FlyBase:JBrowse Tracks
Reference Genome
Nucleotide view When zoomed in, the DNA sequence of the Release 6 (R6) (Hoskins et al, 2015) genome is shown as color-coded blocks, G-orange, A-green, T-red, C-blue. When zoomed in further, the bases are also labeled (GATC). Above and below the base representation, the three-frame translation for the plus and minus strands is shown using the single-letter amino acid code. Start codons (M and L) are indicated in green and stop codons are marked in red.
Gene: gene span view Shows the extent of all annotated gene models with direction of transcription indicated by a small arrow at the downstream edge. Protein-coding genes are shown in blue with the different shades further indicating direction of transcription. Non-protein-coding genes are shown in red, tRNA genes in purple and pseudogenes in pink. Each gene glyph is hyperlinked to a pop-up window containing an automated gene summary and links to the FlyBase Gene Report and NCBI gene report.
Gene: transcript view Shows a condensed transcript summary of all annotated gene models with direction of transcription indicated by a small arrow at the downstream edge. For each annotated gene, all transcripts are shown with the complete intron/exon structure (exons indicated by wider bars, introns by black lines). For protein-coding genes, coding regions are shown in orange and untranslated regions in gray. Non-protein-coding genes are shown in red, tRNA genes in purple and pseudogenes in pink. Like in the gene span view track, each transcript summary glyph is hyperlinked to a pop-up window containing an automated gene summary and links to the FlyBase Gene Report and NCBI gene report; labels show FlyBase transcript symbols. For links to individual FlyBase transcript reports, please see the RNA track.
RNA Like the Gene:transcript view track, this track shows the complete intron/exon structure (exons indicated by wider bars, introns by black lines) of each annotated transcript with direction of transcription indicated by a small arrow at the downstream edge. For protein-coding genes, coding regions are shown in orange and untranslated regions in gray. Non-protein-coding genes are shown in red, tRNA genes in purple and pseudogenes in pink. Each transcript glyph is hyperlinked to its individual FlyBase Transcript Report; labels show FlyBase transcript symbols.
CDS Shows extent of sequence encoding each specific polypeptide, with direction of transcription indicated by a small arrow; introns indicated as narrow lines. Each CDS glyph is hyperlinked to a FlyBase Polypeptide Report; labels show FlyBase polypeptide symbols.
Orthologs Pale yellow bar indicates the extent of the orthologous region. Each glyph is hyperlinked to a pop-up window containing links for orthologs of the gene. The ortholog box will contain the drosophilid orthologs on the left (which link to a FlyBase Gene Report) and other orthologs on the right (which link to a GenBank report).
Natural TE Shows the extent of a natural transposable element in the sequenced strain (at the time it was sequenced). Directionality is indicated by a small arrow at the downstream edge. Each TE glyph is hyperlinked to a FlyBase Natural Transposon Report; labels show FlyBase natural transposon symbols.
Repeat region Regions of genomic repeats and low complexity DNA sequences, as computed using RepeatMasker and RepeatRunner (Smith, et al., 2007)
Estimated Cytological band Approximate extent of the classical cytological chromosome bands described by Bridges. See Computed cytological data in FlyBase for a detailed description of how this computed cytological location is calculated. See FlyBase Maps for a collection of polytene chromosome images.
Genome Level Features
Chromatin Features
- Chromatin Domains (5-state model, Kc cells) Whole-genome DamID binding profiles of 53 chromatin proteins in Drosophila Kc167 cells were generated and/or analyzed. In the same array platform, ChIP-chip profiles of histone H3, H1, H3K9me2, H3K27me3, H3K4me2, and H3K79me3 were obtained. These were correlated with gene expression, which was measured by RNA-tag profiling. See the Chromatin_types_NKI.Kc167 FlyBase Dataset Report and references therein for more information.
- Chromatin Domains (9-state model, S2 cells) Demarcation of chromatin domains of nine major types based on analysis of 18 histone modification profiles. See the Chromatin_types_mE1.S2 FlyBase Dataset Report and references therein for more information.
- Chromatin Domains (9-state model, BG3 cells) Demarcation of chromatin domains of nine major types based on analysis of 18 histone modification profiles. See the Chromatin_types_mE2.BG3 FlyBase Dataset Report and references therein for more information.
- His3 modifications (ChIP-seq, embryonic mesoderm) Peak calls for ChIP-seq of histone modifications obtained from purified embryonic mesodermal nuclei. Data are available for H3K4me1, H3K4me3, H3K27Ac, H3K27me3, H3K36me3, H3K79me3 and RNA Pol II and are displayed as one compiled track. Data were kindly provided by Eileen Furlong's lab (EMBL), as published in Bonn et al., 2012. Data analysis methods by Matthias Monfort (of the Furlong group) are described here. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data. See the below FlyBase Dataset Reports and references therein for more information.
Transcriptional Regulatory Elements
- Insulators (modENCODE, class I) Insulators identified by ChIP-chip of Cp190, BEAF-32 and CTCF in embryos. Class I insulators are defined as having at least two binding sites among Cp190, BEAF-32 and CTCF with peak overlap of less than 250bp. See the Insulator_Class_I.mE01 FlyBase Dataset Report and references therein for more information. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data.
- Insulators (modENCODE, class II) Insulators identified by ChIP-chip of su(Hw) in embryos. Class I insulators are defined as having only su(Hw) binding sites. See the Insulator_Class_II.mE01 FlyBase Dataset Report and references therein for more information. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data.
- Putative PREs (modENCODE) Genomic sequences identified by ChIP-chip of HDAC and histone modifications as putative polycomb response elements (silencers) in embryos. See the mE1_HDAC_PRE FlyBase Dataset Report and references therein for more information. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data.
