hub GCF_000002765.6 genome assembly shortLabel malaria parasite P. falciparum (v6 3D7 2016) longLabel malaria parasite P. falciparum (v6 3D7 2016)/Plasmodium falciparum 3D7/GCF_000002765.6_GCA_000002765 genome assembly useOneFile on email genome-www@soe.ucsc.edu descriptionUrl html/GCF_000002765.6_GCA_000002765.description.html genome GCF_000002765.6 taxId 36329 groups groups.txt description malaria parasite P. falciparum (v6 3D7 2016) twoBitPath GCF_000002765.6.2bit twoBitBptUrl GCF_000002765.6.2bit.bpt chromSizes GCF_000002765.6.chrom.sizes.txt chromAliasBb GCF_000002765.6.chromAlias.bb organism GCA_000002765 Apr. 2016 defaultPos NC_037283.1:1097312-1107312 scientificName Plasmodium falciparum 3D7 htmlPath html/GCF_000002765.6_GCA_000002765.description.html blat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/765/GCF_000002765.6 transBlat dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/765/GCF_000002765.6 isPcr dynablat-01.soe.ucsc.edu 4040 dynamic GCF/000/002/765/GCF_000002765.6 track assembly longLabel Assembly shortLabel Assembly visibility hide colorByStrand 150,100,30 230,170,40 color 150,100,30 altColor 230,170,40 bigDataUrl bbi/GCF_000002765.6_GCA_000002765.assembly.bb type bigBed 6 html html/GCF_000002765.6_GCA_000002765.assembly searchIndex name searchTrix ixIxx/GCF_000002765.6_GCA_000002765.assembly.ix url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel NCBI Nucleotide database: group map track cytoBandIdeo shortLabel Chromosome Band (Ideogram) longLabel Ideogram for Orientation group map visibility dense type bigBed 4 + bigDataUrl bbi/GCF_000002765.6_GCA_000002765.cytoBand.bb track gc5Base shortLabel GC Percent longLabel GC Percent in 5-Base Windows group map visibility dense autoScale Off maxHeightPixels 128:36:16 graphTypeDefault Bar gridDefault OFF windowingFunction Mean color 0,0,0 altColor 128,128,128 viewLimits 30:70 type bigWig 0 100 bigDataUrl bbi/GCF_000002765.6_GCA_000002765.gc5Base.bw html html/GCF_000002765.6_GCA_000002765.gc5Base track tanDups shortLabel Tandem Dups longLabel Paired identical sequences compositeTrack on visibility hide type bigBed 12 group map html html/GCF_000002765.6_GCA_000002765.tanDups track tandemDups parent tanDups on shortLabel Tandem Dups longLabel Paired exactly identical sequence survey over entire genome assembly bigDataUrl bbi/GCF_000002765.6_GCA_000002765.tandemDups.bb type bigBed 12 track repeatMasker shortLabel RepeatMasker longLabel RepeatMasker Repetitive Elements type bigRmsk 9 + visibility pack group varRep bigDataUrl bbi/GCF_000002765.6_GCA_000002765.rmsk.bb xrefDataUrl bbi/GCF_000002765.6_GCA_000002765.rmsk.align.bb maxWindowToDraw 5000000 html html/GCF_000002765.6_GCA_000002765.repeatMasker track simpleRepeat shortLabel Simple Repeats longLabel Simple Tandem Repeats by TRF group varRep visibility dense type bigBed 4 + bigDataUrl bbi/GCF_000002765.6_GCA_000002765.simpleRepeat.bb html html/GCF_000002765.6_GCA_000002765.simpleRepeat track refSeqComposite compositeTrack on shortLabel NCBI RefSeq longLabel RefSeq gene predictions from NCBI group genes visibility pack type bigBed dragAndDrop subTracks allButtonPair on dataVersion INSDC submitter (2023-10-05) html html/GCF_000002765.6_GCA_000002765.refSeqComposite priority 2 track ncbiRefSeq parent refSeqComposite on color 12,12,120 shortLabel RefSeq All type bigGenePred urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$" labelFields name2,geneName,geneName2 defaultLabelFields name2 searchIndex name searchTrix ixIxx/GCF_000002765.6_GCA_000002765.ncbiRefSeq.ix bigDataUrl bbi/GCF_000002765.6_GCA_000002765.ncbiRefSeq.bb longLabel NCBI RefSeq genes, curated and predicted sets (NM_*, XM_*, NR_*, XR_*, NP_* or YP_*) idXref ncbiRefSeqLink mrnaAcc name