Difference between revisions of "FlyBase:JBrowse Tracks"

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== Reference Sequence ==
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== Reference Genome ==
  
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'''Estimated Cytological band''' Approximate extent of the classical cytological chromosome bands described by Bridges. See [http://{{SERVERNAME}}/wiki/FlyBase:Computed_cytological_data Computed cytological data] in FlyBase for a detailed description of how this computed cytological location is calculated. See [http://{{SERVERNAME}}/wiki/FlyBase:Maps FlyBase Maps] for a collection of polytene chromosome images.
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'''Nucleotide View''' When zoomed in, the DNA sequence of the Release 6 (R6) [http://flybase.org/reports/FBrf0227719.html (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.
  
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'''Reference Sequence''' When zoomed in, the DNA sequence of the Release 6 (R6) [http://flybase.org/reports/FBrf0227719.html (Hoskins et al, 2015)] genome is shown. The bases are color-coded, G-yellow, A-green, T-red, C-blue. When zoomed in (150 bp or less) the bases are colored and labeled (GATC). Between 150 and 750 bp, the bases are colored but not labeled. 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.
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'''Gene span''' 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 displays a pop-up window containing an automated gene summary when moused over and links to the FlyBase Gene Report when clicked.
  
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== Reference Genome Annotations [http://flybase.org/reports/FBsn0000272.html (iso-1)] ==
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'''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. Each transcript summary glyph is hyperlinked to a pop-up window containing an automated gene summary; labels show FlyBase transcript symbols. For links to individual FlyBase transcript reports, please see the RNA track.
  
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'''Gene''' Shows all annotated genes (including non-coding genes), with direction of transcription indicated by small arrow at downstream edge. For each annotated gene, all transcripts are shown with the complete intron/exon structure (exon (wider bars) and intron (black line)). Coding regions are shown in blue and untranslated regions are uncolored. The gene region is hyperlinked to a pop-up window containing an automated gene summary and links to the FlyBase Gene Report and NCBI gene report; labels shows FlyBase transcript symbols.  
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'''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.
  
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'''RNA''' {{flybaseorg|cgi-bin/cvreport.html?rel=is_a&id=SO:0000673|SO:0000673}}  Shows the exon (wider bars) and intron (black line) structure of each annotated coding transcript, with direction of transcription indicated with a small arrow at the downstream edge. Coding regions are shown in tan and untranslated regions are uncolored. Each transcript is hyperlinked to a FlyBase Transcript Report; label shows FlyBase transcript symbol.
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'''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.
  
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'''Natural TE''' [http://{{SERVERNAME}}/cgi-bin/cvreport.html?id=SO:0000101 SO:0000101] Shows the extent of a natural transposable element in the sequenced strain (at the time it was sequenced). Hyperlinked to Natural Transposon report; label shows FlyBase Natural transposon symbol.
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'''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).
  
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'''Repeat region''' Regions of genomic repeats and low complexity DNA sequences (in pink), as computed using RepeatMasker and RepeatRunner [http://{{SERVERNAME}}/reports/FBrf0194515.html (Smith, et al., 2007)]. {{flybaseorg|/blast/|BLAST}}
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'''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.
  
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== Aligned Evidence ==
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'''Repeat region''' Regions of genomic repeats and low complexity DNA sequences, as computed using RepeatMasker and RepeatRunner [http://{{flybaseorg}}/reports/FBrf0194515.html (Smith, et al., 2007)]
  
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'''EST''' ("expressed sequence tag") Partial sequence of a cDNA; Indicated in medium green (darker than cDNAs). Partial sequence of a cDNA; shows the exon (wider bars) and intron (narrow bars) structure, and direction of transcription. When zoomed out to greater than 100kb, a density plot is shown. Link to GenBank entry. Sequences are aligned to release 6 by NCBI and submitted to FlyBase.
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'''Estimated Cytological band''' Approximate extent of the classical cytological chromosome bands described by Bridges. See [http://{{flybaseorg}}/wiki/FlyBase:Computed_cytological_data Computed cytological data] in FlyBase for a detailed description of how this computed cytological location is calculated. See [http://{{flybaseorg}}/wiki/FlyBase:Maps FlyBase Maps] for a collection of polytene chromosome images.
  
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'''cDNA''' D. melanogaster cDNA sequences from large-scale submissions submitted to the sequence databases; Indicated in light green. Shows the exon (wider bars) and intron (black line) structure, and direction of transcription. Link to GenBank 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.
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== Aberrations ==
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'''Aberration junctions''' Location of aberration breakpoint reported in the literature. Often the exact breakpoint location is unknown and the feature indicates a range within which the breakpoint has been mapped.
  
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'''RNA-Seq based exon junctions''' Indicated in blue. Orientation of the junction is indicated with an arrow. Links go to FlyBase exon junction reports containing read counts from modENCODE or Baylor. See the [http://{{SERVERNAME}}/reports/FBlc0000204.html BCM_1_RNAseq_junctions] and [http://{{SERVERNAME}}/reports/FBlc0000203.html modENCODE_mRNA-Seq_U_junctions] Dataset Reports.
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'''Deficiencies''' (formerly Deleted segment) Glyphs correspond to the extent of deleted sequences. For convenience, labels for deficiencies without stocks available at Drosophila stock centers are red. Hover over each glyph to view a pop-up window with stock center availability. Click on each glyph to expand the pop-up window with a list of affected genes and a link to the relevant FlyBase Aberration Report with further information including links to the relevant Stock Report with stock ordering information. For tracks displaying only deficiencies with stocks available, please see the 'Deficiency Stocks' and 'Deficiency Kit' tracks in this section.
  
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'''other aligned sequences''' D. melanogaster aligned nucleotides submitted to the sequence databases. Link to a report which includes 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.
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'''Duplications''' Glyphs correspond to the extent of duplicated sequences. For convenience, labels for duplications without stocks available at Drosophila stock centers are red. Hover over each glyph to view a pop-up window with stock center availability. Click on each glyph to expand the pop-up window with a list of affected genes and a link to the relevant FlyBase Aberration Report with further information including links to the relevant Stock Report with stock ordering information. Many of these duplications were generated by transgenic methods and belong to several curated collections. See the [http://{{flybaseorg}}/reports/FBlc0000500.html Dps(X)DC_set1], [http://{{flybaseorg}}/reports/FBlc0003379.html Dps_BAC_Retrofit], [http://{{flybaseorg}}/reports/FBlc0003380.html Dps_GenetiVision], and [http://{{flybaseorg}}/reports/FBlc0000499.html Dps(X)BSC_set1] FlyBase Dataset Reports for more details on these collections.  For tracks displaying only duplications with stocks available, please see the 'Duplication Stocks' track in this section.
  