- Transcriptional Regulatory Regions (REDfly) Locations of regulatory regions reported in the literature, as compiled by FlyBase and/or REDfly). See the REDfly CRMs FlyBase Dataset Report and references therein for more information. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data.
Transcription Factor Binding Sites
- Transcription Factor Binding Sites (REDfly) Locations of protein binding sites reported in the literature, as compiled by FlyBase and/or RedFly). See the REDfly TFBSs FlyBase Dataset Report and references therein for more information. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data.
- Transcription Factor Binding Sites (Furlong lab compiled, ChIP-chip, mesodermal TFs) ChIP-chip binding peak calls for 13 TFs that control mesodermal development at various points of embryogenesis. There are 28 samples in all, compiled into five tracks by stage of embryogenesis. These data were kindly provided by Eileen Furlong's lab (EMBL), comprising several studies: Zinzen et al., 2009, Bonn et al., 2012, Junion et al., 2012, Rembold et al., 2014 and Ciglar et al., 2014. These 28 ChIP-chip datasets were processed in parallel by Matthias Monfort of the Furlong group, as described here. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data. See the below FlyBase Dataset Reports and references therein for more information.
- ChIP (embryo, 2-4h) - Mef2 sna tin twi
- ChIP (embryo, 4-6h) - Doc2 pMad Mef2 pan pnr slp1 tin twi
- ChIP (embryo, 6-8h) - bap bin Doc2 lmd pMad Mef2 pan pnr slp1 tin ttk twi
- ChIP-chip_bap_E6-8h_organism
- ChIP-chip_bin_E6-8h_organism
- ChIP-chip_Doc2_E6-8h_organism
- ChIP-chip_lmd_E6-8h_organism
- ChIP-chip_pMad_E6-8h_organism
- ChIP-chip_Mef2_E6-8h_organism
- ChIP-chip_pan_E6-8h_organism
- ChIP-chip_pnr_E6-8h_organism
- ChIP-chip_slp1_E6-8h_organism
- ChIP-chip_tin_E6-8h_organism
- ChIP-chip_ttk_E6-8h_organism
- ChIP-chip_twi_E6-8h_organism
- ChIP-chip_bap_E6-8h_organism
- ChIP (embryo, 8-10h) - bin Mef2
- ChIP (embryo, 10-12h) - bin Mef2
- Transcription Factor HOT spot analysis (modENCODE compiled, ChIP-chip, whole embryo) Genomic sequences identified as unique regions of transcription factor (TF) binding using HOT spot analysis (HSA); one or many TFs may bind in a given region. A synthesis of ChIP-chip data sets for 41 different transcription factors. TF binding profiles used in this analysis were assayed at early embryo stages. Each glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data. See the mE1_TFBS_HSA FlyBase Dataset Report and references therein for more information.
- Zinc Finger TF Binding Sites (modENCODE compiled, ChIP-chip, whole embryo) Binding sites for transcriptions factors that contain one or more zinc finger domains. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data. See the below FlyBase Dataset Reports and references therein for more information.
- Homeodomain TF Binding Sites (modENCODE compiled, ChIP-chip, whole embryo) Binding sites for transcriptions factors that contain one or more homeodomains. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data. See the below FlyBase Dataset Reports and references therein for more information.
- Helix-loop-helix TF Binding Sites (modENCODE compiled, ChIP-chip, whole embryo) Binding sites for transcription factors that contain one or more helix-loop-helix domains. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data. See the below FlyBase Dataset Reports and references therein for more information.
- BTB/POZ ChIP TF Binding Sites (modENCODE compiled, ChIP-chip, whole embryo) Binding sites for transcriptions factors that contain one or more BTB/POZ domains. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data. See the below FlyBase Dataset Reports and references therein for more information.
- Other classes TF Binding Sites (modENCODE compiled, ChIP-chip, whole embryo) Binding sites for transcriptions factors that do not fall into one of the other categories. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data. See the below FlyBase Dataset Reports and references therein for more information.
Other Sequence Elements
- Origins of replication Genome profile of early activating origins of replication in Kc, BG3 and S2 cell lines identified by BrdU label/RepliSeq. See the mE_Early_Replication_Origins_cells FlyBase Dataset Report and references therein for more information. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data.
Transcript Level Features
cDNA
- Sequenced cDNAs D. melanogaster cDNA sequences from large-scale submissions to sequence databases. Shows the exon (wider bars) and intron (black lines) structure, and direction of transcription. Each cDNA glyph is hyperlinked to its GenBank nucleotide entry. cDNA sequences are aligned to release 6 by NCBI and submitted to FlyBase. Some genomic DNA submissions, including third party submissions, are included in this tier.
- Inferred transcript sequences D. melanogaster aligned nucleotides submitted to sequence databases. Each glyph is hyperlinked to a pop-up window containing the ID, position, length, DNA sequence, and more. Sequences are aligned to release 6 by NCBI and submitted to FlyBase. Some genomic DNA submissions, including third party submissions, are included in this tier.
EST (Expressed Sequence Tag)
Partial sequence of a cDNA. Shows the exon (wider bars) and intron (black lines) structure, and direction of transcription. When zoomed out to greater than 100kb, a density plot is shown. Each cDNA glyph is hyperlinked to its GenBank nucleotide entry. Sequences are aligned to release 6 by NCBI and submitted to FlyBase.
Transcription Start Sites
- Transcription start sites (modENCODE), embryo Transcription start site (TSS) regions identified by integrative analysis of ESTs, CAGE or RLM-RACE; glyphs indicate the range over which 90 percent of the TSS signal is located. The arrow points in the direction of transcription. Hyperlinked to the relevant Sequence Feature Report. Note: data for embryonic stages only. See the mE_Transcription_Start_Sites FlyBase Dataset Report and references therein for more information.
