96688b9c02671c5a1119ee2a75ac0130edf711e9
hiram
  Tue Nov 26 13:27:04 2019 -0800
adding rules for regenCho1 refs #24568

diff --git src/hg/makeDb/schema/all.joiner src/hg/makeDb/schema/all.joiner
index c4fa8e1..ed0e264 100644
--- src/hg/makeDb/schema/all.joiner
+++ src/hg/makeDb/schema/all.joiner
@@ -31,31 +31,31 @@
 set cavApe cavApe1
 set cavPor cavPor3
 set cb cb1,cb3,cb4
 set ce ce2,ce4,ce6,ce9,ce10,ce11
 set cebCap cebCap1
 set cerAty cerAty1
 set cerSim cerSim1
 set chiLan chiLan1
 set choHof choHof1
 set chlSab chlSab2
 set chrPic chrPic1,chrPic2
 set ci ci1,ci2,ci3
 set cioSav cioSav1,cioSav2
 set colAng colAng1
 set cotJap cotJap2
-set criGri criGri1,criGriChoV1,criGriChoV2
+set criGri criGri1,criGriChoV1,criGriChoV2,regenCho1
 set danRer danRer3,danRer4,danRer5,danRer6,danRer7,danRer10,danRer11
 set dasNov dasNov2,dasNov3
 set dipOrd dipOrd1,dipOrd2
 set dm dm1,dm2,dm3,dm6
 set dp dp2,dp3
 set droEre droEre1
 set droMoj droMoj1,droMoj2
 set droMult droAna1,droAna2,droMoj1,droMoj2,droVir1,droVir2,droEre1,droSim1,droGri1,droPer1,droSec1
 set droVir droVir1,droVir2
 set droYak droYak1,droYak2
 set eboVir eboVir3
 set echTel echTel1,echTel2
 set equCab equCab1,equCab2,equCab3
 set eriEur eriEur1,eriEur2
 set eulFla eulFla1
@@ -150,31 +150,31 @@
 
 
 # Define all organism/assembly-specific databases.
 set gbd $ailMel,$allMis,$ambMex,$anaPla,$anoCar,$anoGam,$aotNan,$apiMel,$aplCal,$aptMan,$aquChr,$astMex,$balAcu,$bisBis,$bosTau,$braFlo,$bruMal,$caeAng,$caeJap,$caePb,$caeRem,$caeSp11,$canFam,$calJac,$calMil,$casCan,$cavApe,$cavPor,$cb,$ce,$cebCap,$cerAty,$cerSim,$chiLan,$choHof,$chlSab,$chrPic,$ci,$cioSav,$colAng,$cotJap,$criGri,$danRer,$dasNov,$dipOrd,$dm,$dp,$droMult,$droYak,$eboVir,$echTel,$equCab,$eriEur,$eulFla,$eulMac,$felCat,$ficAlb,$fr,$fukDam,$gadMor,$galGal,$gasAcu,$galVar,$geoFor,$gorGor,$haeCon,$hetGla,$hg,$jacJac,$latCha,$lepOcu,$loxAfr,$manPen,$macEug,$macNem,$macFas,$manLeu,$melGal,$melHap,$melInc,$melUnd,$mesAur,$micMur,$micOch,$mm,$monDom,$musFur,$myoLuc,$nanGal,$nanPar,$nasLar,$neoSch,$nomLeu,$ochPri,$octDeg,$orcOrc,$oreNil,$ornAna,$oryCun,$oryLat,$otoGar,$oviAri,$oxyTri,$panPan,$panManBai,$panTro,$papAnu,$papHam,$pelSin,$petMar,$perMan,$poeFor,$ponAbe,$priPac,$proCap,$proCoq,$pteVam,$rheMac,$rhiBie,$rhiRox,$rn,$rouAeg,$sacCer,$saiBol,$sarHar,$sorAra,$speTri,$staAur,$strPur,$susScr,$taeGut,$tarSyr,$tetNig,$thaSir,$triMan,$tupBel,$tupChi,$turTru,$vicPac,$xenLae,$xenTro,$xipMac
 
