomLeu3
 set ochPri ochPri2,ochPri3
 set octDeg octDeg1
 set orcOrc orcOrc1
 set oreNil oreNil1,oreNil2,oreNil3
 set ornAna ornAna1,ornAna2
 set oryCun oryCun2
 set oryLat oryLat2
 set otoGar otoGar1,otoGar3
 set oviAri oviAri1,oviAri3,oviAri4
 set oxyTri oxyTri2
-set panPan panPan1,panPan2
+set panPan panPan1,panPan2,panPan3
 set panManBai panManBai1
 set panTro panTro1,panTro2,panTro3,panTro4,panTro5,panTro6
 set papAnu papAnu2,papAnu3,papAnu4
 set papHam papHam1
 set petMar petMar1,petMar2,petMar3
 set pelSin pelSin1
 set perMan perManBai1
 set poeFor poeFor1
 set ponAbe ponAbe2,ponAbe3
 set priPac priPac1,priPac2,priPac3
 set proCap proCap1
 set proCoq proCoq1
 set pteVam pteVam1
 set rheMac rheMac2,rheMac3,rheMac8,rheMac10
 set rhiBie rhiBie1
@@ -6029,31 +6029,31 @@
     $hgSplit,hg19,!hg18.gl.frag $split chopAfter=_
     $hg,!hg16,!hg17,!hg18.gold.frag
     $hgSplit,!hg18.gold.frag $split
     hg18.gl.frag $split chopAfter=_ minCheck=0.95
     hg18.gold.frag $split minCheck=0.90
 
 identifier wgsContigAccession typeOf=seqExtFile
 "Genbank accession.version of whole-genome shotgun contig"
     $wgs.contigAcc.acc
 
 identifier wgsContigName
 "Sequencing project name for whole-genome shotgun contigs."
     $wgs.contigAcc.contig
     $wgs,!panTro1.gold.frag $split full
 
-set notProteinAccession !ailMel1,!allMis1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!ci3,!colAng1,!cotJap2,!criGriChoV1,criGri1,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!dm3,!dm6,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat8,!felCat9,!fr2,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!manPen1,!macFas5,!manLeu1,!micMur2,!micMur3,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAr4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!petMar2,!priPac3,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!susScr3,!taeGut2,!tarSyr2,!vicPac2,!xenLae2,!xenTro7,!xenTro9
+set notProteinAccession !ailMel1,!allMis1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!ci3,!colAng1,!cotJap2,!criGriChoV1,criGri1,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!dm3,!dm6,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat8,!felCat9,!fr2,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!manPen1,!macFas5,!manLeu1,!micMur2,!micMur3,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAr4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!petMar2,!priPac3,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!susScr3,!taeGut2,!tarSyr2,!vicPac2,!xenLae2,!xenTro7,!xenTro9
 
 identifier proteinAccession fuzzy
 "Genbank protein accession."
     $kgDb.kgProtAlias.alias
     $kgDb.kgSpAlias.alias minCheck=0.1
     $kgDb.kgXref.protAcc
     hgFixed.refLink.protAcc
 
 identifier estOrMrnaAccession
 "Genbank EST or mRNA accession."
     hgFixed.gbSeq.acc
     hgFixed.gbCdnaInfo.acc unique
     hgFixed.imageClone.acc
     $gbd,!ce2,!hg16,!hg17,!hg18,!mm7.altGraphX.mrnaRefs comma
     ce2.altGraphX.mrnaRefs comma minCheck=0.96
@@ -6617,52 +6617,52 @@
 "An image cDNA clone ID"
     hgFixed.imageClone.imageId
 
 identifier humanFosmidId
 "Human Fosmid (~50kb genomic sequence) clone"
     $hg.fosEndPairs.name dupeOk
 
 identifier humanFosmidEndId
 "Identifier of read from one end of human formid."
     $hg.all_fosends.qName dupeOk
     $hg.fosEndPairs.lfNames comma
 
 ## TYPED TO HERE %%%
 # Mapping Stuff, STS, etc.
 
-set notDbStsId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!braFlo2,!bosTau8,!bosTau9,!calJac3,!calMil1,!canFam4,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!equCab3,!ficAlb1,!fr2,!fukDam1,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
+set notDbStsId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!braFlo2,!bosTau8,!bosTau9,!calJac3,!calMil1,!canFam4,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!equCab3,!ficAlb1,!fr2,!fukDam1,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
 
 identifier dbStsId external=dbSts fuzzy
 "NCBI dbSTS (Sequenced Tagged Site, aka mapping sequence) ID"
     $hg.all_sts_primer.qName chopBefore=dbSTS_
     $gbd,$notDbStsId.all_sts_seq.qName
     $gbd,$notDbStsId.stsInfo2.dbSTSid
 
 identifier ucscStsId
 "UCSC STS (Sequenced Tagged Site, aka mapping sequence) ID"
     $gbd.stsInfo2.identNo
     $gbd.stsAlias.identNo
     $gbd.stsMap.identNo
 
 identifier ucscMouseStsId
 "UCSC Mouse STS (Sequenced Tagged Site, aka mapping sequence) ID"
     $mm.stsInfoMouseNew.identNo
     $mm.stsAlias.identNo
     $mm.all_sts_primer.qName chopAfter=_ minCheck=0.99
     $mm.stsMapMouseNew.identNo
 