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'''PeptideAtlas peptides''' Indicated in red. 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 [https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=352 Peptide Atlas]
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'''Deficiency 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. Click on each glyph to view a pop-up window with a list of affected genes and a link to the relevant FlyBase Aberration Report with further information including links to the relevant Stock Report with stock ordering information.
  
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'''Protein domains (PFAM)''' [http://pfam.xfam.org/ Pfam] protein domains identified in annotated proteins, as obtained from [https://www.ebi.ac.uk/interpro/download.html InterPro], are mapped to the genome. The feature glyph links to a Pfam report for the domain.
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'''The Bloomington Deficiency Kit'''  
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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. The BDSC Deficiency Kit includes deficiencies with molecularly mapped breakpoints as well as deficiencies with breakpoints that have not been mapped molecularly, primarily to provide coverage of gaps between the molecularly defined deficiencies. These two classes of deficiencies are separated into the following two tracks.  
  
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'''Protein domains (SMART)''' [http://smart.embl-heidelberg.de/ SMART] protein domains identified in annotated proteins are mapped to the genome. The feature glyph links to an InterPro report for the domain.
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:'''BDSC Deficiency Kit: deleted segment''' Molecularly defined deficiencies. Click on each glyph to view a pop-up window with a list of affected genes and a link to the relevant FlyBase Aberration Report with further information including links to the relevant Stock Report with stock ordering information.
  
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'''Transcription Start Sites (modENCODE), embryo''' Transcription start site (TSS) regions identified by integrative analysis of ESTs, CAGE or RLM-RACE are depicted as green glyphs indicating the range over which 90 percent of the TSS signal is located. The arrow points in the direction of transcription. Clicking on the TSS feature links to the relevant Sequence Feature report. Note: data for embryonic stages only. See the [http://{{SERVERNAME}}/reports/FBlc0000202.html mE_Transcription_Start_Sites] Dataset Report.  
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:'''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. 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 JBrowse display. The endpoints of gap filling segments are derived primarily from overlapping deficiency endpoints and complementation with annotated genes. Each glyph is hyperlinked to a FlyBase Aberration Report with further information including links to the relevant Stock Report with stock ordering information.
  
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'''Transcription Start Sites (RAMPAGE), peak calls''' Transcription start site regions (peak calls) identified by RAMPAGE-Seq across 36 stages of development, depicted as green glyphs. The arrow points in the direction of transcription. The feature glyph links to the relevant Sequence Feature report.
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'''Duplication Stocks in Bloomington, Kyoto''' (formerly Stock Center Aberrations: duplicated segment) This track contains only duplications available from the Bloomington or Kyoto Stock Centers. Click on each glyph to view a pop-up window with a list of affected genes and a link to the relevant FlyBase Aberration Report with further information including links to the relevant Stock Report with stock ordering information.
  
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== Mapped Mutations ==
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== Transgenic Insertions ==
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'''Transgenic Insertions'''(formerly Transgenic insertion site) Insertions are indicated by blue diamonds with an arrow indicating orientation if known. An arrow pointing to the right indicates a transposable element 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 arrow pointing to the left indicates a transposable element 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, a dotted line represents the region of uncertainty. Hover over each insertion glyph to view a pop-up window with basic information and click to go to its FlyBase Insertion Report with further information including links to the relevant Stock Report with stock ordering information.
  
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'''Transgenic insertion site''' [http://{{SERVERNAME}}/cgi-bin/cvreport.html?rel=is_a&id=SO:0000368 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.
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'''Transgenic Insertion Stocks in Bloomington, Kyoto''' This track contains only insertions available from the Bloomington and Kyoto Stock Centers. Insertions are indicated by blue diamonds with an arrow indicating orientation if known. An arrow pointing to the right indicates a transposable element 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 arrow pointing to the left indicates a transposable element 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, a dotted line represents the region of uncertainty. Hover over each insertion glyph to view a pop-up window with basic information and click to go to its FlyBase Insertion Report with further information including links to the relevant Stock Report with stock ordering information.
  
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'''Point mutation''' [http://{{SERVERNAME}}/cgi-bin/cvreport.html?rel=is_a&id=SO:1000008 SO:1000008] 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.
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== Mutations & Sequence Variants ==
  
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'''Sequence variant''' [http://{{SERVERNAME}}/cgi-bin/cvreport.html?rel=is_a&id=SO:0000109 SO:0000109] 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 vertical bar and labeled with the FlyBase allele symbol. The feature glyph is linked to the related Allele Report.
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=== Mutations & Experimentally Induced Variants ===
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:'''Substitutions''' Substitutions include point mutations in which a single nucleotide has been changed into another nucleotide as well as multiple nucleotide variants (MNV) in which the inserted sequence is the same length as the replaced sequence. The location of the mutation is indicated with a vertical bar and labeled with the FlyBase allele symbol. Point mutations are labeled in blue while MNVs are labeled in red to allow the user to easily distinguish substitution types. Each feature glyph is hyperlinked to the related FlyBase Allele Report.
  
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'''Uncharacterized change in nucleotide sequence''' [http://{{SERVERNAME}}/cgi-bin/cvreport.html?rel=is_a&id=SO:1000007 SO:1000007] The nature of the nucleotide substitution is either uncharacterized or only partially characterized. The location of the mutation is indicated with a bar and labeled with the FlyBase allele symbol. The feature glyph is linked to the related Allele Report.
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:'''Insertions, Deletions''' This track shows insertions or deletions of one or more nucleotides as well as delins, alterations which include both an insertion and a deletion of 2 or more nucleotides. In the case of deletions and delins, the extent of the lesion is indicated by a yellow bar. In the case of nucleotide insertions, the location of the insertion is indicated by a vertical line. Mutations are labeled with the FlyBase allele symbol, insertions in green, deletions in red and delins in black. Each feature glyph is hyperlinked to the related FlyBase Allele Report.
  
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'''Aberration junction''' [http://{{SERVERNAME}}/cgi-bin/cvreport.html?rel=is_a&id=SO:0000687 SO:0000687] 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 available in the Aberration Report which can be accessed directly by clicking on the feature.
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:'''Complex Substitutions''' 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. Each feature glyph is hyperlinked to the related FlyBase Allele Report.
  