- Transcription start sites (RAMPAGE), peak calls Transcription start site regions (peak calls) identified by RAMPAGE-Seq across 36 stages of development. The arrow points in the direction of transcription. Hyperlinked to the relevant FlyBase Sequence Feature Report. See the TSS_RAMPAGE FlyBase Dataset Report and references therein for more information.
- Transcription start sites (RAMPAGE), early embryo 0-12hr, stranded RNA-Seq Profile of capped transcript 5' ends observed by RAMPAGE-Seq for 12 stages of early embryogenesis. See the TSS_RAMPAGE FlyBase Dataset Report and references therein for more information.
- Transcription start sites (RAMPAGE), late embryo 13-24hr, stranded RNA-Seq Profile of capped transcript 5' ends observed by RAMPAGE-Seq for 12 stages of late embryogenesis. See the TSS_RAMPAGE FlyBase Dataset Report and references therein for more information.
- Transcription start sites (RAMPAGE), larva/pupa/adult, stranded RNA-Seq Profile of capped transcript 5' ends observed by RAMPAGE-Seq for 12 larval, pupal or adult stages. See the TSS_RAMPAGE FlyBase Dataset Report and references therein for more information.
- Transcription start sites (MachiBase), stranded RNA-Seq Profile of capped transcript 5' ends observed by MachiBase CAGE-Seq for embryonic, larval, adult male and female (young or old) and S2 cell line samples. See the TSS_MachiBase FlyBase Dataset Report and references therein for more information.
Please note that the signal shown for the Transcription Start Site data (RAMPAGE and MachiBase) is one base off: i.e., the signal is shown one base to the left of where it should be. In the example to the right, the signal should map to the first base (3R:6864324, A) of the ftz transcript, but is instead shown one base to the left (3R:6864323, C). This is a known bug and we're working to fix this.
RNA-seq Exon Junctions
Orientation of the junction is indicated with an arrow. Each exon junction glyph is hyperlinked to a FlyBase exon junction Sequence Feature Report containing read counts from a modENCODE or Baylor dataset. See the BCM_1_RNAseq_junctions and modENCODE_mRNA-Seq_U_junctions FlyBase Dataset Reports and references therein for more information.
Polyadenylation Sites
D. melanogaster polyadenylation sites identified in various tissues. Arrows indicate orientation (i.e., pointing toward the side to which the polyA extension is added). Each glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data. See pA_sites_Lai and pA_sites_Moreira FlyBase Dataset Reports and references therein for more information.
RNA Editing Sites
A-to-I RNA editing sites. Each glyph is hyperlinked to a FlyBase Sequence Feature Report containing read counts by developmental stage. See mE_A-to-I_RNA_Editing_Sites and Rosbash_Adult_Head_A-to-I_Editing_Sites FlyBase Dataset Reports and references therein for more information.
Protein Level Features
Protein Domains
- Protein domains (Pfam) Pfam protein domains identified in annotated proteins, as obtained from InterPro, are mapped to the genome. Hyperlinked to a Pfam report for the domain.
- Protein domains (SMART) SMART protein domains identified in annotated proteins are mapped to the genome. Hyperlinked to an InterPro report for the domain.
Peptide Sequences
- Developmental Proteome (Casas-Vila et al.) Alignment of peptide sequences identified in the developmental proteome of Casas-Vila et al., 2017 to the reference genome. Each peptide glyph is hyperlinked to a FlyBase Sequence Feature Report with the peptide sequence. See the Casas-Vila_proteome_development FlyBase Dataset Report and references therein for more information.
- Peptide Atlas Alignment of peptide sequences determined by mass spectroscopy, derived from polypeptides isolated from the sequenced strain at various developmental stages. Contributed by the Center for Model Organism Proteomes, SystemsX and Research Priority Project of the University of Zurich, Switzerland. For more information, see Peptide Atlas
Reagents
Deficiencies
- Deficiencies with stocks in Bloomington, Kyoto (formerly Stock Center Aberrations: deleted segment under Stocks) This track contains only deficiencies with stocks available from the Bloomington and Kyoto Stock Centers. Links to the relevant Stock Report can be found at the bottom of the Aberration Report, which is linked from the feature glyph.
- The Bloomington Deficiency Kit
- The Bloomington Deficiency Kit is a set of stocks defined by the Bloomington Drosophila Stock Center (BDSC) to provide maximal coverage of the genome with the minimal number of deficiencies having molecularly mapped breakpoints. The BDSC Deficiency Kit also includes deficiencies with breakpoints that have not been mapped molecularly, primarily to provide coverage of gaps between the molecularly defined deficiencies. Since the ends of cytologically characterized deficiencies cannot be placed on the genome map with certainty, the BDSC has defined segments of these deficiencies that fill gaps in molecularly defined coverage for GBrowse display. The endpoints of gap filling segments are derived primarily from overlapping deficiency endpoints and complementation with annotated genes.
- BDSC Deficiency Kit: deleted segment Molecularly defined deficiencies are indicated in red. Click the deficiency to go to the Aberration Report. Links to the relevant Stock Report can be found at the bottom of the Aberration Report.
- Dfs_BSC_set2 Dataset report.
- Dfs_BSC_set1 Dataset report.
- Dfs_BSC_set2 Dataset report.
- BDSC Deficiency Kit: gap filling or haploinsufficiency flanking segment. Segments of cytologically defined deficiencies that fill gaps between molecularly defined deficiencies or flank haploinsufficient loci are indicated in yellow. Click the segment icon to go to the Aberration Report for the full deficiency. Links to the relevant Stock Report can be found at the bottom of the Aberration Report.
