knownGene knownGene exact knownGene 0 1 Known Genes Based on SWISS-PROT, TrEMBL, mRNA, and RefSeq (knownGene) blastHg16KG blastHg16KG prefix psl 1 select tName,tStart,tEnd,qName from %s where qName like '%s%%' 1 Human Proteins (hg16) Mapped by Chained tBLASTn (blastHg16KG) ccdsGene ccdsGene exact genePred 0 select chrom,txStart,txEnd,name from %s where name like '%s' 1.1 Consensus CDS (ccdsGene) refLink refGene exact refGene 0 2 RefSeq Genes (refGene) grepIndex genbankGrep/refLink.mrnaAccProduct\ xenoRefGene xenoRefGene exact refGene 0 2.1 Non-C. savignyi RefSeq Genes (xenoRefGene) grepIndex refLinkGrep/refLink.mrnaAccProduct\ transMapRefGene transMapRefGene exact genePred 0 select chrom,txStart,txEnd,name from %s where name like '%s' 2.31 TransMap RefSeq Gene Predictions (transMapRefGene) transMapMRnaGene transMapMRnaGene exact genePred 0 select chrom,txStart,txEnd,name from %s where name like '%s' 2.32 TransMap Protein-Coding mRNA Predictions (transMapMRnaGene) pseudoGeneLink pseudoGeneLink exact 0 select chrom, chromStart,chromEnd, refSeq from %s where refSeq = '%s' refLink select mrnaAcc, name from %s where name like '%s%%' 2.5 pseudoGeneLink pseudoGeneUniProt pseudoGeneLink exact 0 select chrom, chromStart,chromEnd, kgName from %s where kgName = '%s' kgXref select kgID, spDisplayID from %s where spDisplayID = '%s' 2.6 pseudoGeneLink retroMrnaInfo retroMrnaInfo prefix bed 0 select chrom,chromStart,chromEnd,name from %s where name like '%s%%' 3.5 retroMrnaInfo retroMrnaInfoRefSeq retroMrnaInfo exact 0 select chrom, chromStart,chromEnd, refSeq from %s where refSeq = '%s' refLink select mrnaAcc, name from %s where name like '%s%%' 3.51 retroMrnaInfo pseudoGIS pseudoGIS exact genePred 0 select chrom,txStart,txEnd,name from %s where name like '%s' 4 pseudoGIS pseudoHavana pseudoHavana exact genePred 0 select chrom,txStart,txEnd,name from %s where name like '%s' 4 pseudoHavana pseudoYaleEncode pseudoYaleEncode exact genePred 0 select chrom,txStart,txEnd,name from %s where name like '%s' 4 pseudoYaleEncode assemblyAcc gold prefix 1 ^[A-Z]{4}[0-9]{8,10}(\\.[0-9]+)?$ select chrom,chromStart,chromEnd,frag from %s where frag like '%s' contigAcc select contig,acc from %s where acc like '%s%%' 5 Assembly from Fragments (gold) allenBrainAli allenBrainAli exact psl 1 ^RP_.+$ select tName,tStart,tEnd,qName from %s where qName like '%s' 5 Allen Brain Atlas Probes (allenBrainAli) ctgPos ctgPos exact 1 ^(ctg|NT_|NG_|NC_)[0-9]+$ select chrom,chromStart,chromEnd,contig from %s where contig like '%s' 5 Physical Map Contigs (ctgPos) superfamily superfamily fuzzy bed 0 select chrom,chromStart,chromEnd,name from %s where name like '%s' sfDescription select name,description from %s where description like '%%%s%%' 6 Description of Superfamily Protein padding 100\ cytoBand cytoBand exact cytoBand 1 ^(x|y|[1-9][0-9]?)(p|q)[0-9]+(\\.[0-9]+)?$ 6 cytoBand padding 500000\ fishClones fishClones exact bed 0 ^(RP|CT|GS)[[:alnum:]]+-[[:alnum:]]+$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 7 Clones Placed on Cytogenetic Map Using FISH (fishClones) clonePosNoVers clonePos prefix 1 ^[a-z][a-z0-9]_?[0-9]+$ select chrom,chromStart,chromEnd,name from %s where name like '%s.%%' 7 Clone Coverage/Fragment Position (clonePos) dontCheck [a-z][a-z0-9]_?[0-9]+.[0-9]+\ clonePos clonePos exact bed 1 ^[a-z]+_?[0-9]+\\.