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'''Complex substitution''' [http://{{SERVERNAME}}/cgi-bin/cvreport.html?rel=is_a&id=SO:1000005 SO:1000005] 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 grey bar and labeled with the FlyBase allele symbol. Feature is linked to the related Allele Report.
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:'''Roughly Mapped Mutations''' (formerly Uncharacterized change in nucleotide sequence) The mutation has only been roughly mapped molecularly, e.g. to a restriction fragment. The location of the mutation is indicated with a red bar and labeled with the FlyBase allele symbol. Each feature glyph is hyperlinked to the related FlyBase Allele Report.
  
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'''Indels''' [http://{{SERVERNAME}}/cgi-bin/cvreport.html?rel=is_a&id=SO:1000032 SO:1000032] 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.
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:'''FlyBase Mutations/Variants on Alliance''' These represent the portion of FlyBase curated mutation data shared with the [https://www.alliancegenome.org/ Alliance of Genome Resources]. The same data is contained in the other tracks in this section, as well as in the Transgenic Insertions track, and can be viewed separately by mutation type therein. Here, the differently-shaped glyphs represent mutation type- deletions are rectangles, insertions are inverted triangles and point mutations are diamonds. Hovering over each glyph brings up a window with further information.
  
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'''Rescue fragment''' [http://{{SERVERNAME}}/cgi-bin/cvreport.html?rel=is_a&id=SO:0000411 SO:0000411] Locations of transgenic rescue fragment reported in the literature. Labeled with FlyBase allele symbol designation. Features are linked to the related Allel Reports which contain genetic data.
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=== Polymorphisms & Natural Population Variants ===
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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.
  
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== Noncoding Features ==
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:'''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.
  
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'''Insulators class I''' [http://{{SERVERNAME}}/reports/FBlc0000058.html Insulator_Class_I.mE01] Dataset Report
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:'''DGRP Variants''' These are SNPs and indels observed in the set of [http://flybase.org/reports/FBlc0000504 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.
  
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'''Insulators class II''' [http://{{SERVERNAME}}/reports/FBlc0000059.html Insulator_Class_II.mE01 ] Dataset Report
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== Misc. Reagents ==
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=== Putative Enhancer Lines ===
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:'''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. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data and links to the relevant Stock Report with stock ordering information. See the [http://{{flybaseorg}}/reports/FBlc0000201.html GMR_Brain_exp_1] FlyBase Dataset Report and references therein for more information on this collection.
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:'''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 [http://{{flybaseorg}}/reports/FBlc0000718.html VDRC-VT] FlyBase Dataset Report and references therein for more information on this collection.
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=== sgRNA Reagents ===
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:'''TRiP-OE-VPR 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 [http://{{flybaseorg}}/reports/FBlc0003381.html TRiP-OE-VPR] FlyBase Dataset Report and references therein for more information.
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:'''TRiP-OE-flySAM 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 [http://{{flybaseorg}}/reports/FBlc0003482.html TRiP-OE-flySAM] and [http://{{flybaseorg}}/reports/FBlc0003483.html TRiP-OE-flySAM.dCas9] FlyBase Dataset Reports and references therein for more information.
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:'''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 [http://{{flybaseorg}}/reports/FBlc0003382.html TRiP-KO] FlyBase Dataset Report and references therein for more information.
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:'''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  [http://{{flybaseorg}}/reports/FBlc0003496.html Weizmann_CRISPR_reagents] FlyBase Dataset Report and references therein for more information.
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:'''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 [http://{{flybaseorg}}/reports/FBlc0003497.html HD_CFD] FlyBase Dataset Report and references therein for more information.
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:'''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 [http://{{flybaseorg}}/reports/FBlc0003481.html DRSC_sgRNA_designs] FlyBase Dataset Report and references therein for more information.
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=== RNAi Reagents ===
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:'''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 [http://{{flybaseorg}}/reports/FBlc0000026.html DRSC_dsRNA] FlyBase Dataset Report and references therein for more information.
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:'''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 [http://{{flybaseorg}}/reports/FBlc0000041.html VDRC-GD], [http://{{flybaseorg}}/reports/FBlc0000055.html VDRC-KK] and [http://{{flybaseorg}}/reports/FBlc0003376.html VDRC-SH] FlyBase Dataset Reports and references therein for more information.
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:'''TRiP RNAi amplicons''' Extents of the amplicons are indicated with an orange bar. See the [http://{{flybaseorg}}/reports/FBlc0000048.html TRiP-1],  [http://{{flybaseorg}}/reports/FBlc0000153.html TRiP-2], [http://{{flybaseorg}}/reports/FBlc0000185.html TRiP-3],  [http://{{flybaseorg}}/reports/FBlc0000186.html TRiP-4] and  [http://{{flybaseorg}}/reports/FBlc0000416.html TRiP-5] FlyBase Dataset Reports and references therein for more information.
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:'''BKNA RNAi amplicons''' RNAi amplicons from the GenomeRNAi database. Extents of the amplicons are indicated with an orange bar. See the [http://{{flybaseorg}}/reports/FBlc0000030.html HD2] FlyBase Dataset Report and references therein for more information.
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:'''HFA RNAi amplicons''' Extents of the amplicons are indicated with an orange bar. See the [http://{{flybaseorg}}/reports/FBlc0000031.html HFA] FlyBase Dataset Report and references therein for more information.
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:'''NIG-Fly RNAi amplicons''' Extents of the amplicons are indicated with an orange bar. See the [http://{{flybaseorg}}/reports/FBlc0000491.html NIG_RNAi_Fly-1] FlyBase Dataset Report and references therein for more information.
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=== Rescue fragments === 
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Locations of transgenic rescue fragments reported in the literature. Labeled with FlyBase allele symbol designation. Each feature glyph is linked to the related FlyBase Allele Report which contains genetic data.
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=== Genomic Libraries ===
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:'''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 [http://{{flybaseorg}}/reports/FBlc0000783.html CHORI-321_BAC] FlyBase Dataset Report and references therein for more information.
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:'''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 [http://{{flybaseorg}}/reports/FBlc0000784.html CHORI-322_BAC] FlyBase Dataset Report and references therein for more information.
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=== 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 [http://{{flybaseorg}}/reports/FBlc0000327.html 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 [http://{{flybaseorg}}/reports/FBlc0000029.html Affymetrix_GeneChip_v2] FlyBase Dataset Report for more information.
 +
 