Duplications
- Duplicated segment Aberrations representing duplicated segments are split out into various tracks. The duplicated region is indicated in blue. When one or more aberrations cover the region being viewed, a darker blue bar labeled "Spanning aberration(s)" will be seen. When moused-over, a pop-up box containing all the aberrations that cover the region being viewed will appear. Click one of the aberration symbols to go to the Aberration Report. When mousing over a lighter blue bar labeled with a duplication symbol, a list of genes within the aberration extent pops up. Clicking on one of the gene symbols within the pop up will link to the Gene Report. Clicking on the bar itself links to the Aberration Report.
- Y linked duplication Interchromosomal duplications inserted onto the Y chromosome.
- Transgenic duplication Interchromosomal duplications generated by transgenic methods, excluding those carried on the Y chromosome. Duplicated region is indicated in blue.
- Stock Center Aberration: duplicated segment This track functions just as the "Duplicated Segment" track described above. This track contains only duplications available from the Bloomington Stock Center. Links to the relevant Stock Report can be found at the bottom of the Aberration Report, which is linked from the feature glyph.
Transgenic Insertions
- Transgenic insertions in stocks, Bloomington SO:0000368 This track functions just as the "Transgenic Insertion Site" track described above. This track contains only insertions available from the Bloomington Stock Center. Links to the relevant Stock Report can be found at the bottom of the Insertion Report, which is linked from the feature glyph.
- Transgenic insertions in stocks, Kyoto SO:0000368 This track functions just as the "Transgenic Insertion Site" track described above. This track contains only insertions available from the Kyoto Stock Center. Links to the relevant Stock Report can be found at the bottom of the Insertion Report, which is linked from the feature glyph.
Putative Enhancer Lines
- Putative Brain Enhancers (Janelia GAL4 lines) Putative enhancers used to generate fly stocks carrying GAL4 transgenic constructs designed to be expressed in the adult brain. See the GMR_Brain_exp_1 FlyBase Dataset Report and references therein for more information. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data. Stocks are available from the Bloomington Stock Center. See the "Stocks" section for associated fly stocks at Bloomington.
- Putative Enhancers (Vienna Tile GAL4 lines) Putative enhancers used to generate fly stocks carrying GAL4 transgenic constructs. Stocks are available from the Vienna Drosophila Resource Center. Each feature glyph is hyperlinked to a FlyBase Sequence Feature report with supporting data and links to the related FlyBase Stock Report. See the VDRC-VT
sgRNA Reagents
- TRiP-OE sgRNAs (overexpression) Genomic sequences used as short guide RNAs in constructs designed to target genes for CRISPR/Cas9-VPR-based overexpression. Two nearby sgRNAs are used in a single construct to target the upstream region of a given gene. Each glyph indicating the extent of sgRNAs (arrows indicate orientation) is hyperlinked to a FlyBase Sequence Feature Report containing associated data. See the TRiP-OE-VPR FlyBase Dataset Report and references therein for more information.
- TRiP-OE-flySAM.dCas9 sgRNAs (overexpression) Genomic sequences used as short guide RNAs in constructs designed to target genes for overexpression by a "synergistic activation mediator" (flySAM). These sgRNAs have been fused to MS2 loops for recruitment of MCP-tagged transcriptional activator, in addition to the sgRNA-recruited nuclease-dead Cas9 fused to a transcriptional activator. Two nearby sgRNAs are used in a single construct to target the upstream region of a given gene. Each glyph indicating the extent of sgRNAs (arrows indicate orientation) is hyperlinked to a FlyBase Sequence Feature Report containing associated data. See the TRiP-OE-flySAM FlyBase Dataset Report and references therein for more information.
- TRiP-KO sgRNAs (knockout) Genomic sequences used as short guide RNAs in constructs designed to target genes for CRISPR/Cas9-based mutation. Each glyph indicating the extent of sgRNAs (arrows indicate orientation) is hyperlinked to a FlyBase Sequence Feature Report containing associated data. See the TRiP-KO FlyBase Dataset Report and references therein for more information.
- Weizmann KO sgRNAs (knockout) Genomic sequences used as short guide RNAs in constructs designed to target genes for CRISPR/Cas9-based mutation. Only some of these sgRNAs have been incorporated into flies, while the rest are available as plasmid stocks. Each glyph indicating the extent of sgRNAs (arrows indicate orientation) is hyperlinked to a FlyBase Sequence Feature Report containing associated data. See the Weizmann_CRISPR_reagents FlyBase Dataset Report and references therein for more information.
- Heidelberg CFD KO sgRNAs (conditional knockout) Genomic sequences used as short guide RNAs in UAS constructs designed to target genes for CRISPR/Cas9-based mutation. Each glyph indicating the extent of sgRNAs (arrows indicate orientation) is hyperlinked to a FlyBase Sequence Feature Report containing associated data. See the HD_CFD FlyBase Dataset Report and references therein for more information.
- Predicted sgRNAs Sequences predicted to be suitable as sgRNAs for genome engineering. These comprise all possible 23-mers in the D. melanogaster Release6 genome assembly that have 1) a 3-prime PAM sequence (NGG) and 2) a 15 bp sequence that is unique to the genome (including the PAM sequence). The seed score for each sgRNA, which ranges from 12 to 15 bases, indicates the uniqueness of the base pairing end of the sgRNA (excluding the PAM sequence). The frameshift score is the percent of frameshift changes predicted by micro-homology around the target site; the higher the score, the better suited the sgRNA for knockout. Because base pair mismatches can be tolerated outside the seed region, predicted sgRNAs were evaluated for potential off-target sites allowing for 3, 4 or 5 mismatches; potential sgRNA sequences are sorted into five browser tracks based on their predicted specificity at different stringencies. Each glyph indicating the extent of sgRNAs (arrows indicate orientation) is hyperlinked to a pop-up window containing associated data. See the DRSC_sgRNA_designs FlyBase Dataset Report and references therein for more information.
