Dear Browser friends, I have seen a problem with the display of different bases of ESTs / mRNAs from other species in the human assembly (hg18) genome browser in a few cases. To reproduce:
1) go to hg18.chr9:140,190,658-140,190,658. 2) switch off all tracks 3) switch on "other ESTs" 4) configure "other ESTs" track to show "different item bases" This should give the following error message: "baseColorDrawSetup: CT565720: mRNA size (1542) != psl qSize (1541)" I have attached a screen shot and text version saved session as well. Hope this is helpful. Best, Jakob
HInvGeneMrna hide NumtSeq hide acembly hide acescan hide affyAllExonSuper hide affyGnf1h hide affyRatio hide affyTxnPhase3Super hide affyU133 hide affyU133Plus2 hide affyU95 hide agilentCgh hide allenBrainAli hide augustus hide bacEndPairs hide bamSLDenisova hide burgeRnaSeqGemMapperAlign hide c chr9 c chr9 ccdsGene hide centerLabels 1 cgapSage hide chainNetAnoCar1 hide chainNetAplCal1 hide chainNetBosTau4 hide chainNetBraFlo1 hide chainNetCalJac1 hide chainNetCanFam2 hide chainNetCavPor3 hide chainNetDanRer5 hide chainNetEquCab1 hide chainNetFelCat3 hide chainNetFr2 hide chainNetGalGal3 hide chainNetGasAcu1 hide chainNetMm9 hide chainNetMonDom4 hide chainNetOrnAna1 hide chainNetOryLat2 hide chainNetPanTro2 hide chainNetPetMar1 hide chainNetPonAbe2 hide chainNetRheMac2 hide chainNetRn4 hide chainNetStrPur2 hide chainNetTaeGut1 hide chainNetTetNig1 hide chainNetXenTro2 hide chainSelf hide chromName chr9 clade mammal clonePos hide cnp hide command start compGenoSubmit submit cons44way hide cons44wayViewalign.align.bosTau4 0 cons44wayViewalign.align.calJac1 0 cons44wayViewalign.align.cavPor3 0 cons44wayViewalign.align.choHof1 0 cons44wayViewalign.align.danRer5 0 cons44wayViewalign.align.dasNov2 0 cons44wayViewalign.align.dipOrd1 0 cons44wayViewalign.align.echTel1 0 cons44wayViewalign.align.equCab2 0 cons44wayViewalign.align.eriEur1 0 cons44wayViewalign.align.felCat3 0 cons44wayViewalign.align.fr2 0 cons44wayViewalign.align.gorGor1 0 cons44wayViewalign.align.mafChain 1 cons44wayViewalign.align.micMur1 0 cons44wayViewalign.align.myoLuc1 0 cons44wayViewalign.align.ochPri2 0 cons44wayViewalign.align.oryCun1 0 cons44wayViewalign.align.oryLat2 0 cons44wayViewalign.align.otoGar1 0 cons44wayViewalign.align.panTro2 0 cons44wayViewalign.align.petMar1 0 cons44wayViewalign.align.ponAbe2 0 cons44wayViewalign.align.proCap1 0 cons44wayViewalign.align.pteVam1 0 cons44wayViewalign.align.rn4 0 cons44wayViewalign.align.sorAra1 0 cons44wayViewalign.align.speTri1 0 cons44wayViewalign.align.taeGut1 0 cons44wayViewalign.align.tarSyr1 0 cons44wayViewalign.align.tetNig1 0 cons44wayViewalign.align.tupBel1 0 cons44wayViewalign.align.turTru1 0 cons44wayViewalign.align.vicPac1 0 cons46way full cons46wayViewalign.align.anoCar1 0 cons46wayViewalign.align.bosTau4 0 cons46wayViewalign.align.calJac1 0 cons46wayViewalign.align.cavPor3 0 cons46wayViewalign.align.choHof1 0 cons46wayViewalign.align.dasNov2 0 cons46wayViewalign.align.dipOrd1 0 cons46wayViewalign.align.echTel1 0 cons46wayViewalign.align.equCab2 0 cons46wayViewalign.align.eriEur1 0 cons46wayViewalign.align.felCat3 0 cons46wayViewalign.align.fr2 0 cons46wayViewalign.align.gasAcu1 0 cons46wayViewalign.align.gorGor1 0 cons46wayViewalign.align.macEug1 0 cons46wayViewalign.align.mafChain 1 cons46wayViewalign.align.micMur1 0 cons46wayViewalign.align.myoLuc1 0 cons46wayViewalign.align.ochPri2 