 set metaGbd $gbd
 
 # Define organism databases based on whole-genome shotgun projects
 # (Assembly based on WGS project contigs accessioned in Genbank)
 set wgs $ailMel,$allMis,$aplCal,$balAcu,$bisBis,$bosTau,$bruMal,$calJac,$calMil,$canFam,$cavPor,$choHof,$chrPic,$cioSav,$colAng,$cotJap,$criGri,$dasNov,$dipOrd,$echTel,$eriEur,$eulFla,$eulMac,$felCat,$fr,$galGal,$haeCon,$hetGla,$manPen,$macEug,$macNem,$macFas,$manLeu,$melGal,$melHap,$melInc,$micMur,$monDom,$musFur,$myoLuc,$nanPar,$nasLar,$neoSch,$nomLeu,$ochPri,$otoGar,$oryCun,$oryLat,$oviAri,$panPan,$panTro,$proCap,$proCoq,$pteVam,$rn,$sarHar,$sorAra,$speTri,$susScr,$taeGut,$tarSyr,$tetNig,$tupBel,$tupChi,$turTru,$vicPac
 
 # Define organism databases for which we build a xenoRefGene track:
 set xrg $ailMel,$allMis,$anoCar,$anoGam,$aotNan,$aplCal,$aquChr,$balAcu,$bisBis,$bosTau,$braFlo,$bruMal,$caeAng,$caeJap,$caePb,$caeRem,$caeSp11,$calJac,$calMil,$canFam,$casCan,$cavApe,$cb,$ce,$cebCap,$cerAty,$cerSim,$chlSab,$choHof,$chrPic,$ci,$colAng,$cotJap,$criGri,danRer6,danRer7,danRer10,danRer11,$dasNov,$dipOrd,dm6,$dp,$droMult,$droYak,$echTel,$eriEur,$equCab,$eulFla,$eulMac,$felCat,$ficAlb,$fukDam,$gadMor,$galGal,$galVar,$geoFor,$gorGor,$haeCon,$hetGla,$hg,$latCha,$loxAfr,$manPen,$macEug,$macNem,$macFas,$manLeu,$melGal,$melHap,$melInc,$melUnd,$mesAur,$micMur,$micOch,$mm,$monDom,$musFur,$myoLuc,$nanPar,$nasLar,$neoSch,$nomLeu,$ornAna,$ochPri,$orcOrc,$oreNil,$oryCun,$oryLat,$otoGar,$oviAri,$panPan,$panTro,$papAnu,$papHam,$petMar,$ponAbe,$priPac,$proCap,$proCoq,$pteVam,$rheMac,$rhiBie,$rhiRox,$rn,$rouAeg,$saiBol,$sarHar,$sorAra,$speTri,$staAur,$strPur,$susScr,$taeGut,$tarSyr,$thaSir,$triMan,$tupBel,$tupChi,$turTru,$vicPac,$xenLae,$xenTro
 