RNAi Reagents
- DRSC RNAi amplicons DNA fragments amplified from D. melanogaster genomic DNA (OregonR) by the Drosophila Genomics Resource Center (DGRC), using gene-specific primers made by Incyte and designed to target transcribed regions with minimal sequence similarity to other genes. Used for the DGRC genome-wide RNAi library. Each glyph indicating the extent of the amplicon (arrows indicate orientation) is hyperlinked to a pop-up window containing associated data. See the DRSC_dsRNA FlyBase Dataset Report and references therein for more information.
- VDRC RNAi amplicons DNA segments used to create RNAi libraries from the Vienna Drosophila RNAi Center. This track is a composite of three VDRC RNAi library collections- GD, KK and shRNA. Each glyph indicating the extent of the amplicon (arrows indicate orientation) is hyperlinked to a pop-up window containing associated data. See the VDRC-GD,
VDRC-KK and VDRC-SH FlyBase Dataset Reports and references therein for more information.
- TRiP RNAi amplicons Extents of the amplicons are indicated with an orange bar. See the TRiP-1, TRiP-2, TRiP-3, TRiP-4 and TRiP-5 FlyBase Dataset Reports and references therein for more information.
- BKNA RNAi amplicons RNAi amplicons from the GenomeRNAi database. Extents of the amplicons are indicated with an orange bar. See the
HD2 FlyBase Dataset Report and references therein for more information.
- HFA RNAi amplicons Extents of the amplicons are indicated with an orange bar. See the
HFA FlyBase Dataset Report and references therein for more information.
- NIG-Fly RNAi amplicons Extents of the amplicons are indicated with an orange bar. See the
NIG_RNAi_Fly-1 FlyBase Dataset Report and references therein for more information.
Rescue fragments
Locations of transgenic rescue fragment reported in the literature. Labeled with FlyBase allele symbol designation. Features are linked to the related Allele Reports which contain genetic data.
Genomic Libraries
- Pacman Chori-321_BAC A BAC library containing genomic DNA fragments (average size of 83 kb) in the attB-P[acman]-CmR-BW vector. The glyphs indicate the extent of the BAC, inferred from the mapping of the sequenced BAC insert ends. Each feature glyph is hyperlinked to a FlyBase Clone Report with supporting data. See the CHORI-321_BAC FlyBase Dataset Report and references therein for more information.
- Pacman Chori-322_BAC A BAC library containing genomic DNA fragments (average size of 21 kb) in the attB-P[acman]-CmR-BW vector. The glyphs indicate the extent of the BAC, inferred from the mapping of the sequenced BAC insert ends. Each feature glyph is hyperlinked to a FlyBase Clone Report with supporting data. See the CHORI-322_BAC FlyBase Dataset Report and references therein for more information.
Microarrays
- Affymetric v1 Oligonucleotides (25-mers) designed by Affymetrix to correspond to annotated transcripts in D. melanogaster. Used for the Affymetrix GeneChip Drosophila Genome Array DrosGenome1 microarray, release date February 19, 2002. Each glyph is hyperlinked to a pop-up window containing sequence data. See the Affymetrix_GeneChip_v1 FlyBase Dataset Report for more information.
- Affymetric v2 Oligonucleotides (25-mers) designed by Affymetrix to correspond to annotated transcripts in D. melanogaster. Used for the Affymetrix GeneChip Drosophila Genome 2.0 Array, release date July 1, 2004. Each glyph is hyperlinked to a pop-up window containing sequence data. See the Affymetrix_GeneChip_v2 FlyBase Dataset Report for more information.
- DGRC-1 amplicons DNA fragments amplified from D. melanogaster genomic DNA (OregonR) by the Drosophila Genomics Resource Center (DGRC), using gene-specific primers made by Incyte and designed to target transcribed regions with minimal sequence similarity to other genes. Used for the DGRC-D.melanogaster-DGRC1-15552-v5 amplicon microarray, release date June 2, 2006 (original release of v1, May 2004) . Each glyph is hyperlinked to a pop-up window containing sequence data. See the DGRC-1 FlyBase Dataset Report for more information.
- DGRC-2 oligos "Long oligos" (65-69mers) designed to correspond to annotated transcripts in D. melanogaster (r4.3); synthesized by FlyChip in collaboration with the International Drosophila Array Consortium INDAC and the Drosophila Genomics Resource Center (DGRC). Used for the DGRC-D.melanogaster-DGRC2-17328-v1 oligonucleotide microarray, release date June 20,2006. Each glyph is hyperlinked to a pop-up window containing sequence data. See the DGRC-2 FlyBase Dataset Report for more information.
Chromosomal and Sequence Variation
Aberrations
All annotated aberration junctions Location of aberration breakpoint reported in the literature. Labeled with FlyBase aberration symbol designation and the numerical designation of the breakpoint mapped (where known). Often the exact breakpoint location is unknown and the feature indicates a range within which the breakpoint has been mapped. Genetic data is available in the Aberration Report which can be accessed directly by clicking on the feature.