baseColorUseCds given baseColorDefault genomicCodons priority 1 track ncbiRefSeqPredicted color 12,12,120 parent refSeqComposite on shortLabel RefSeq Predicted longLabel NCBI RefSeq genes, predicted subset (XM_* or XR_*) type bigGenePred urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$" labelFields name2,geneName,geneName2 defaultLabelFields name2 searchIndex name searchTrix ixIxx/GCF_000002765.6_GCA_000002765.ncbiRefSeqPredicted.ix idXref ncbiRefSeqLink mrnaAcc name bigDataUrl bbi/GCF_000002765.6_GCA_000002765.ncbiRefSeqPredicted.bb baseColorUseCds given baseColorDefault genomicCodons priority 3 track ncbiRefSeqOther color 32,32,32 parent refSeqComposite on shortLabel RefSeq Other longLabel NCBI RefSeq other annotations (not NM_*, NR_*, XM_*, XR_*, NP_* or YP_*) priority 4 searchIndex name searchTrix ixIxx/GCF_000002765.6_GCA_000002765.ncbiRefSeqOther.ix bigDataUrl bbi/GCF_000002765.6_GCA_000002765.ncbiRefSeqOther.bb type bigBed 12 + labelFields name skipEmptyFields on urls GeneID="https://www.ncbi.nlm.nih.gov/gene/$$" MIM="https://www.ncbi.nlm.nih.gov/omim/$$" HGNC="http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=$$" FlyBase="http://flybase.org/reports/$$" WormBase="http://www.wormbase.org/db/gene/gene?name=$$" RGD="https://rgd.mcw.edu/rgdweb/search/search.html?term=$$" SGD="https://www.yeastgenome.org/locus/$$" miRBase="http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=$$" ZFIN="https://zfin.org/$$" MGI="http://www.informatics.jax.org/marker/$$" track ncbiRefSeqPsl priority 5 parent refSeqComposite off shortLabel RefSeq Alignments longLabel RefSeq Alignments of RNAs type bigPsl searchIndex name bigDataUrl bbi/GCF_000002765.6_GCA_000002765.bigPsl.bb indelDoubleInsert on indelQueryInsert on showDiffBasesAllScales . showDiffBasesMaxZoom 10000.0 showCdsMaxZoom 10000.0 showCdsAllScales . baseColorDefault diffCodons pslSequence no baseColorUseSequence lfExtra baseColorUseCds table given color 0,0,0 track cpgIslands compositeTrack on shortLabel CpG Islands longLabel CpG Islands (Islands < 300 Bases are Light Green) group regulation visibility dense type bigBed 4 + html html/GCF_000002765.6_GCA_000002765.cpgIslands track cpgIslandExt parent cpgIslands off shortLabel CpG Islands longLabel CpG Islands (Islands < 300 Bases are Light Green) type bigBed 4 + priority 1 bigDataUrl bbi/GCF_000002765.6_GCA_000002765.cpgIslandExt.bb track cpgIslandExtUnmasked parent cpgIslands on shortLabel Unmasked CpG longLabel CpG Islands on All Sequence (Islands < 300 Bases are Light Green) type bigBed 4 + priority 2 bigDataUrl bbi/GCF_000002765.6_GCA_000002765.cpgIslandExtUnmasked.bb track windowMasker shortLabel WM + SDust longLabel Genomic Intervals Masked by WindowMasker + SDust group varRep visibility dense type bigBed 3 bigDataUrl bbi/GCF_000002765.6_GCA_000002765.windowMasker.bb html html/GCF_000002765.6_GCA_000002765.windowMasker track augustus shortLabel Augustus longLabel Augustus Gene Predictions group genes visibility dense color 180,0,0 type bigGenePred bigDataUrl bbi/GCF_000002765.6_GCA_000002765.augustus.bb html html/GCF_000002765.6_GCA_000002765.augustus track xenoRefGene shortLabel RefSeq mRNAs longLabel RefSeq mRNAs mapped to this assembly group rna visibility pack color 180,0,0 type bigGenePred bigDataUrl bbi/GCF_000002765.6_GCA_000002765.xenoRefGene.bb url https://www.ncbi.nlm.nih.gov/nuccore/$$ urlLabel NCBI Nucleotide database: labelFields name,geneName,geneName2 defaultLabelFields geneName searchIndex name searchTrix ixIxx/GCF_000002765.6_GCA_000002765.xenoRefGene.ix html html/GCF_000002765.6_GCA_000002765.xenoRefGene track EST_Alignments bigDataUrl contrib/VEuPathDB/bbi/EST_Alignments.bb html contrib/VEuPathDB/html/blat_ests.html longLabel