 # Ensembl gene track lists constructed from update procedure
-set ensGeneDb ailMel1,anaPla1,anoCar2,anoGam3,astMex1,bosTau6,calJac3,canFam2,canFam3,cavApe1,cavPor3,ce10,ce11,chiLan1,chlSab2,choHof1,ci2,ci3,cioSav2,criGri1,criGriChoV1,criGriChoV2,danRer10,danRer11,danRer7,dasNov2,dasNov3,dipOrd1,dipOrd2,dm3,dm6,echTel1,echTel2,equCab2,eriEur1,eriEur2,felCat3,felCat5,ficAlb1,fr2,fr3,fukDam1,gadMor1,galGal3,galGal4,galGal5,gasAcu1,gorGor3,gorGor4,hetGla1,hetGla2,hg16,hg17,hg18,hg19,hg38,jacJac1,latCha1,lepOcu1,loxAfr3,macEug1,melGal1,mesAur1,micMur1,micMur2,micOch1,mm10,mm7,mm8,mm9,monDom5,musFur1,myoLuc2,nanGal1,nomLeu1,nomLeu3,ochPri2,ochPri3,octDeg1,oreNil1,ornAna1,ornAna2,oryCun2,oryLat2,otoGar3,oviAri3,panTro2,panTro4,papAnu2,papAnu3,papAnu4,pelSin1,perManBai1,petMar2,poeFor1,ponAbe2,proCap1,pteVam1,rheMac2,rheMac8,rn3,rn4,rn5,rn6,sacCer3,saiBol1,sarHar1,sorAra1,sorAra2,speTri2,susScr1,susScr11,susScr3,taeGut1,tarSyr1,tetNig2,tupBel1,turTru1,vicPac1,vicPac2,xenTro3,xipMac1
+set ensGeneDb ailMel1,anaPla1,anoCar2,anoGam3,astMex1,bosTau6,calJac3,canFam2,canFam3,cavApe1,cavPor3,ce10,ce11,chiLan1,chlSab2,choHof1,ci2,ci3,cioSav2,criGri1,criGriChoV1,criGriChoV2,danRer10,danRer11,danRer7,dasNov2,dasNov3,dipOrd1,dipOrd2,dm3,dm6,echTel1,echTel2,equCab2,eriEur1,eriEur2,felCat3,felCat5,ficAlb1,fr2,fr3,fukDam1,gadMor1,galGal3,galGal4,galGal5,gasAcu1,gorGor3,gorGor4,hetGla1,hetGla2,hg16,hg17,hg18,hg19,hg38,jacJac1,latCha1,lepOcu1,loxAfr3,macEug1,melGal1,mesAur1,micMur1,micMur2,micOch1,mm10,mm7,mm8,mm9,monDom5,musFur1,myoLuc2,nanGal1,nomLeu1,nomLeu3,ochPri2,ochPri3,octDeg1,oreNil1,ornAna1,ornAna2,oryCun2,oryLat2,otoGar3,oviAri3,panTro2,panTro4,papAnu2,papAnu3,papAnu4,pelSin1,perManBai1,petMar2,poeFor1,ponAbe2,proCap1,pteVam1,regenCho1,rheMac2,rheMac8,rn3,rn4,rn5,rn6,sacCer3,saiBol1,sarHar1,sorAra1,sorAra2,speTri2,susScr1,susScr11,susScr3,taeGut1,tarSyr1,tetNig2,tupBel1,turTru1,vicPac1,vicPac2,xenTro3,xipMac1
 
 # Databases from the old days when we split some large tables into one table per chrom
 # Some databases are excluded here because they're excluded from databasesChecked, e.g. cb2, ce3
 set oldSplit anoGam1,apiMel2,bosTau3,bosTau4,braFlo1,caeJap1,caePb1,caePb2,caeRem2,caeRem3,canFam1,canFam2,cb1,cb3,cb4,ce10,ce2,ce4,ce6,ce9,danRer3,danRer4,dm1,dm2,dm3,dp3,droSim1,droYak1,droYak2,equCab1,equCab2,fr1,fr2,galGal2,galGal3,gasAcu1,hg16,hg17,hg18,mm10,mm7,mm8,mm9,monDom1,monDom4,panTro1,panTro2,ponAbe2,priPac1,rheMac2,rn3,rn4,sacCer1,sacCer2,sacCer3,strPur2,susScr1,susScr2,taeGut1,tetNig1,tetNig2
 
 set hgSplit hg16,hg17,hg18
 
 # Obsolete archived Ensembl gene tracks
 set obsoleteEnsGeneDb danRer7,hg16,hg38,rn3
 
 set ensGeneWgs chlSab2,choHof1,dasNov2,dipOrd1,echTel1,echTel2,eriEur1,eriEur2,felCat3,gadMor1,micMur1,myoLuc2,ochPri2,ochPri3,otoGar1,proCap1,pteVam1,sorAra1,sorAra2,speTri1,tarSyr1,tupBel1,turTru1,vicPac1,vicPac2
 
 set ensGeneScaffold choHof1,dasNov2,dipOrd1,echTel1,echTel2,eriEur1,eriEur2,felCat3,gadMor1,micMur1,ochPri2,ochPri3,otoGar1,proCap1,pteVam1,sorAra1,sorAra2,speTri1,tarSyr1,tupBel1,turTru1,vicPac1,vicPac2
 
 # Define organism databases for which we host the vegaGenes
@@ -6051,52 +6051,52 @@
 "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,!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,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
+set notDbStsId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!braFlo2,!bosTau8,!bosTau9,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!equCab3,!ficAlb1,!fr2,!fukDam1,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$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,!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,!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,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
+set notStsName !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$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,!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"
@@ -6182,31 +6182,31 @@
     $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,!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,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn3,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
+set notWormBaseId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$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,!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
@@ -6226,31 +6226,31 @@
 