0 cons46wayViewalign.align.ornAna1 0 cons46wayViewalign.align.oryCun2 0 cons46wayViewalign.align.oryLat2 0 cons46wayViewalign.align.otoGar1 0 cons46wayViewalign.align.panTro2 0 cons46wayViewalign.align.papHam1 0 cons46wayViewalign.align.petMar1 0 cons46wayViewalign.align.ponAbe2 0 cons46wayViewalign.align.proCap1 0 cons46wayViewalign.align.pteVam1 0 cons46wayViewalign.align.rn4 0 cons46wayViewalign.align.sorAra1 0 cons46wayViewalign.align.speTri1 0 cons46wayViewalign.align.taeGut1 0 cons46wayViewalign.align.tarSyr1 0 cons46wayViewalign.align.tetNig2 0 cons46wayViewalign.align.tupBel1 0 cons46wayViewalign.align.turTru1 0 cons46wayViewalign.align.vicPac1 0 consIndelsHgMmCanFam hide contrastGene hide cpgIslandExt hide ctgPos hide ctgPos2 hide cutters hide cytoBand hide darned hide db hg18 decipher hide denisovaModernHumans hide dgv hide dinkL 2.0 dinkR 2.0 dragSelection 1 ecoresTetNig1 hide eioJcviNAS hide enableAdvancedJavascript 1 encodeAffyChipSuper hide encodeAffyEcSuper hide encodeAffyRnaSuper hide encodeBUORChID hide encodeBuFirstExon hide encodeEgaspSuper hide encodeGencodeSuper hide encodeIndels hide encodeMsaTbaDec07 hide encodeNhgriDukeDnaseHs hide encodePseudogene hide encodeRegions hide encodeRikenCage hide encodeRna hide encodeSangerChipSuper hide encodeStanfordChipSuper hide encodeStanfordPromoters hide encodeStanfordRtPcr hide encodeUViennaRnaz hide encodeUcDavisChipSuper hide encodeUcsdChipSuper hide encodeUncFaire hide encodeUppsalaChipSuper hide encodeUtexChipSuper hide encodeUvaDnaRepSuper hide encodeUwDnaseSuper hide encodeYaleChipSuper hide encodeYaleRnaSuper hide ensGene hide eponine hide est hide evofold hide exaptedRepeats hide exoniphy hide firstEF hide fishClones hide fosEndPairs hide fox2ClipSeqComp hide gad hide gap hide gc5Base hide geneid hide genomicSuperDups hide genscan hide gnfAtlas2 hide gold hide guidelines 1 gwasCatalog hide hapmapLdPh hide hapmapSnps hide hg18ContigDiff hide hg19ContigDiff hide hgFind.matches rs1130793, hgIkmc hide hgS_loadUrlName hgS_otherUserName hgS_otherUserSessionName hgS_saveLocalFileCompress none hgS_saveLocalFileName problem.v2.txt hgTracksConfigPage hgdpFst hide hgdpGeo hide hgdpHzy hide hgdpIhs hide hgdpXpehh hide hgsid 184361055 hgt.labelWidth 17 hgt.suggest hgt_configGroupTarget none hgt_doJsCommand hgta_compressType gzip hgta_group varRep hgta_outFileName ancestral.gz hgta_outputType primaryTable hgta_regionType genome hgta_table hgdpGeo hgta_track hgdpGeo hgtgroup_compGeno_close 0 hgtgroup_denisova_close 0 hgtgroup_encodeChip_close 1 hgtgroup_encodeChrom_close 1 hgtgroup_encodeCompAndVar_close 1 hgtgroup_encodeGenes_close 1 hgtgroup_encodeTxLevels_close 1 hgtgroup_expression_close 0 hgtgroup_genes_close 0 hgtgroup_map_close 0 hgtgroup_neandertal_close 0 hgtgroup_phenDis_close 1 hgtgroup_regulation_close 0 hgtgroup_rna_close 0 hgtgroup_varRep_close 0 hinv70Composite hide ideogram 1 illuminaProbes hide insideX 118 intronEst hide jaxQtlMapped hide jsh_pageVertPos 0 kiddEichlerDisc hide knownAlt hide knownGene hide knownGene.label.gene 1 knownGeneOld3 hide l 140190657 laminB1Super hide lastPosition chr9:140190658-140190658 leftLabels 1 mammalPsg hide mgcFullMrna hide microsat hide mostConserved28way hide mrna hide multiz17way hide multiz28way hide multiz44way.speciesOrder rheMac2 mm9 canFam2 loxAfr2 monDom4 ornAna1 galGal3 anoCar1 xenTro2 gasAcu1 multiz46way.speciesOrder rheMac2 