[0-9]+$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 7 Clone Coverage/Fragment Position (clonePos) bacEndPairs bacEndPairs exact bed 0 ^([[:alnum:]_ ]+|((RP|CT|GS|CH|TAM|MSMG)[[:alnum:]]+)?(-[[:alnum:]_]+)+)$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 8 BAC End Pairs (bacEndPairs) gold gold exact gold 1 ^[abuz].[0-9]+(\\.[0-9]+)?$ 8 Assembly from Fragments (gold) fosEndPairs fosEndPairs exact bed 0 ^([[:alnum:]]+|(RP|CT|GS)[[:alnum:]]+-[[:alnum:]]+|-[[:alnum:]]+-[[:alnum:]]+)$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 9 Fosmid End Pairs (fosEndPairs) knownGeneAcc knownGene exact knownGene 1 ^[a-z][a-z0-9][0-9]+$ 9 Known Genes Based on SWISS-PROT, TrEMBL, mRNA, and RefSeq (knownGene) semiShortCircuit 1\ fosEndPairsBad fosEndPairsBad exact bed 0 ^([[:alnum:]]+|(RP|CT|GS)[[:alnum:]]+-[[:alnum:]]+|-[[:alnum:]]+-[[:alnum:]]+)$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 10 Orphan, Short and Incorrectly Oriented Fosmid End Pairs (fosEndPairsBad) mrnaAcc all_mrna prefix mrnaAcc 1 ^[a-z][a-z0-9][0-9]+$ 10 C. savignyi mRNAs from Genbank (all_mrna) semiShortCircuit 1\ stsMapAliasComprehensive stsMap exact bed 0 ^[^[:space:]]+$ select chrom,chromStart,chromEnd,name from %s where name like '%s' stsAlias select trueName,alias from %s where alias like '%s' 11 Alias of STS Marker padding 100000\ searchBoth on\ encodeRegionsConsensus encodeRegionsConsensus prefix bed 1 ^EN[rm][0-9]+(_[0-9]+)?$ select chrom,chromStart,chromEnd,name from %s where name like '%s%%' 11 Consensus Orthology of ENCODE Regions from LiftOver and Mercator (Freeze 3) (encodeRegionsConsensus) encodeRegions encodeRegions prefix bed 1 ^EN[rm][0-9]+(_[0-9]+)?$ select chrom,chromStart,chromEnd,name from %s where name like '%s%%' 11 encodeRegions stsMapAliasMrnaAcc stsMap exact bed 1 ^[a-z][a-z0-9][0-9]+$ select chrom,chromStart,chromEnd,name from %s where name like '%s' stsAlias select trueName,alias from %s where alias like '%s' 11 Alias of STS Marker padding 100000\ searchBoth on\ semiShortCircuit 1\ snp126Short snp126 exact bed 1 ^(rs[0-9]{3}[0-9]+)$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 12 Simple Nucleotide Polymorphisms (dbSNP build 126) (snp126) dontCheck ([0-9]+|rs[0-9][0-9]?[0-9]?)\ padding 250\ semiShortCircuit 1\ snp127Short snp127 exact bed 1 ^(rs[0-9]{3}[0-9]+)$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 12 Simple Nucleotide Polymorphisms (dbSNP build 127) (snp127) dontCheck ([0-9]+|rs[0-9][0-9]?[0-9]?)\ padding 250\ semiShortCircuit 1\ snp125Short snp125 exact bed 1 ^(rs[0-9]{3}[0-9]+)$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 12 Simple Nucleotide Polymorphisms (dbSNP build 125) (snp125) dontCheck ([0-9]+|rs[0-9][0-9]?[0-9]?)\ padding 250\ semiShortCircuit 1\ snpShort snp exact bed 1 ^(rs[0-9]{3}[0-9]+|SNP_A-[0-9]+(_[0-9]+)?)$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 12 Simple Nucleotide Polymorphisms (SNPs) (snp) dontCheck ([0-9]+|rs[0-9][0-9]?[0-9]?)\ padding 250\ semiShortCircuit 1\ snpMapShort snpMap exact bed 1 ^(rs[0-9]{3}[0-9]+|SNP_A-[0-9]+(_[0-9]+)?)$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 12 Simple Nucleotide Polymorphisms (SNPs) (snpMap) dontCheck ([0-9]+|rs[0-9][0-9]?[0-9]?)\ padding 250\ semiShortCircuit 1\ mrnaKeyword all_mrna exact mrnaKeyword 0 15 C. savignyi mRNAs from Genbank (all_mrna) grepIndex genbankGrep\ snp126Long snp126 exact bed 1 ^([0-9]+|rs[0-9][0-9]?[0-9]?)