 +
:'''DGRC-1 amplicons''' DNA fragments amplified from D. melanogaster genomic DNA (OregonR) by the [https://dgrc.bio.indiana.edu/Home/ Drosophila Genomics Resource Center (DGRC)], using gene-specific primers made by [https://www.incyte.com/ 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 [http://{{flybaseorg}}/reports/FBlc0000027.html 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 [https://www.sysbiol.cam.ac.uk/CSBC/FlyChip FlyChip] in collaboration with the International Drosophila Array Consortium INDAC and the [https://dgrc.bio.indiana.edu/Home/ 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 [http://{{flybaseorg}}/reports/FBlc0000028.html DGRC-2] FlyBase Dataset Report for more information.
 +
 
 +
== 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 [http://{{flybaseorg}}/reports/FBlc0000187.html Chromatin_types_NKI.Kc167] FlyBase Dataset Report and references therein for more information. The 5-state model track legend is as follows.
 +
::[[File:5_state.png|450px]]<br/>
 +
 
 +
:'''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 [http://{{flybaseorg}}/reports/FBlc0000199.html 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 [http://{{flybaseorg}}/reports/FBlc0000200.html Chromatin_types_mE2.BG3] FlyBase Dataset Report and references therein for more information. The 9-state model track legend is as follows.
 +
::[[File:9_state.png|450px]]<br/>
 +
 
 +
:'''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 [http://{{flybaseorg}}/reports/FBrf0217348.html Bonn et al., 2012]. Data analysis methods by Matthias Monfort (of the Furlong group) are described [http://{{flybaseorg}}/reports/FBrf0227761.html 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.
 +
 
 +
::[http://{{flybaseorg}}/reports/FBlc0000710.html ChIP-seq_H3K4me1_E6-8h_mesoderm]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000715.html ChIP-seq_H3K27Ac_E6-8h_mesoderm]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000711.html ChIP-seq_H3K4me3_E6-8h_mesoderm]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000709.html ChIP-seq_RpII33_E6-8h_mesoderm]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000713.html ChIP-seq_H3K79me3_E6-8h_mesoderm]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000714.html ChIP-seq_H3K36me3_E6-8h_mesoderm]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000712.html ChIP-seq_H3K27me3_E6-8h_mesoderm]<br />
 +
 
 +
=== 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 [http://{{flybaseorg}}/reports/FBlc0000058.html Insulator_Class_I.mE01] FlyBase Dataset Report and references therein for more information. Each diamond-shaped feature glyph displays a pop-up window with basic information when hovered over and links to a FlyBase Sequence Feature Report with further 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 [http://{{flybaseorg}}/reports/FBlc0000059.html Insulator_Class_II.mE01 ] FlyBase Dataset Report and references therein for more information. Each diamond-shaped feature glyph displays a pop-up window with basic information when hovered over and links to a FlyBase Sequence Feature Report with further supporting data.
 
   
 
   
−
'''Protein binding site'''. Indicated by grey bar. Locations of protein binding site reported in the literature, as compiled by FlyBase and/or [http://redfly.ccr.buffalo.edu/ RedFly]). Reference and supporting information available on related Sequence Feature reports (click feature glyph to access report). See also the [http://{{SERVERNAME}}/reports/FBlc0000494.html REDfly TFBSs] dataset report.
+
:'''Putative PREs (modENCODE)''' Genomic sequences identified by ChIP-chip of HDAC and histone modifications as putative polycomb response elements (silencers) in embryos. See the [http://{{flybaseorg}}/reports/FBlc0000414.html 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 [http://redfly.ccr.buffalo.edu/ REDfly]). See the [http://{{flybaseorg}}/reports/FBlc0000493.html 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 [http://redfly.ccr.buffalo.edu/ RedFly]). See the [http://{{flybaseorg}}/reports/FBlc0000494 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: [http://{{flybaseorg}}/reports/FBrf0209262.html Zinzen et al., 2009], [http://{{flybaseorg}}/reports/FBrf0217348.html Bonn et al., 2012], [http://{{flybaseorg}}/reports/FBrf0217404.html Junion et al., 2012], [http://{{flybaseorg}}/reports/FBrf0223915.html Rembold et al., 2014] and [http://{{flybaseorg}}/reports/FBrf0225471.html Ciglar et al., 2014]. These 28 ChIP-chip datasets were processed in parallel by Matthias Monfort of the Furlong group, as described [http://{{flybaseorg}}/reports/FBrf0227761.html 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.<br />
 +
 
 +
::'''ChIP (embryo, 2-4h) - Mef2 sna tin twi'''
 +
 
 +
:::[http://{{flybaseorg}}/reports/FBlc0000689.html ChIP-chip_Mef2_E2-4h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000700.html ChIP-chip_sna_E2-4h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000701.html ChIP-chip_tin_E2-4h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000705.html ChIP-chip_twi_E2-4h_organism]<br />
 +
 
 +
::'''ChIP (embryo, 4-6h) - Doc2 pMad Mef2 pan pnr slp1 tin twi'''
 +
 
 +
:::[http://{{flybaseorg}}/reports/FBlc0000684.html ChIP-chip_Doc2_E4-6h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000696.html ChIP-chip_pMad_E4-6h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000690.html ChIP-chip_Mef2_E4-6h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000686.html ChIP-chip_pan_E4-6h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000694.html ChIP-chip_pnr_E4-6h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000698.html ChIP-chip_slp1_E4-6h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000702.html ChIP-chip_tin_E4-6h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000706.html ChIP-chip_twi_E4-6h_organism]<br />
 +
 
 +
::'''ChIP (embryo, 6-8h) - bap bin Doc2 lmd pMad Mef2 pan pnr slp1 tin ttk twi'''
 +
 
 +
:::[http://{{flybaseorg}}/reports/FBlc0000680.html ChIP-chip_bap_E6-8h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000681.html ChIP-chip_bin_E6-8h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000685.html ChIP-chip_Doc2_E6-8h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000688.html ChIP-chip_lmd_E6-8h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000697.html ChIP-chip_pMad_E6-8h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000691.html ChIP-chip_Mef2_E6-8h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000687.html ChIP-chip_pan_E6-8h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000695.html ChIP-chip_pnr_E6-8h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000699.html ChIP-chip_slp1_E6-8h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000703.html ChIP-chip_tin_E6-8h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000704.html ChIP-chip_ttk_E6-8h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000707.html ChIP-chip_twi_E6-8h_organism]<br />
 +
 