-set notStsName !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!canFam4,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
+set notStsName !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!canFam4,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
 
 identifier stsName fuzzy
 "STS (Sequenced Tagged Site, aka mapping sequence) Name"
     $hg.fishClones.stsNames comma
     $gbd,$notStsName.stsInfo2.otherNames comma
     $mm.stsInfoMouseNew.alias separator=;
 
 identifier stsTrueName typeOf=stsName
 "STS (Sequenced Tagged Site, aka mapping sequence) Unique Name"
     $gbd,!hg16.stsInfo2.name
     $gbd.stsAlias.trueName
     $gbd.stsMap.name
 
 identifier stsTrueNameHg16 typeOf=stsName
 "STS (Sequenced Tagged Site, aka mapping sequence) Unique Name for hg16"
@@ -6748,31 +6748,31 @@
     $hg.jaxOrtholog.mouseSymbol
     hgFixed.refLink.name
     visiGene.gene.name
 
 # Model Organism Database Identifiers
 
 identifier jaxMgiId
 "Jackson Labs Mouse Gene Identifier"
     $hg.jaxOrtholog.mgiId
 
 identifier wormBaseIsoformCluster
 "Overlapping (after splicing) WormBase transcripts"
     $ce.sangerCanonical.clusterId
     $ce.sangerIsoforms.clusterId full
 
-set notWormBaseId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!canFam4,!casCan1,!cavApe1,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn3,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
+set notWormBaseId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!canFam4,!casCan1,!cavApe1,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn3,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
 
 identifier wormBaseId external=WormBase dependency
 "WormBase (C. elegans) ORF ID"
     $ce.sangerGene.name
     $gbd,$notWormBaseId.ceBlastTab.target minCheck=0.90
     $ce.kimExpDistance.query minCheck=0.68
     $ce.kimExpDistance.target minCheck=0.66
     $ce.orfToGene.name
     $ce.sangerBlastTab.query
     $ce.sangerBlastTab.target
     $ce.sangerCanonical.transcript
     $ce.sangerIsoforms.transcript
     $ce.sangerLinks.orfName minCheck=0.96
     $ce.sangerPep.name minCheck=0.96
     $ce.sangerToKim.name
@@ -6792,31 +6792,31 @@
 
 identifier wormBaseRnaGene external=WormBase dependency
 "WormBase (C. elegans) RNA genes"
     $ce.sangerRnaGene.name
 
 identifier flyBaseRefId
 "FlyBase (Drosophila) Reference (Literature)"
     $dm.fbRef.id
     $dm.fbPhenotype.fbRef
 
 identifier flyBaseAlleleId
 "FlyBase (Drosophila) Allele ID"
     $dm.fbAllele.id
     $dm.fbPhenotype.fbAllele exclude=0
 
-set notFlyBaseGeneId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!canFam4,!casCan1,!cavApe1,!ce2,!ce4,!ce6,!ce9,!ce10,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!eboVir3,!danRer3,!danRer7,!danRer10,!danRer11,!dipOrd2,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg17,!hg18,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm7,!mm8,!mm9,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn3,!rn4,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer1,!sacCer2,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
+set notFlyBaseGeneId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!canFam4,!casCan1,!cavApe1,!ce2,!ce4,!ce6,!ce9,!ce10,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!eboVir3,!danRer3,!danRer7,!danRer10,!danRer11,!dipOrd2,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg17,!hg18,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm7,!mm8,!mm9,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn3,!rn4,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sacCer1,!sacCer2,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
 
 identifier flyBaseGeneId external=FlyBase
 "FlyBase (Drosophila) Gene ID"
     $dm.fbGene.geneId
     $dm.bdgpExprLink.flyBaseId minCheck=0.95
     dm1.bdgpGeneInfo.flyBaseId minCheck=0.95
     dm1.bdgpNonCodingInfo.flyBaseId minCheck=0.20
     dm1.bdgpSwissProt.flyBaseId minCheck=0.95
     $dm.fbAllele.geneId
     $dm.fbPhenotype.geneId
     $dm.fbSynonym.geneId
     $dm.fbTranscript.geneId minCheck=0.95
     dm1.flyBaseSwissProt.flyBaseId minCheck=0.95
     $dm,!dm1.flyBase2004Xref.fbgn minCheck=0.90
     $dm,!dm1.pscreen.geneIds comma minCheck=0.95
@@ -6910,31 +6910,31 @@
     $dm.flyreg2.name minCheck=0.8
 
 identifier sgdIsoformCluster
 "Overlapping (after splicing) SGD (Yeast) transcripts"
     $sacCer.sgdCanonical.clusterId
     $sacCer.sgdIsoforms.clusterId full
 
 identifier sgdProtHomologId
 "sacCer protHomolog protein ID"
     $sacCer.protHomolog.proteinID dupeOk
     $sacCer.samSubdir.proteinId
 
 identifier sgdId external=SGD
 "Sacchromyces Genome Database ID - Coding or other"
 