Transcriptomics__BLAT_and_Blast_Alignments__EST_Alignments.gff3.bed.bb maxWindowToDraw 200000 shortLabel EST Alignments type bigBed 9 visibility dense track Long_ncRNA bigDataUrl contrib/VEuPathDB/bbi/Long_ncRNA.bb html contrib/VEuPathDB/html/noncoding_rna.html longLabel Gene_Models__Transcripts__Long_non-coding_RNA_for_P._falciparum.gff3.bed.bb shortLabel Long ncRNA type bigBed 9 visibility pack track Curated_transcript bigDataUrl contrib/VEuPathDB/bbi/Curated_transcript.bb html contrib/VEuPathDB/html/annotated_transcripts.html longLabel Gene_Models__Transcripts__Annotated_Transcripts.gff3.bed.bb shortLabel Curated transcript type bigBed 12 visibility pack track Long_Read_RNA bigDataUrl contrib/VEuPathDB/bbi/Long_Read_RNA.bb html contrib/VEuPathDB/html/Long_Read_RNA.html longLabel Gene_Models__Transcripts__Long_Read_RNA_for_P._falciparum.gff3.bed.bb shortLabel Long Read RNA type bigBed 9 visibility squish track Annotated_Introns bigDataUrl contrib/VEuPathDB/bbi/Annotated_Introns.bb html contrib/VEuPathDB/html/annotated_introns.html labelFields none longLabel Annotated introns that are confirmed by RNASeq reads mouseOverField readCount shortLabel Annotated Introns type bigBed 9+1 visibility pack track Unannotated_Introns bigDataUrl contrib/VEuPathDB/bbi/Unannotated_Introns.bb html contrib/VEuPathDB/html/unannotated_introns.html labelFields none longLabel Unannotated introns that are suggested by RNASeq reads mouseOverField readCount shortLabel Unannotated Introns type bigBed 9+1 visibility pack track Combined_RNA-Seq aggregate transparentOverlay container multiWig html contrib/VEuPathDB/html/Combined_RNA-Seq.html longLabel Combined RNA-Seq data mirrored from plasmodb.org shortLabel Combined RNA-Seq showSubtrackColorOnUi on type bigWig 0 756 track Bartfai_IDC_2018_plus bigDataUrl contrib/VEuPathDB/bbi/Bartfai_IDC_2018_plus.bw color 130,100,130 longLabel Bartfai_IDC_2018_firststrand_merged parent Combined_RNA-Seq shortLabel Bartfai_IDC_2018_plus type bigWig 0 121 track Bartfai_IDC_2018_minus bigDataUrl contrib/VEuPathDB/bbi/Bartfai_IDC_2018_minus.bw color 120,100,120 longLabel Bartfai_IDC_2018_secondstrand_merged parent Combined_RNA-Seq shortLabel Bartfai_IDC_2018_minus type bigWig 0 116 track 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parent Combined_RNA-Seq shortLabel Duffy_Ring-Schiz-Tropho_minus type bigWig 0 38 track Gomez-Diaz_asexual_stages_plus bigDataUrl contrib/VEuPathDB/bbi/Gomez-Diaz_asexual_stages_plus.bw color 110,110,150 longLabel Gomez-Diaz_asexual_stages_firststrand_merged parent Combined_RNA-Seq shortLabel Gomez-Diaz_asexual_stages_plus type bigWig 0 55 track Gomez-Diaz_asexual_stages_minus bigDataUrl contrib/VEuPathDB/bbi/Gomez-Diaz_asexual_stages_minus.bw color 110,110,140 longLabel Gomez-Diaz_asexual_stages_secondstrand_merged parent Combined_RNA-Seq shortLabel Gomez-Diaz_asexual_stages_minus type bigWig 3 60 track Josling_Schizont_Transcriptomes_plus bigDataUrl contrib/VEuPathDB/bbi/Josling_Schizont_Transcriptomes_plus.bw color 110,110,130 longLabel Josling_Schizont_Transcriptomes_firststrand_merged parent Combined_RNA-Seq shortLabel Josling_Schizont_Transcriptomes_plus type bigWig 0 29 track Josling_Schizont_Transcriptomes_minus bigDataUrl contrib/VEuPathDB/bbi/Josling_Schizont_Transcriptomes_minus.bw color 110,110,120 longLabel Josling_Schizont_Transcriptomes_secondstrand_merged parent Combined_RNA-Seq shortLabel Josling_Schizont_Transcriptomes_minus type bigWig 0 26 track Kamaliddin_Sequestration_plus bigDataUrl contrib/VEuPathDB/bbi/Kamaliddin_Sequestration_plus.bw color 110,150,110 longLabel Kamaliddin_Sequestration_firststrand_merged parent Combined_RNA-Seq shortLabel Kamaliddin_Sequestration_plus type bigWig 0 80 track Kamaliddin_Sequestration_minus bigDataUrl