Deficiencies
- All annotated deficiencies Indicated in red. Dashed lines indicate uncertainty in breakpoint location, and demarcate the region to which the breakpoint has been mapped. When one or more aberrations overlap the region being viewed, a darker red bar labeled "Spanning aberration(s)" will be seen. When moused-over, a pop-up box containing all the aberrations that span the region being viewed will appear. Click one of the aberration symbols to go to the Aberration Report. When mousing over a lighter red bar labeled with a deficiency symbol, a list of genes within the aberration extents pops up. Clicking on one of the gene symbols within the pop up will link to the Gene Report. Clicking on the bar itself links to the Aberration Report.
- Deficiencies with stocks in Bloomington, Kyoto (formerly Stock Center Aberrations: deleted segment under Stocks) This track contains only deficiencies with stocks available from the Bloomington and Kyoto Stock Centers. Links to the relevant Stock Report can be found at the bottom of the Aberration Report, which is linked from the feature glyph.
- The Bloomington Deficiency Kit:
The Bloomington Deficiency Kit is a set of stocks defined by the Bloomington Drosophila Stock Center (BDSC) to provide maximal coverage of the genome with the minimal number of deficiencies having molecularly mapped breakpoints. The BDSC Deficiency Kit also includes deficiencies with breakpoints that have not been mapped molecularly, primarily to provide coverage of gaps between the molecularly defined deficiencies. Since the ends of cytologically characterized deficiencies cannot be placed on the genome map with certainty, the BDSC has defined segments of these deficiencies that fill gaps in molecularly defined coverage for GBrowse display. The endpoints of gap filling segments are derived primarily from overlapping deficiency endpoints and complementation with annotated genes.
- BDSC Deficiency Kit: deleted segment Molecularly defined deficiencies are indicated in red. Click the deficiency to go to the Aberration Report. Links to the relevant Stock Report can be found at the bottom of the Aberration Report.
Dfs_BSC_set2 Dataset report.
Dfs_BSC_set1 Dataset report.
- BDSC Deficiency Kit: gap filling or haploinsufficiency flanking segment. Segments of cytologically defined deficiencies that fill gaps between molecularly defined deficiencies or flank haploinsufficient loci are indicated in yellow. Click the segment icon to go to the Aberration Report for the full deficiency. Links to the relevant Stock Report can be found at the bottom of the Aberration Report.
Duplications Aberrations representing duplicated segments are split out into various tracks. The duplicated region is indicated in blue. When one or more aberrations cover the region being viewed, a darker blue bar labeled "Spanning aberration(s)" will be seen. When moused-over, a pop-up box containing all the aberrations that cover the region being viewed will appear. Click one of the aberration symbols to go to the Aberration Report. When mousing over a lighter blue bar labeled with a duplication symbol, a list of genes within the aberration extent pops up. Clicking on one of the gene symbols within the pop up will link to the Gene Report. Clicking on the bar itself links to the Aberration Report.
- Y linked duplication Interchromosomal duplications inserted onto the Y chromosome.
- Transgenic duplication Interchromosomal duplications generated by transgenic methods, excluding those carried on the Y chromosome. Duplicated region is indicated in blue.
- Other duplicated segment Duplicated segments not part of the Y-linked or transgenic duplication series. Duplicated region is indicated in blue.
- Stock Center Aberration: duplicated segment This track functions just as the "Duplicated Segment" track described above. This track contains only duplications available from the Bloomington Stock Center. Links to the relevant Stock Report can be found at the bottom of the Aberration Report, which is linked from the feature glyph.
Transgenic Insertions
Transgenic insertion site SO:0000368 Indicated by vertical bars with an arrow indicating orientation if known. An insertion indicated with an arrow pointing to the right is oriented with its conventional 5' terminus to the left (assuming view is in conventional orientation of the Drosophila chromosome); this is described as being in the "plus" orientation. An insertion indicated with an arrow pointing to the left is oriented with its conventional 5' terminus to the right (assuming view is in conventional orientation of the Drosophila chromosome); this is described as being in the "minus" orientation. An insertion with no arrow has an unknown orientation. For all insertions, if the estimated insertion site is larger than 10 nucleotides, the insertion is shown as a blue box rather than a vertical line. In those cases, see the Insertion Report for more information about localization. Insertions are linked to their respective Insertion Report.
Transgenic insertions in stocks, Bloomington SO:0000368 This track functions just as the "Transgenic Insertion Site" track described above. This track contains only insertions available from the Bloomington Stock Center. Links to the relevant Stock Report can be found at the bottom of the Insertion Report, which is linked from the feature glyph.
Transgenic insertions in stocks, Kyoto SO:0000368 This track functions just as the "Transgenic Insertion Site" track described above. This track contains only insertions available from the Kyoto Stock Center. Links to the relevant Stock Report can be found at the bottom of the Insertion Report, which is linked from the feature glyph.
Mutations
Point mutation A single nucleotide has been changed into another nucleotide. Location of mutation is indicated with a vertical bar and labeled with the FlyBase allele symbol. The feature glyph is linked to the related Allele Report.
Insertions, Deletions The junction where an insertion or deletion of one or more nucleotides occurred. Location of mutation is indicated and labeled with the FlyBase allele symbol. In the case of deletions, the extent of the deletion is indicated by a red bar. In the case of nucleotide insertions, the location of the nucleotide(s) insertion is indicated by a vertical line. Features are linked to the related Allele Report.
Complex substitution The mutation does not fall simply into any of the other categories and is often a combination of events, e.g. deletion of 20 bases and insertion of 11 unrelated bases. Location of mutation is indicated with a red bar and labeled with the FlyBase allele symbol. Feature is linked to the related Allele Report.
Roughly mapped mutations (formerly Uncharacterized change in nucleotide sequence) The nature of the nucleotide substitution is either uncharacterized or only partially characterized. The location of the mutation is indicated with a red box and labeled with the FlyBase allele symbol. The feature glyph is linked to the related Allele Report.