 +
::'''ChIP (embryo, 8-10h) - bin Mef2'''
 +
 
 +
:::[http://{{flybaseorg}}/reports/FBlc0000682.html ChIP-chip_bin_E8-10h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000692.html ChIP-chip_Mef2_E8-10h_organism]<br />
 +
 
 +
::'''ChIP (embryo, 10-12h) - bin Mef2'''
 +
 
 +
:::[http://{{flybaseorg}}/reports/FBlc0000683.html ChIP-chip_bin_E10-12h_organism]<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000693.html ChIP-chip_Mef2_E10-12h_organism]<br />
 +
 
 +
:'''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 [http://{{flybaseorg}}/reports/FBlc0000258.html 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.
 +
 
 +
::[http://{{flybaseorg}}/reports/FBlc0000293.html mE1_TFBS_disco]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000299.html mE1_TFBS_ftz-f1]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000300.html mE1_TFBS_GATAe]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000303.html BDTNP1_TFBS_hb]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000304.html mE1_TFBS_hkb]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000308.html BDTNP1_TFBS_kni]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000309.html mE1_TFBS_Kr]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000314.html mE1_TFBS_sbb]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000315.html mE1_TFBS_sens]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000316.html BDTNP1_TFBS_shn]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000318.html BDTNP1_TFBS_sna]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000320.html BDTNP1_TFBS_tll]<br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000326.html mE1_TFBS_zfh1]<br />
 +
 
 +
:'''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.
 +
 
 +
::[http://{{flybaseorg}}/reports/FBlc0000287.html BDTNP1_TFBS_bcd] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000288.html mE1_TFBS_cad] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000295.html mE1_TFBS_Dll] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000296.html mE1_TFBS_en] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000297.html mE1_TFBS_eve] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000298.html BDTNP1_TFBS_ftz] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000305.html mE1_TFBS_inv] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000312.html BDTNP1_TFBS_prd] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000324.html mE1_TFBS_Ubx] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000325.html BDTNP1_TFBS_z] <br />
 +
 
 +
:'''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.
 +
 
 +
::[http://{{flybaseorg}}/reports/FBlc0000292.html BDTNP1_TFBS_da ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000302.html mE1_TFBS_h ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000307.html mE1_TFBS_kn ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000323.html BDTNP1_TFBS_twi ] <br />
 +
 
 +
:'''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.
 +
 
 +
::[http://{{flybaseorg}}/reports/FBlc0000286.html mE1_TFBS_bab1 ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000289.html mE1_TFBS_chinmo ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000321.html mE1_TFBS_Trl ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000322.html mE1_TFBS_ttk ] <br />
 +
 
 +
:'''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.
 +
 
 +
::[http://{{flybaseorg}}/reports/FBlc0000290.html mE1_TFBS_cnc ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000291.html mE1_TFBS_D ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000294.html BDTNP1_TFBS_dl ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000301.html BDTNP1_TFBS_gt ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000306.html mE1_TFBS_jumu ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000310.html BDTNP1_TFBS_Mad ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000311.html BDTNP1_TFBS_Med ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000313.html mE1_TFBS_run ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000317.html BDTNP1_TFBS_slp1 ] <br />
 +
::[http://{{flybaseorg}}/reports/FBlc0000319.html mE1_TFBS_Stat92E ] <br />
 +
 
 +
=== 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 [http://{{flybaseorg}}/reports/FBlc0000188.html 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''' Mostly 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. A few genomic DNA submissions, including third party submissions, are included in this tier.
 +
 
 +
:'''Inferred transcript sequences''' Mostly D. melanogaster sequences designated as [https://www.ncbi.nlm.nih.gov/genbank/tpa-inf/ Third Party Annotation:Inferential]. 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 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 are dotted lines with TSS peak profile overlaid. The arrow points in the direction of transcription. Hover over glyph for a pop-up window with basic information, click to go to the relevant Sequence Feature Report. Note: data for embryonic stages only. See the [http://{{flybaseorg}}/reports/FBlc0000202.html 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 [http://{{flybaseorg}}/reports/FBlc0000537.html 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 [http://{{flybaseorg}}/reports/FBlc0000537.html 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 [http://{{flybaseorg}}/reports/FBlc0000537.html 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 [http://{{flybaseorg}}/reports/FBlc0000537.html 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 [http://{{flybaseorg}}/reports/FBlc0000725.html TSS_MachiBase] FlyBase Dataset Report and references therein for more information.
 +
 
 +
:[[File:TopoViewOneOff.png|200px|right|Known bug.]]
 +
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. The portion of exons confirmed by RNA-Seq reads are represented by blue bars while introns are represented as lines. Hover over each exon junction glyph to view a pop-up window containing read counts from modENCODE and/or Baylor datasets and click to go to a FlyBase exon junction Sequence Feature Report. See the [http://{{flybaseorg}}/reports/FBlc0000204.html BCM_1_RNAseq_junctions] and [http://{{flybaseorg}}/reports/FBlc0000203.html 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 [http://{{flybaseorg}}/reports/FBlc0003700 pA_sites_Lai] and [http://{{flybaseorg}}/reports/FBlc0003702 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 [http://{{flybaseorg}}/reports/FBlc0000259 mE_A-to-I_RNA_Editing_Sites] and [http://{{flybaseorg}}/reports/FBlc0000519 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)''' [http://pfam.xfam.org/ Pfam] protein domains identified in annotated proteins, as obtained from [https://www.ebi.ac.uk/interpro/download.html InterPro], are mapped to the genome. Hyperlinked to a Pfam report for the domain.
 +
 
 +
:'''Protein domains (SMART)''' [http://smart.embl-heidelberg.de/ SMART] protein domains identified in annotated proteins are mapped to the genome. Hyperlinked to an InterPro report for the domain.
 +
 
 +
=== Peptide Sequences ===
 +
:'''Developmental Proteomes''' Alignment of peptide sequences identified in various developmental proteomes to the reference genome. Each peptide glyph is hyperlinked to a FlyBase Sequence Feature Report with the peptide sequence. Data obtained from: [http://{{flybaseorg}}/reports/FBrf0235991 Casas-Vila et al., 2017], [http://{{flybaseorg}}/reports/FBrf0246020 Cao et al., 2020].
 +
 
 +
:'''Peptide Atlas''' Alignment of peptide sequences determined by mass spectroscopy, derived from polypeptides isolated from the sequenced strain at various developmental stages and from various tissues. Contributed by the Center for Model Organism Proteomes, SystemsX and Research Priority Project of the University of Zurich, Switzerland. For more information, see [https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=352 Peptide Atlas]
 +
 
 +
==Expression==
 +
===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.
  