mm9 canFam2 loxAfr3 monDom5 galGal3 xenTro2 danRer6 nestedRepeats hide nestedRepeatsRM327 hide newWinWidth 1 nextExonArrows 1 nextItemArrows 0 nscan hide ntHumChimpCodingDiff hide ntModernHumans hide ntOoaHaplo hide ntSeqContigs hide ntSeqReads hide ntSssSnps hide ntSssTop5p hide ntSssZScorePMVar hide o 73585648 oligoMatch hide omimGene hide oreganno hide orfeomeMrna hide org Human pgSnp hide phastConsElements17way hide phenDisSubmit submit phyloPCons28way hide pix 800 placentalChainNet hide polyA hide position chr9:140190658-140190658 primateChainNet hide r 140190658 rdmr hide recombRate hide refGene hide regPotential7X hide revCmplDisp 0 rgdQtl hide rgdRatQtl hide rmsk hide rmskRM327 hide rnaCluster hide rnaGene hide ruler dense rulerClickHeight 22 sendToGalaxy 0 sendToGreat 0 sestanBrainAtlas hide sgpGene hide sibGene hide sibTxGraph hide simpleRepeat hide snp126 hide snp128 hide snp129 hide snp130 hide snp131 pack snpArray hide stsMap hide switchDbTss hide t 73587770 tRNAs hide tajD hide tajdSnp hide targetScanS hide textSize 8 tfbsConsSites hide trackControlsOnMain 1 transMap hide transMapAlnMRna.baseColorDrawOpt diffBases transMapAlnMRna.indelDoubleInsert 1 transMapAlnMRna.indelPolyA 0 transMapAlnMRna.indelQueryInsert 1 transMapAlnMRna.label.acc 0 transMapAlnMRna.label.db 0 transMapAlnMRna.label.gene 0 transMapAlnMRna.label.orgAbbrv 0 transMapAlnMRna.label.orgCommon 0 transMapAlnRefSeq.label.acc 1 transMapAlnRefSeq.label.orgCommon 1 transMapAlnSplicedEst pack transMapAlnSplicedEst.baseColorDrawOpt diffBases transMapAlnSplicedEst.indelDoubleInsert 1 transMapAlnSplicedEst.indelPolyA 0 transMapAlnSplicedEst.indelQueryInsert 1 transMapAlnSplicedEst.label.acc 0 transMapAlnSplicedEst.label.db 0 transMapAlnSplicedEst.label.gene 0 transMapAlnSplicedEst.label.orgAbbrv 0 transMapAlnSplicedEst.label.orgCommon 1 transMapAlnUcscGenes.label.acc 1 transMapAlnUcscGenes.label.orgCommon 1 ucsfBrainMethyl hide uniGene_3 hide uppsalaChipSuper hide uwNucOcc hide vegaGeneComposite hide vertebrateChainNet hide vistaEnhancers hide wgEncodeAffyRnaChip hide wgEncodeBroadChipSeq hide wgEncodeBuOrchid hide wgEncodeCaltechRnaSeq hide wgEncodeChromatinMap hide wgEncodeCshlLongRnaSeq hide wgEncodeCshlShortRnaSeq hide wgEncodeDNAseSuper hide wgEncodeDnaMethylSuper hide wgEncodeDukeAffyExonArray hide wgEncodeGencode hide wgEncodeGisChipPetAll hide wgEncodeGisDnaPet hide wgEncodeGisPet hide wgEncodeGisRnaPet hide wgEncodeGisRnaSeq hide wgEncodeHelicosRnaSeq hide wgEncodeHudsonalphaChipSeq hide wgEncodeHudsonalphaCnv hide wgEncodeHudsonalphaMethyl27 hide wgEncodeHudsonalphaMethylSeq hide wgEncodeHudsonalphaRnaSeq hide wgEncodeMapability hide wgEncodeNhgriBip hide wgEncodeReg hide wgEncodeRikenCage hide wgEncodeRnaSeqSuper hide wgEncodeSangerGencode hide wgEncodeSunyalbanyRnaGeneChip hide wgEncodeUcsdNgTaf1Super hide wgEncodeUwAffyExonArray hide wgEncodeUwChIPSeq hide wgEncodeUwDGF hide wgEncodeUwDnaseSeq hide wgEncodeYaleChIPseq hide wgEncodeYaleRNAseq hide wgRna hide wikiTrack hide winEnd 140190658 winStart 140190657 xenoEst pack xenoEst.baseColorDrawOpt none xenoEst.indelDoubleInsert 1 xenoEst.indelPolyA 0 xenoEst.indelQueryInsert 1 xenoEstFt red xenoEstLt and xenoEst_acc xenoEst_aut xenoEst_cel xenoEst_des xenoEst_gen xenoEst_key xenoEst_lib xenoEst_org xenoEst_pro xenoEst_tis xenoMrna hide xenoRefGene hide yaleBertoneTars hide
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