$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 16 Simple Nucleotide Polymorphisms (dbSNP build 126) (snp126) dontCheck (rs[0-9]{3}[0-9]+)\ padding 250\ semiShortCircuit 1\ snp127Long snp127 exact bed 1 ^([0-9]+|rs[0-9][0-9]?[0-9]?)$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 16 Simple Nucleotide Polymorphisms (dbSNP build 127) (snp127) dontCheck (rs[0-9]{3}[0-9]+)\ padding 250\ semiShortCircuit 1\ snp125Long snp125 exact bed 1 ^([0-9]+|rs[0-9][0-9]?[0-9]?)$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 16 Simple Nucleotide Polymorphisms (dbSNP build 125) (snp125) dontCheck (rs[0-9]{3}[0-9]+)\ padding 250\ semiShortCircuit 1\ snpLong snp exact bed 1 ^([0-9]+|rs[0-9][0-9]?[0-9]?)$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 16 Simple Nucleotide Polymorphisms (SNPs) (snp) dontCheck (rs[0-9]{3}[0-9]+|SNP_A-[0-9]+(_[0-9]+)?)\ padding 250\ semiShortCircuit 1\ snpMapLong snpMap exact bed 1 ^([0-9]+|rs[0-9][0-9]?[0-9]?)$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 16 Simple Nucleotide Polymorphisms (SNPs) (snpMap) dontCheck (rs[0-9]{3}[0-9]+|SNP_A-[0-9]+(_[0-9]+)?)\ padding 250\ semiShortCircuit 1\ blastDm1FBGene blastDm1FB prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s' dm1.blastFBRef00 select acc,geneId from %s where geneId like '%s%%' 25 D. melanogaster Proteins (dm1) Mapped by Chained tBLASTn (blastDm1FB) blastDm2FBGene blastDm2FB prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s' dm2.blastFBRef01 select acc,geneId from %s where geneId like '%s%%' 25 D. melanogaster Proteins (dm2) Mapped by Chained tBLASTn (blastDm2FB) blastHg18KGGene blastHg18KG prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s' hg18.blastKGRef04 select acc,geneId from %s where geneId like '%s%%' 25 Human Proteins Mapped by Chained tBLASTn (blastHg18KG) blastHg18KGSprot blastHg18KG prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s' hg18.blastKGRef04 select acc,extra1 from %s where extra1 like '%s%%' 25 Human Proteins Mapped by Chained tBLASTn (blastHg18KG) blastHg17KGGene blastHg17KG prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s' hg17.blastKGRef01 select acc,geneId from %s where geneId like '%s%%' 25 Hg17 Proteins Mapped by Chained tBLASTn (blastHg17KG) blastHg17KGSprot blastHg17KG prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s' hg17.blastKGRef01 select acc,extra1 from %s where extra1 like '%s%%' 25 Hg17 Proteins Mapped by Chained tBLASTn (blastHg17KG) blastHg16KGSprot blastHg16KG prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s' hg16.blastKGRef00 select acc,extra1 from %s where extra1 like '%s%%' 25 Human Proteins (hg16) Mapped by Chained tBLASTn (blastHg16KG) blastSacCer1SGSprot blastSacCer1SG prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s' sacCer1.blastSGRef00 select acc,extra1 from %s where extra1 like '%s%%' 25 Yeast Proteins from SGD Mapped by Chained tBLASTn (blastSacCer1SG) blastSacCer1SG blastSacCer1SG prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s%%' 25 Yeast Proteins from SGD Mapped by Chained tBLASTn (blastSacCer1SG) blastDm1FB blastDm1FB prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s%%' 25 D. melanogaster Proteins (dm1) Mapped by Chained tBLASTn (blastDm1FB) blastDm2FB blastDm2FB prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s%%' 25 D. melanogaster Proteins (dm2) Mapped by Chained tBLASTn (blastDm2FB) jgiGene jgiGene prefix genePred 1 ^ci[0-9]+?