 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,!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,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn3,!rn4,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sacCer1,!sacCer2,!sacCer3,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
+set notFlyBaseGeneId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce2,!ce4,!ce6,!ce9,!ce10,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!eboVir3,!danRer3,!danRer7,!danRer10,!danRer11,!dipOrd2,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg17,!hg18,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm7,!mm8,!mm9,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$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,!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
@@ -6344,31 +6344,31 @@
     $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,!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,!$orcOrc,!oreNil3,!ornAna1,!ornAna2,!otoGar3,!oviAri3,!oviAri4,!oxyTri2,!panPan1,!panPan2,!panTro5,!panTro6,!papAnu2,!papAnu3,!papAnu4,!petMar2,!petMar3,!ponAbe3,!priPac3,!proCoq1,!rheMac8,!rheMac10,!rhiBie1,!rhiRox1,!rn5,!rn6,!regenRn0,!regenRn1,!rouAeg1,!sorAra2,!speTri2,!staAur1,!staAur2,!susScr3,!susScr11,!taeGut2,tarSyr2,!thaSir1,!tupChi1,!vicPac2,!xenLae2,!xenTro7,!xenTro9
+set notSgdCodingId !ailMel1,!allMis1,!ambMex1,!anoGam3,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!calJac3,!calMil1,!casCan1,!cavApe1,!ce11,!cebCap1,!cerAty1,!cerSim1,!chlSab2,!chrPic2,!ci3,!colAng1,!cotJap2,!criGriChoV1,!criGriChoV2,criGri1,!dipOrd2,!dm6,!eboVir3,!danRer7,!danRer10,!danRer11,!dasNov3,!echTel2,!eriEur2,!eulFla1,!eulMac1,!felCat3,!felCat8,!felCat9,!equCab3,!ficAlb1,!fr2,!fukDam1,!galGal5,!galGal6,!galGal4,!gasAcu1,!hg38,!hg19,!galVar1,!gorGor5,!gorGor6,!loxAfr3,!mm10,!manPen1,!macNem1,!macFas5,!manLeu1,!melGal5,!micMur2,!micMur3,!micOch1,!myoLuc2,!nanPar1,!nasLar1,!neoSch1,!nomLeu1,!ochPri3,!$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,!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
@@ -6486,31 +6486,31 @@
 "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,!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,!regenRn0,!regenRn1,!rhiBie1,!rhiRox1,!rouAeg1,!staAur1,!staAur2,!taeGut2,!tarSyr2,!thaSir1,!tupChi1,!xenLae2,!xenTro7,!xenTro9
+set notEnsemblTranscriptId !allMis1,!ambMex1,!aotNan1,!aptMan1,!aquChr2,!balAcu1,!bisBis1,!bosTau8,!bosTau9,!braFlo2,!ce10,!calMil1,!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,!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
@@ -7883,30 +7883,34 @@
 dependency $pbDb.pbAaDistM $pbDb.knownGenePep
 dependency $pbDb.pbAaDistN $pbDb.knownGenePep
 dependency $pbDb.pbAaDistP $pbDb.knownGenePep
 dependency $pbDb.pbAaDistQ $pbDb.knownGenePep
 dependency $pbDb.pbAaDistR $pbDb.knownGenePep
 dependency $pbDb.pbAaDistS $pbDb.knownGenePep
 dependency $pbDb.pbAaDistT $pbDb.knownGenePep
 dependency $pbDb.pbAaDistV $pbDb.knownGenePep
 dependency $pbDb.pbAaDistW $pbDb.knownGenePep
 dependency $pbDb.pbAaDistY $pbDb.knownGenePep
 
 
 
 # Ignored tables - no linkage here that we check at least.
 
+tablesIgnored regenCho1
+    regenAGP
+    regenAGPGap
+
 tablesIgnored go
     instance_data
     source_audit
 
 tablesIgnored visiGene
     vgPrbAli
     vgPrbAliAll
     tableDescriptions
 
 tablesIgnored hgFixed
     omimTitle
     cutters
     rebaseRefs
 
 tablesIgnored $gbd