-set notSgdCodingId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!canFam4,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
+set notSgdCodingId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!canFam4,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenCho1,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
 
 identifier sgdCodingId typeOf=sgdId dependency
 "Sacchromyces Genome Database ID"
     $sacCer.sgdGene.name
     $gbd,$notSgdCodingId.scBlastTab.target minCheck=0.90
     $sacCer.sgdBlastTab.query
     $sacCer.sgdBlastTab.target
     $sacCer.ceBlastTab.query
     $sacCer.dmBlastTab.query
     $sacCer,!sacCer1.drBlastTab.query
     $sacCer.hgBlastTab.query minCheck=0.999
     $sacCer.mmBlastTab.query
     $sacCer.rnBlastTab.query
     sacCer2.knownBlastTab.query
     $sacCer.choExpDistance.target minCheck=0.60
@@ -7052,31 +7052,31 @@
 "Ensemble Gene ID"
     $gbd.ensemblXref3.gene dupeOk
 
 identifier ensemblProteinId external=Ensembl
 "Ensemble Translated Protein ID"
     $gbd.ensTranscript.translation_name dupeOk
     $gbd.ensGtp.protein chopAfter=.
     $gbd.sfAssign.seqID minCheck=0.01
 
 identifier ensemblProteinId3 external=Ensembl
 "Ensemble Translated Protein ID"
     $gbd.ensemblXref3.protein dupeOk
     $gbd.sfAssign.seqID minCheck=0.01
 
 
-set notEnsemblTranscriptId !allMis1,!ambMex1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!ce10,!calMil1,!canFam4,!casCan1,!cebCap1,!cerAty1,!cerSim1,!chrPic2,!$colAng,!cotJap2,!eboVir3,!eulFla1,!eulMac1,!equCab3,!felCat8,!felCat9,!galGal6,!galVar1,!gorGor5,!gorGor6,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur3,!nanPar1,!nasLar1,!neoSch1,!$orcOrc,!oreNil3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!petMar3,!ponAbe3,!priPac3,!proCoq1,!regenCho1,!regenRn0,!regenRn1,!rhiBie1,!rhiRox1,!rouAeg1,!staAur1,!staAur2,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
+set notEnsemblTranscriptId !allMis1,!ambMex1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!ce10,!calMil1,!canFam4,!casCan1,!cebCap1,!cerAty1,!cerSim1,!chrPic2,!$colAng,!cotJap2,!eboVir3,!eulFla1,!eulMac1,!equCab3,!felCat8,!felCat9,!galGal6,!galVar1,!gorGor5,!gorGor6,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur3,!nanPar1,!nasLar1,!neoSch1,!$orcOrc,!oreNil3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panPan3,!panTro5,!panTro6,!petMar3,!ponAbe3,!priPac3,!proCoq1,!regenCho1,!regenRn0,!regenRn1,!rhiBie1,!rhiRox1,!rouAeg1,!staAur1,!staAur2,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!wuhCor1,!xenLae2,!xenTro7,!xenTro9
 
 identifier ensemblTranscriptId external=Ensembl dependency
 "Ensembl Transcript ID"
     $ensGeneDb,$notEnsemblTranscriptId.ensGene.name dupeOk
     $gbd,$notEnsemblTranscriptId.ensGeneXref.transcript_name minCheck=0.95
     $ensGeneDb,$notEnsemblTranscriptId.ensGtp.transcript minCheck=0.94
     $ensGeneDb,$notEnsemblTranscriptId.ensPep.name minCheck=0.93
     $gbd,$notEnsemblTranscriptId.ensTranscript.transcript_name minCheck=0.20
     $gbd,$notEnsemblTranscriptId.ensInfo.name minCheck=0.9
     $ensGeneDb,$notEnsemblTranscriptId.ensemblToGeneName.name minCheck=0.94
     $ensGeneDb,$notEnsemblTranscriptId.ensemblSource.name minCheck=0.96
     !hg38,$kgDb.knownToEnsembl.value chopAfter=.
     $kgDb.rgdGene2ToEnsembl.value chopAfter=.
     $danRer.ensZfishBlastTab.query
     $danRer.ensZfishBlastTab.target