$ select chrom,txStart,txEnd,name from %s where name like '%s%%' 49 JGI Gene Predictions (jgiGene) eponine eponine exact bed 0 ^chr[0-9]+[.][0-9]+$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 50 Eponine Predicted Transcription Start Sites (eponine) nscanGene nscanGene exact genePred 0 ^(chr)?.*\\.[0-9]+\\.[0-9]+\\.[a-z]$ select chrom,txStart,txEnd,name from %s where name like '%s' 50 nscanGene phastConsTopPaper phastConsTopPaper exact bed 0 ^pc[a-z][a-z].[[:alnum:]]+$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 50 PhastCons Highly Conserved Elements (HCEs) (phastConsTopPaper) rnaCluster rnaCluster exact bed 0 ^chr[0-9a-z_]+[.][0-9]+$ select chrom,chromStart,chromEnd,name from %s where name like '%s' 50 Gene Boundaries as Defined by RNA and Spliced EST Clusters (rnaCluster) NIAGene NIAGene prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s%%' 50 NIAGene rgdGene rgdGene exact genePred 0 select chrom,txStart,txEnd,name from %s where name like '%s' 50 Rat Genome Database Curated Genes (rgdGene) rgdEst rgdEst exact psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s' 50 RGD EST (rgdEst) rgdSslp rgdSslp exact bed 0 select chrom,chromStart,chromEnd,name from %s where name like '%s' 50 Rat Genome Database Simple Sequence Length Polymorphisms (rgdSslp) rgdQtl rgdQtl fuzzy bed 0 select chrom,chromStart,chromEnd,name from %s where name like '%%%s%%' 50 Quantitative Trait Locus (from RGD) (rgdQtl) slamHuman slamHuman exact genePred 0 ^[[:alnum:]_]+\\.[0-9]+\\.[0-9]+$ select chrom,txStart,txEnd,name from %s where name like '%s' 50 slamHuman slamMouse slamMouse exact genePred 0 ^[[:alnum:]_]+\\.[0-9]+\\.[0-9]+$ select chrom,txStart,txEnd,name from %s where name like '%s' 50 slamMouse slamRat slamRat exact genePred 0 ^[[:alnum:]_]+\\.[0-9]+\\.[0-9]+$ select chrom,txStart,txEnd,name from %s where name like '%s' 50 slamRat vegaPseudoGene vegaPseudoGene exact genePred 0 select chrom,txStart,txEnd,name from %s where name like '%s' 50 vegaPseudoGene vegaGene vegaGene exact genePred 0 select chrom,txStart,txEnd,name from %s where name like '%s' 50 vegaGene sangerGene sangerGene exact genePred 0 select chrom,txStart,txEnd,name from %s where name like '%s' 50 sangerGene ECgene ECgene exact genePred 0 ^[[:alnum:]_]+\\.[0-9]+$ select chrom,txStart,txEnd,name from %s where name like '%s' 50 ECgene Gene Predictions with Alt-Splicing (ECgene) geneid geneid prefix genePred 0 ^chr[^_]+_(random_|h2_hap[0-9]_|cox_hap[0-9]_|qbl_hap[0-9]_|hla_hap[0-9]_)?[0-9]+(\\.[0-9]+)?$ select chrom,txStart,txEnd,name from %s where name like '%s%%' 50 Geneid Gene Predictions (geneid) sgpGene sgpGene exact genePred 0 ^chr[^_]+_(random_|h2_hap[0-9]_|cox_hap[0-9]_|qbl_hap[0-9]_|hla_hap[0-9]_)?[0-9]+(\\.[0-9]+)?$ select chrom,txStart,txEnd,name from %s where name like '%s' 50 SGP Gene Predictions Using Mouse/Human Homology (sgpGene) twinscan twinscan exact genePred 0 ^(chr)?.*\\.[0-9]+\\.[0-9]+\\.[a-z]$ select chrom,txStart,txEnd,name from %s where name like '%s' 50 Twinscan Gene Predictions Using Mouse/Human Homology (twinscan) genscan genscan exact genePred 0 ^[[:alnum:]_]+\\.[0-9]+$ select chrom,txStart,txEnd,name from %s where name like '%s' 50 Genscan Gene Predictions (genscan) acembly acembly exact genePred 0 ^[^[:space:]]+$ select chrom,txStart,txEnd,name from %s where name like '%s' 50 AceView Gene Models With Alt-Splicing (acembly) softberryGene softberryGene exact genePred 0 ^C[A-Z0-9][A-Z0-9][0-9]+$ select chrom,txStart,txEnd,name from %s where name like '%s' 50 Fgenesh++ Gene Predictions (softberryGene) genieAlt genieAlt exact genePred 0 ^A\\.chr.