contrib/VEuPathDB/bbi/Kamaliddin_Sequestration_minus.bw color 110,140,110 longLabel Kamaliddin_Sequestration_secondstrand_merged parent Combined_RNA-Seq shortLabel Kamaliddin_Sequestration_minus type bigWig 0 77 track Lasonder_Bartfai_Gametocytes_plus bigDataUrl contrib/VEuPathDB/bbi/Lasonder_Bartfai_Gametocytes_plus.bw color 110,130,110 longLabel Lasonder_Bartfai_Gametocytes_firststrand_merged parent Combined_RNA-Seq shortLabel Lasonder_Bartfai_Gametocytes_plus type bigWig 0 34 track Lasonder_Bartfai_Gametocytes_minus bigDataUrl contrib/VEuPathDB/bbi/Lasonder_Bartfai_Gametocytes_minus.bw color 110,120,110 longLabel Lasonder_Bartfai_Gametocytes_secondstrand_merged parent Combined_RNA-Seq shortLabel Lasonder_Bartfai_Gametocytes_minus type bigWig 0 38 track Lee_Gambian_plus bigDataUrl contrib/VEuPathDB/bbi/Lee_Gambian_plus.bw color 150,110,110 longLabel Lee_Gambian_firststrand_merged parent Combined_RNA-Seq shortLabel Lee_Gambian_plus type bigWig 0 762 track Lee_Gambian_minus bigDataUrl contrib/VEuPathDB/bbi/Lee_Gambian_minus.bw color 140,110,110 longLabel Lee_Gambian_secondstrand_merged parent Combined_RNA-Seq shortLabel Lee_Gambian_minus type bigWig 0 756 track Lindner_Oocyst_Salivary_plus bigDataUrl contrib/VEuPathDB/bbi/Lindner_Oocyst_Salivary_plus.bw color 130,110,110 longLabel Lindner_Oocyst_Salivary_Sporo_firststrand_merged parent Combined_RNA-Seq shortLabel Lindner_Oocyst_Salivary_plus type bigWig 0 34 track Lindner_Oocyst_Salivary_minus bigDataUrl contrib/VEuPathDB/bbi/Lindner_Oocyst_Salivary_minus.bw color 120,110,110 longLabel Lindner_Oocyst_Salivary_Sporo_secondstrand_merged parent Combined_RNA-Seq shortLabel Lindner_Oocyst_Salivary_minus type bigWig 0 40 track Newbold_nostrand bigDataUrl contrib/VEuPathDB/bbi/Newbold_nostrand.bw color 110,150,150 longLabel Newbold_unstranded_merged parent Combined_RNA-Seq shortLabel Newbold_nostrand type bigWig 1 105 track DC_UTR_2020_nostrand bigDataUrl contrib/VEuPathDB/bbi/DC_UTR_2020_nostrand.bw color 110,140,140 longLabel DC_UTR_RNASeq_2020_unstranded_merged parent Combined_RNA-Seq shortLabel DC_UTR_2020_nostrand type bigWig 0 95 track Febrile_temps_plus bigDataUrl contrib/VEuPathDB/bbi/Febrile_temps_plus.bw color 110,130,130 longLabel Febrile_temps_RNASeq_firststrand_merged parent Combined_RNA-Seq shortLabel Febrile_temps_plus type bigWig 0 86 track Febrile_temps_minus bigDataUrl contrib/VEuPathDB/bbi/Febrile_temps_minus.bw color 110,120,120 longLabel Febrile_temps_RNASeq_secondstrand_merged parent Combined_RNA-Seq shortLabel Febrile_temps_minus type bigWig 0 81 track Scherf_Intraerythrocytic_cycle_plus bigDataUrl contrib/VEuPathDB/bbi/Scherf_Intraerythrocytic_cycle_plus.bw color 150,110,150 longLabel Scherf_Intraerythrocytic_cycle_firststrand_merged parent Combined_RNA-Seq shortLabel Scherf_Intraerythrocytic_cycle_plus type bigWig 0 68 track Scherf_Intraerythrocytic_cycle_minus bigDataUrl contrib/VEuPathDB/bbi/Scherf_Intraerythrocytic_cycle_minus.bw color 140,110,140 longLabel Scherf_Intraerythrocytic_cycle_secondstrand_merged parent Combined_RNA-Seq shortLabel Scherf_Intraerythrocytic_cycle_minus type bigWig 0 67 track Scherf_Ring_Oocyst_Sporozoite_plus bigDataUrl contrib/VEuPathDB/bbi/Scherf_Ring_Oocyst_Sporozoite_plus.bw color 130,110,130 longLabel Scherf_Ring_Oocyst_Sporozoite_firststrand_merged parent Combined_RNA-Seq shortLabel Scherf_Ring_Oocyst_Sporozoite_plus type bigWig 0 47 track 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type bigWig 0 25 track invitro_versus_mosquito_minus bigDataUrl contrib/VEuPathDB/bbi/invitro_versus_mosquito_minus.bw color 120,120,120 longLabel invitro_versus_mosquito_produced_sporozoite_RNASeq_secondstrand_merged parent Combined_RNA-Seq shortLabel invitro_versus_mosquito_minus type bigWig 0 31