−
'''Enhancers''' [http://{{SERVERNAME}}/reports/FBlc0000415.html mE1_CBP_Enhancers ] Dataset Report. Genomic sequences identified as putative embryo-only enhancers by virtue of embryo-specific CBP-binding in ChIP assays.
+
:'''modENCODE transcriptomes'''
  
−
'''Silencers''' [http://{{SERVERNAME}}/reports/FBlc0000414.html mE1_HDAC_PRE ] Dataset Report. Genomic sequences identified as putative polycomb response elements (silencers) in embryos.
+
::'''Developmental stages, unique reads''' [http://{{flybaseorg}}/reports/FBlc0000085.html modENCODE_mRNA-Seq_U] Dataset report. These tracks contain RNA-Seq expression data for several different stages of development.
  
−
'''Regulatory region'''. Indicated by grey bar. Locations of regulatory regions reported in the literature, as compiled by FlyBase and/or [http://redfly.ccr.buffalo.edu/ REDfly]). Reference and supporting information available on related Sequence Feature reports (click feature glyph to access report). See also the [http://{{SERVERNAME}}/reports/FBlc0000493.html REDfly CRMs] dataset report.
+
::'''Tissues
 +
:::'''Digestive system''' <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000227.html mE_mRNA_L3_Wand_dig_sys]<br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000219.html mE_mRNA_A_1d_dig_sys] <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000223.html mE_mRNA_A_4d_dig_sys] <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000221.html mE_mRNA_A_20d_dig_sys] <br />
  
−
'''TFBS – HOT spot analysis''' [http://{{SERVERNAME}}/reports/FBlc0000258.html mE1_TFBS_HSA ] Dataset Report. 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 data sets for 41 different transcription factors. TF binding profiles used in this analysis were assayed at early embryo stages. Mousing over the feature pops up a box that lists the transcription factor genes that bind within the region. Clicking on the feature links to the related Sequence Feature report.  
+
:::'''Fat body and salivary glands''' <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000228.html mE_mRNA_L3_Wand_fat] <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000233.html mE_mRNA_WPP_fat] <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000235.html mE_mRNA_P8_fat] <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000230.html mE_mRNA_L3_Wand_saliv]<br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000234.html mE_mRNA_WPP_saliv] <br />
  
−
'''TFBS – zinc finger domain''' Binding sites for transcriptions factors that contain one or more zinc finger domains. Clicking on the feature links to the related Sequence Feature report. The following Dataset Reports comprise the data found in this track.
+
:::'''Imaginal disc and other carcass''' <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000229.html mE_mRNA_L3_Wand_imag_disc]  <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000226.html mE_mRNA_L3_Wand_carcass]  <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000218.html mE_mRNA_A_1d_carcass]  <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000222.html mE_mRNA_A_4d_carcass]  <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000220.html mE_mRNA_A_20d_carcass]  <br />
  
−
[http://{{SERVERNAME}}/reports/FBlc0000293.html mE1_TFBS_disco]<br />
+
:::'''CNS and adult head''' <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000299.html mE1_TFBS_ftz-f1]<br />
+
::::[http://{{flybaseorg}}/reports/FBlc0000225.html mE_mRNA_L3_CNS] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000300.html mE1_TFBS_GATAe]<br />
+
::::[http://{{flybaseorg}}/reports/FBlc0000224.html mE_mRNA_P8_CNS] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000303.html BDTNP1_TFBS_hb]<br />
+
::::[http://{{flybaseorg}}/reports/FBlc0000209.html mE_mRNA_A_MateM_1d_head] <br />  
−
[http://{{SERVERNAME}}/reports/FBlc0000304.html mE1_TFBS_hkb]<br />
+
::::[http://{{flybaseorg}}/reports/FBlc0000216.html mE_mRNA_A_MateM_4d_head] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000308.html BDTNP1_TFBS_kni]<br />
+
::::[http://{{flybaseorg}}/reports/FBlc0000214.html mE_mRNA_A_MateM_20d_head] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000309.html mE1_TFBS_Kr]<br />
+
::::[http://{{flybaseorg}}/reports/FBlc0000210.html mE_mRNA_A_VirF_1d_head] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000314.html mE1_TFBS_sbb]<br />
+
::::[http://{{flybaseorg}}/reports/FBlc0000211.html mE_mRNA_A_VirF_4d_head] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000315.html mE1_TFBS_sens]<br />
+
::::[http://{{flybaseorg}}/reports/FBlc0000231.html mE_mRNA_A_VirF_20d_head] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000316.html BDTNP1_TFBS_shn]<br />
+
::::[http://{{flybaseorg}}/reports/FBlc0000207.html mE_mRNA_A_MateF_1d_head] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000318.html BDTNP1_TFBS_sna]<br />
+
::::[http://{{flybaseorg}}/reports/FBlc0000213.html mE_mRNA_A_MateF_4d_head] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000320.html BDTNP1_TFBS_tll]<br />
+
::::[http://{{flybaseorg}}/reports/FBlc0000212.html mE_mRNA_A_MateF_20d_head] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000326.html mE1_TFBS_zfh1]<br />
 
  
−
'''TFBS – homeodomain''' Binding sites for transcriptions factors that contain one or more homeodomains. The following Dataset Reports comprise the data found in this track.
+
:::'''Gonads and male accessory glands'''<br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000217.html mE_mRNA_A_MateM_4d_testis] <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000215.html mE_mRNA_A_MateM_4d_acc_gland] <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000232.html mE_mRNA_A_VirF_4d_ovary] <br />
 +
::::[http://{{flybaseorg}}/reports/FBlc0000208.html mE_mRNA_A_MateF_4d_ovary]<br />
  
−
[http://{{SERVERNAME}}/reports/FBlc0000287.html BDTNP1_TFBS_bcd] <br />
+
::'''Tissue culture cells, by strand (modENCODE Transcription Group)''' [http://{{flybaseorg}}/reports/FBlc0000260.htm modENCODE_mRNA-Seq_cell.B] Dataset report.
−
[http://{{SERVERNAME}}/reports/FBlc0000288.html mE1_TFBS_cad] <br />
 