*-.*\\.[0-9]+$ select chrom,txStart,txEnd,name from %s where name like '%s' 50 Genie Gene Predictions from Affymetrix (genieAlt) ensEstGeneGtpProtein ensEstGene prefix genePred 1 ^ENSESTP[0-9]+(\\.[0-9]+)?$ select chrom,txStart,txEnd,name from %s where name like '%s' ensEstGtp select transcript,protein from %s where protein like '%s%%' 50 Ensembl EST Gene Predictions (ensEstGene) ensEstGeneGtpGene ensEstGene prefix genePred 1 ^ENSESTG[0-9]+(\\.[0-9]+)?$ select chrom,txStart,txEnd,name from %s where name like '%s' ensEstGtp select transcript,gene from %s where gene like '%s%%' 50 Ensembl EST Gene Predictions (ensEstGene) ensEstGene ensEstGene prefix genePred 1 ^ENSESTT[0-9]+(\\.[0-9]+)?$ select chrom,txStart,txEnd,name from %s where name like '%s%%' 50 Ensembl EST Gene Predictions (ensEstGene) ensGeneGtpGene ensGene prefix genePred 1 ^ENS([A-Z]{3})?G[0-9]+(\\.[0-9]+)?$ select chrom,txStart,txEnd,name from %s where name like '%s' ensGtp select transcript,gene from %s where gene like '%s%%' 50 Ensembl Gene Predictions (ensGene) ensDotPrefix ensGene exact 1 ^ENS([A-Z]{3})?T[0-9]+$ select chrom,txStart,txEnd,name from %s where name like '%s.%%' 50 Ensembl Gene Predictions (ensGene) dontCheck ENS([A-Z]{3})?T[0-9]+.[0-9]+\ ensGene ensGene exact genePred 1 ^ENS([A-Z]{3})?T[0-9]+(\\.[0-9]+)?$ select chrom,txStart,txEnd,name from %s where name like '%s' 50 Ensembl Gene Predictions (ensGene) snapGene snapGene exact genePred 1 select chrom,txStart,txEnd,name from %s where name like '%s' 50 SNAP Gene Predictions (snapGene) vegaPseudoGene2 vegaPseudoGene prefix 0 select chrom, txStart,txEnd, name from %s where name2 like '%s%%' 50.1 vegaPseudoGene vegaGene2 vegaGene prefix 0 select chrom, txStart,txEnd, name from %s where name2 like '%s%%' 50.1 vegaGene oreg oreganno exact 0 select chrom, chromStart, chromEnd, id from %s where id = '%s' 55 Regulatory elements from ORegAnno (oreganno) padding 500\ blatCioSav1 blatCioSav1 exact bed 1 ^paired_scaffold_[0-9]+?$ select tName,tStart,tEnd,qName from %s where qName like '%s' 60 Ciona savignyi Translated Blat Alignments (blatCioSav1) blastHg18KG blastHg18KG prefix psl 1 select tName,tStart,tEnd,qName from %s where qName like '%s%%' 1000 Human Proteins Mapped by Chained tBLASTn (blastHg18KG) semiShortCircuit 1\ blastHg17KG blastHg17KG prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s%%' 1000 Hg17 Proteins Mapped by Chained tBLASTn (blastHg17KG) blastHg16KGGene blastHg16KG prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s' hg16.blastKGRef00 select acc,geneId from %s where geneId like '%s%%' 1000 Human Proteins (hg16) Mapped by Chained tBLASTn (blastHg16KG) blastSacCer1SGGene blastSacCer1SG prefix psl 0 select tName,tStart,tEnd,qName from %s where qName like '%s' sacCer1.blastSGRef00 select acc,geneId from %s where geneId like '%s%%' 1000 Yeast Proteins from SGD Mapped by Chained tBLASTn (blastSacCer1SG) ensGeneGtpProtein ensGene prefix genePred 1 ^ENS([A-Z]{3})?P[0-9]+(\\.[0-9]+)?$ select chrom,txStart,txEnd,name from %s where name like '%s' ensGtp select transcript,protein from %s where protein like '%s%%' 1000 Ensembl Gene Predictions (ensGene)