Sequence variants
These tracks report single nucleotide polymorphisms (SNPs) and indels observed in various strains of Drosophila melanogaster, relative to the "Release 6" reference genome assembly derived from the iso-1 sequenced strain.
DGRP variants These are SNPs and indels observed in the set of DGRP_wild_type_strains. SNPs are shown in blue, deletions in red and insertions in green. Click on a variant's glyph to obtain additional information on the sequence change, the variant's frequency across the DGRP strains, and a list of the specific strains carrying the variant. Data were mapped to the "Release 6" coordinates and provided in VCF file format by Wen Huang (Michigan State University) and Trudy MacKay (Clemson University). Note that variant data are reported only on the major chromosome arms (X, 2L, 2R, 3L, 3R and 4); note that no variant data are reported in the large 3-4 Mbp regions near the centromeres of chromosome arms X, 2L, 2R, 3L and 3R.
FlyBase annotated variants (formerly Sequence variant) A region of sequence where variation has been observed. Often these refer to natural variants of a protein that lead to two different functions. The location of the mutation is indicated with a red box and labeled with the FlyBase Allele symbol. The feature glyph is linked to the related Allele Report.
Expression Levels: RNA-Seq
These tracks contain RNA-Seq expression data for several different stages of development, specific tissues, types of tissue culture cells, or treatment conditions. Different samples are presented in different colors. The tracks are labeled with the sample identity. Some labels are obscured by the RNA-Seq signal. Moving laterally along the chromosome should take you to a visible label.
Developmental stage subsets, unique reads (modENCODE)modENCODE_mRNA-Seq_U Dataset report. These tracks contain RNA-Seq expression data for several different stages of development.
Digestive system
mE_mRNA_L3_Wand_dig_sys
mE_mRNA_A_1d_dig_sys
mE_mRNA_A_4d_dig_sys
mE_mRNA_A_20d_dig_sys
Fat body and salivary glands
mE_mRNA_L3_Wand_fat
mE_mRNA_WPP_fat
mE_mRNA_P8_fat
mE_mRNA_L3_Wand_saliv
mE_mRNA_WPP_saliv
Imaginal disc and other carcass
mE_mRNA_L3_Wand_imag_disc
mE_mRNA_L3_Wand_carcass
mE_mRNA_A_1d_carcass
mE_mRNA_A_4d_carcass
mE_mRNA_A_20d_carcass
CNS and adult head
mE_mRNA_L3_CNS
mE_mRNA_P8_CNS
mE_mRNA_A_MateM_1d_head
mE_mRNA_A_MateM_4d_head
mE_mRNA_A_MateM_20d_head
mE_mRNA_A_VirF_1d_head
mE_mRNA_A_VirF_4d_head
mE_mRNA_A_VirF_20d_head
mE_mRNA_A_MateF_1d_head
mE_mRNA_A_MateF_4d_head
mE_mRNA_A_MateF_20d_head
Gonads and male accessory glands
mE_mRNA_A_MateM_4d_testis
mE_mRNA_A_MateM_4d_acc_gland
mE_mRNA_A_VirF_4d_ovary
mE_mRNA_A_MateF_4d_ovary
Tissue culture cells, by strand (modENCODE Transcription Group) modENCODE_mRNA-Seq_cell.B Dataset report.
Treatments/Conditions modENCODE_mRNA-Seq_treatments Dataset report.
L3 CNS neuron
Knoblich_mRNA_L3_CNS_neuron
L3 CNS neuroblast
Knoblich_mRNA_L3_CNS_neuroblast
SRA Aggregated RNA-Seq tracks Stranded RNA-Seq coverage data from Justin Fear and Brian Oliver that combines data from thousands of high quality SRA RNA-Seq accessions. These data provide an "average" view of the transcriptome. The exceptional read depth provides insight into regions of low transcription. Tracks are offered with signal cut-off set to 100 (high sensitivity), 1,000 (medium sensitivity) or 10,000 (low sensitivity) for viewing regions of low, medium or high signal, respectively. Signal mapping to the genomic plus strand are shown on top, with signal mapping to the genomic minus strand shown below. See the Oliver_aggregated_RNA-Seq_profile Dataset report for more details.
FlyAtlas2 RNA-seq from larval and adult male or female tissues grouped into the four subsets below. See the FlyAtlas2 FlyBase Dataset report and references therein for further information.