−
[http://{{SERVERNAME}}/reports/FBlc0000295.html mE1_TFBS_Dll] <br />
 
−
[http://{{SERVERNAME}}/reports/FBlc0000296.html mE1_TFBS_en] <br />
 
−
[http://{{SERVERNAME}}/reports/FBlc0000297.html mE1_TFBS_eve] <br />
 
−
[http://{{SERVERNAME}}/reports/FBlc0000298.html BDTNP1_TFBS_ftz] <br />
 
−
[http://{{SERVERNAME}}/reports/FBlc0000305.html mE1_TFBS_inv] <br />
 
−
[http://{{SERVERNAME}}/reports/FBlc0000312.html BDTNP1_TFBS_prd] <br />
 
−
[http://{{SERVERNAME}}/reports/FBlc0000324.html mE1_TFBS_Ubx] <br />
 
−
[http://{{SERVERNAME}}/reports/FBlc0000325.html BDTNP1_TFBS_z] <br />
 
  
−
'''TFBS – helix-loop-helix domain''' Binding sites for transcriptions factors that contain one or more helix-loop-helix domains. The following Dataset Reports comprise the data found in this track.
+
::'''Treatments/Conditions''' [http://{{flybaseorg}}/reports/FBlc0000236.html modENCODE_mRNA-Seq_treatments] Dataset report.
  
−
[http://{{SERVERNAME}}/reports/FBlc0000292.html BDTNP1_TFBS_da ] <br />
+
:'''Knoblich lab- L3 CNS transcriptomes'''
−
[http://{{SERVERNAME}}/reports/FBlc0000302.html mE1_TFBS_h ] <br />
+
::'''L3 CNS neuron'''<br />
−
[http://{{SERVERNAME}}/reports/FBlc0000307.html mE1_TFBS_kn ] <br />
+
:::[http://{{flybaseorg}}/reports/FBlc0000506.html Knoblich_mRNA_L3_CNS_neuron] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000323.html BDTNP1_TFBS_twi ] <br />
+
::'''L3 CNS neuroblast'''<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0000505.html Knoblich_mRNA_L3_CNS_neuroblast] <br />
  
−
'''TFBS – BTB/POZ domain''' Binding sites for transcriptions factors that contain one or more BTB/POZ domains. The following Dataset Reports comprise the data found in this track.
+
:'''Oliver lab- SRA Aggregated RNA-Seq'''
 +
: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 [http://{{flybaseorg}}/reports/FBlc0003484.htm Oliver_aggregated_RNA-Seq_profile] Dataset report for more details.
  
−
[http://{{SERVERNAME}}/reports/FBlc0000286.html mE1_TFBS_bab1 ] <br />
+
:'''FlyAtlas2 transcriptomes''' RNA-seq from larval and adult male or female tissues grouped into the four subsets below. See the [http://{{flybaseorg}}/reports/FBlc0003498 FlyAtlas2] FlyBase Dataset report and references therein for further information.
−
[http://{{SERVERNAME}}/reports/FBlc0000289.html mE1_TFBS_chinmo ] <br />
 
−
[http://{{SERVERNAME}}/reports/FBlc0000321.html mE1_TFBS_Trl ] <br />
 
−
[http://{{SERVERNAME}}/reports/FBlc0000322.html mE1_TFBS_ttk ] <br />
 
  
−
'''TFBS – other''' Binding sites for transcriptions factors that do not fall into one of the other categories. The following Dataset Reports comprise the data found in this track.
+
::'''Nervous system'''<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003650 RNA-Seq_Profile_FlyAtlas2_L3_CNS] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003619 RNA-Seq_Profile_FlyAtlas2_Adult_Female_Brain] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003635 RNA-Seq_Profile_FlyAtlas2_Adult_Male_Brain] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003624.html RNA-Seq_Profile_FlyAtlas2_Adult_Female_Head] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003640 RNA-Seq_Profile_FlyAtlas2_Adult_Male_Head] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003622.html RNA-Seq_Profile_FlyAtlas2_Adult_Female_Eye] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003638 RNA-Seq_Profile_FlyAtlas2_Adult_Male_Eye] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003630 RNA-Seq_Profile_FlyAtlas2_Adult_Female_ThoracicoAbdominalGanglion] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003645 RNA-Seq_Profile_FlyAtlas2_Adult_Male_ThoracicoAbdominalGanglion] <br />
  
−
[http://{{SERVERNAME}}/reports/FBlc0000290.html mE1_TFBS_cnc ] <br />
+
::'''Digestive system'''<br />
−
[http://{{SERVERNAME}}/reports/FBlc0000291.html mE1_TFBS_D ] <br />
+
:::[http://{{flybaseorg}}/reports/FBlc0003620 RNA-Seq_Profile_FlyAtlas2_Adult_Female_Crop] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000294.html BDTNP1_TFBS_dl ] <br />
+
:::[http://{{flybaseorg}}/reports/FBlc0003636 RNA-Seq_Profile_FlyAtlas2_Adult_Male_Crop] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000301.html BDTNP1_TFBS_gt ] <br />
+
:::[http://{{flybaseorg}}/reports/FBlc0003654 RNA-Seq_Profile_FlyAtlas2_L3_Midgut] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000306.html mE1_TFBS_jumu ] <br />
+
:::[http://{{flybaseorg}}/reports/FBlc0003626 RNA-Seq_Profile_FlyAtlas2_Adult_Female_Midgut] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000310.html BDTNP1_TFBS_Mad ] <br />
+
:::[http://{{flybaseorg}}/reports/FBlc0003642 RNA-Seq_Profile_FlyAtlas2_Adult_Male_Midgut] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000311.html BDTNP1_TFBS_Med ] <br />
+
:::[http://{{flybaseorg}}/reports/FBlc0003652 RNA-Seq_Profile_FlyAtlas2_L3_Hindgut] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000313.html mE1_TFBS_run ] <br />
+
:::[http://{{flybaseorg}}/reports/FBlc0003625 RNA-Seq_Profile_FlyAtlas2_Adult_Female_Hindgut] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000317.html BDTNP1_TFBS_slp1 ] <br />
+
:::[http://{{flybaseorg}}/reports/FBlc0003641 RNA-Seq_Profile_FlyAtlas2_Adult_Male_Hindgut] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000319.html mE1_TFBS_Stat92E ] <br />
+
:::[http://{{flybaseorg}}/reports/FBlc0003628 RNA-Seq_Profile_FlyAtlas2_Adult_Female_RectalPad] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003643 RNA-Seq_Profile_FlyAtlas2_Adult_Male_RectalPad] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003655 RNA-Seq_Profile_FlyAtlas2_L3_SalivaryGland] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003629 RNA-Seq_Profile_FlyAtlas2_Adult_Female_SalivaryGland] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003644 RNA-Seq_Profile_FlyAtlas2_Adult_Male_SalivaryGland] <br />
  