Nervous system
RNA-Seq_Profile_FlyAtlas2_L3_CNS
RNA-Seq_Profile_FlyAtlas2_Adult_Female_Brain
RNA-Seq_Profile_FlyAtlas2_Adult_Male_Brain
RNA-Seq_Profile_FlyAtlas2_Adult_Female_Head
RNA-Seq_Profile_FlyAtlas2_Adult_Male_Head
RNA-Seq_Profile_FlyAtlas2_Adult_Female_Eye
RNA-Seq_Profile_FlyAtlas2_Adult_Male_Eye
RNA-Seq_Profile_FlyAtlas2_Adult_Female_ThoracicoAbdominalGanglion
RNA-Seq_Profile_FlyAtlas2_Adult_Male_ThoracicoAbdominalGanglion
Digestive system
RNA-Seq_Profile_FlyAtlas2_Adult_Female_Crop
RNA-Seq_Profile_FlyAtlas2_Adult_Male_Crop
RNA-Seq_Profile_FlyAtlas2_L3_Midgut
RNA-Seq_Profile_FlyAtlas2_Adult_Female_Midgut
RNA-Seq_Profile_FlyAtlas2_Adult_Male_Midgut
RNA-Seq_Profile_FlyAtlas2_L3_Hindgut
RNA-Seq_Profile_FlyAtlas2_Adult_Female_Hindgut
RNA-Seq_Profile_FlyAtlas2_Adult_Male_Hindgut
RNA-Seq_Profile_FlyAtlas2_Adult_Female_RectalPad
RNA-Seq_Profile_FlyAtlas2_Adult_Male_RectalPad
RNA-Seq_Profile_FlyAtlas2_L3_SalivaryGland
RNA-Seq_Profile_FlyAtlas2_Adult_Female_SalivaryGland
RNA-Seq_Profile_FlyAtlas2_Adult_Male_SalivaryGland
Reproductive system
RNA-Seq_Profile_FlyAtlas2_Adult_Female_Ovary
RNA-Seq_Profile_FlyAtlas2_Adult_Female_Virgin_Spermathecum
RNA-Seq_Profile_FlyAtlas2_Adult_Female_Mated_Spermathecum
RNA-Seq_Profile_FlyAtlas2_Adult_Male_Testis
RNA-Seq_Profile_FlyAtlas2_Adult_Male_AccessoryGland
Other systems and whole organism
RNA-Seq_Profile_FlyAtlas2_L3_Trachea
RNA-Seq_Profile_FlyAtlas2_L3_FatBody
RNA-Seq_Profile_FlyAtlas2_Adult_Female_FatBody
RNA-Seq_Profile_FlyAtlas2_Adult_Male_FatBody
RNA-Seq_Profile_FlyAtlas2_L3_MalpighianTubule
RNA-Seq_Profile_FlyAtlas2_Adult_Female_MalpighianTubule
RNA-Seq_Profile_FlyAtlas2_Adult_Male_MalpighianTubule
RNA-Seq_Profile_FlyAtlas2_L3_Carcass
RNA-Seq_Profile_FlyAtlas2_Adult_Female_Carcass
RNA-Seq_Profile_FlyAtlas2_Adult_Male_Carcass
RNA-Seq_Profile_FlyAtlas2_L3_Whole
RNA-Seq_Profile_FlyAtlas2_Adult_Female_Whole
RNA-Seq_Profile_FlyAtlas2_Adult_Male_Whole
Expression Levels: Small RNA-Seq
These tracks contain RNA-Seq expression data for small RNA species (<30nt) that have been consolidated from various independent studies by sample type (developmental stage, tissue or cell line). Different samples are presented in different colors. The tracks are labeled with the sample identity. Some labels are obscured by the RNA-Seq signal. Moving laterally along the chromosome should take you to a visible label.
Tissues, stranded small RNA-Seq (Lai lab) See Lai_shortRNA-Seq_profiles_tissues Dataset Report.
Developmental stages, stranded small RNA-Seq (Lai lab) See Lai_shortRNA-Seq_profiles_development Dataset Report.
Tissue culture cells (Schneider + embryonic), stranded small RNA-Seq (Lai lab) See Lai_shortRNA-Seq_profiles_cells Dataset Report.
Tissue culture cells (imaginal disc), stranded small RNA-Seq (Lai lab) See Lai_shortRNA-Seq_profiles_cells Dataset Report.
Tissue culture cells (CNS, ovary, blood), stranded small RNA-Seq (Lai lab) See Lai_shortRNA-Seq_profiles_cells Dataset Report.
FlyAtlas2 Small RNA-seq from larval and adult male or female tissues grouped into the four subsets below. See the FlyAtlas2 FlyBase Dataset report and references therein for further information.
Nervous system
microRNA-Seq_Profile_FlyAtlas2_L3_CNS
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Brain
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Brain
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Head
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Head
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Eye
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Eye
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_ThoracicoAbdominalGanglion
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_ThoracicoAbdominalGanglion
Digestive system
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Crop
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Crop
microRNA-Seq_Profile_FlyAtlas2_L3_Midgut
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Midgut
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Midgut
microRNA-Seq_Profile_FlyAtlas2_L3_Hindgut
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Hindgut
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Hindgut
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_RectalPad
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_RectalPad
microRNA-Seq_Profile_FlyAtlas2_L3_SalivaryGland
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_SalivaryGland
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_SalivaryGland
Reproductive system
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Ovary
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Virgin_Spermathecum
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Mated_Spermathecum
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Testis
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_AccessoryGland
Other systems and whole organism
microRNA-Seq_Profile_FlyAtlas2_L3_Trachea
microRNA-Seq_Profile_FlyAtlas2_L3_FatBody
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_FatBody
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_FatBody
microRNA-Seq_Profile_FlyAtlas2_L3_MalpighianTubule
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_MalpighianTubule
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_MalpighianTubule
microRNA-Seq_Profile_FlyAtlas2_L3_Carcass
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Carcass
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Carcass
microRNA-Seq_Profile_FlyAtlas2_L3_Whole
microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Whole
microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Whole
Gene Predictions
NCBI Gnomon, 2006 Predicted coding regions generated via a hidden Markov model using transcript alignment constraints and protein hit information, if available; allows prediction of alternatively spliced isoforms; submitted by J. Ostell. Each glyph is hyperlinked to a pop-up window containing supporting data. See the NCBI Gnomon Description Page for more information.
PhyloCSF (CONGO) Exon prediction; region of sequence conservation across multiple Drosophila species, with a pattern of conservation indicative of protein-coding and termini consistent with exon structure (start, splice or stop); submitted by M. Lin and M. Kellis. Each glyph is hyperlinked to a pop-up window containing sequence data. See related publications: Lin MF, Carlson, JW et al. (2007), Lin MF, Jungreis I, and Kellis M. (2011) for more information.