−
'''Origins of replication''' [http://{{SERVERNAME}}/reports/FBlc0000188.html mE_Early_Replication_Origins_cells ] Dataset Report. Genome profile of early activating origins of replication, BrdU label, Kc, BG3 and S2 cell lines.  Links go to relevant Sequence Feature report. <br />
+
::'''Reproductive system'''<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003627 RNA-Seq_Profile_FlyAtlas2_Adult_Female_Ovary] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003633 RNA-Seq_Profile_FlyAtlas2_Adult_Female_Virgin_Spermathecum] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003632 RNA-Seq_Profile_FlyAtlas2_Adult_Female_Mated_Spermathecum] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003647 RNA-Seq_Profile_FlyAtlas2_Adult_Male_Testis] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003648 RNA-Seq_Profile_FlyAtlas2_Adult_Male_AccessoryGland] <br />
  
−
'''Putative brain enhancers''' (Pfeiffer et al.) [http://{{SERVERNAME}}/reports/FBlc0000201.html GMR_Brain_exp_1] Dataset Report. Gray glyphs represent putative enhancers used to generate fly stocks carrying GAL4 transgenic constructs designed to be expressed in adult brain. Stocks are available from the Bloomington Stock Center. Clicking the glyph brings up the associated Sequence Feature report (e.g. http://{{SERVERNAME}}/reports/FBsf0000162377.html). On the Sequence Feature report, under "associated information" there is a construct listed. Clicking this construct link brings up the associated Construct Report (e.g. http://{{SERVERNAME}}/reports/FBtp0058072.html) on which you can find a link to the Stock Report (e.g. http://{{SERVERNAME}}/reports/FBst0045107.html). Sorry it's so roundabout!
+
::'''Other systems and whole organism'''<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003656 RNA-Seq_Profile_FlyAtlas2_L3_Trachea] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003651 RNA-Seq_Profile_FlyAtlas2_L3_FatBody] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003623 RNA-Seq_Profile_FlyAtlas2_Adult_Female_FatBody] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003639 RNA-Seq_Profile_FlyAtlas2_Adult_Male_FatBody] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003653 RNA-Seq_Profile_FlyAtlas2_L3_MalpighianTubule] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003631 RNA-Seq_Profile_FlyAtlas2_Adult_Female_MalpighianTubule] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003646 RNA-Seq_Profile_FlyAtlas2_Adult_Male_MalpighianTubule] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003657 RNA-Seq_Profile_FlyAtlas2_L3_Carcass] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003621 RNA-Seq_Profile_FlyAtlas2_Adult_Female_Carcass] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003637 RNA-Seq_Profile_FlyAtlas2_Adult_Male_Carcass] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003658 RNA-Seq_Profile_FlyAtlas2_L3_Whole] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003634 RNA-Seq_Profile_FlyAtlas2_Adult_Female_Whole] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003649 RNA-Seq_Profile_FlyAtlas2_Adult_Male_Whole] <br />
  
−
'''RNA Editing Sites''' A-to-I RNA editing sites.<br />
+
===Small RNA-Seq===
−
[http://{{SERVERNAME}}/reports/FBlc0000259 mE_A-to-I_RNA_Editing_Sites] Dataset Report. <br />
+
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.
−
[http://{{SERVERNAME}}/reports/FBlc0000519 Rosbash_Adult_Head_A-to-I_Editing_Sites] Dataset Report. <br />
 
  
−
== Similarity==
+
:'''Lai lab transcriptomes'''
  
−
'''Orthologs'''. Indicated by pale yellow bar covering extent of the orthologous region. Clicking on a bar will cause a pop-up box to appear which will contain links for orthologs of the gene. The ortholog box will contain the drosophilid orthologs on the left (link to a GBrowse view of the orthologous region) and other orthologs on the right (link to GenBank report).
+
::'''Developmental stages, stranded small RNA-Seq (Lai lab)''' See [http://flybase.org/cgi-bin/fbidq.html?FBlc0000789 Lai_shortRNA-Seq'''_profiles_development] Dataset Report.
  
−
== RNAi Reagents and Data ==
+
::'''Tissues, stranded small RNA-Seq (Lai lab)''' See [http://flybase.org/cgi-bin/fbidq.html?FBlc0000790 Lai_shortRNA-Seq'''_profiles_tissues] Dataset Report.
  
−
'''DRSC RNAi amplicons''' <br />
+
::'''Cell lines'''
−
Extents of the amplicons are indicated with an orange bar. <br />
+
:::'''Schneider and embryonic-derived'''See [http://flybase.org/cgi-bin/fbidq.html?FBlc0000791 Lai_shortRNA-Seq'''_profiles_cells] Dataset Report.
−
[http://{{SERVERNAME}}/reports/FBlc0000026.html DRSC dsNRA amplicon platform] Dataset Report. 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) . For further information see the [http://{{SERVERNAME}}/reports/FBlc0000027.html DGRC-1 Dataset report].
 
  
−
'''VDRC RNAi amplicons''' <br />
+
:::'''Imaginal disc-derived''' See [http://flybase.org/cgi-bin/fbidq.html?FBlc0000791 Lai_shortRNA-Seq'''_profiles_cells] Dataset Report.
−
Extents of the amplicons are indicated with an orange bar. <br />
 
−
Segment used to create inverted repeat in RNAi construct from the Vienna Drosophila RNAi Center ([http://{{SERVERNAME}}/reports/FBrf0200327.html Dickson B. et al. 2007.7.18]). "GD" identifer also used for allele and construct symbols. <br />
 
  
−
[http://{{SERVERNAME}}/reports/FBlc0000041.html VDRC-1] Dataset Report<br />
+
:::'''CNS-, ovary- and blood-derived''' See [http://flybase.org/cgi-bin/fbidq.html?FBlc0000791 Lai_shortRNA-Seq'''_profiles_cells] Dataset Report.
−
[http://{{SERVERNAME}}/reports/FBlc0000055.html VDRC-2] Dataset Report. <br />
 
  
−
'''TRiP RNAi amplicons''' <br />
+
:'''FlyAtlas2 transcriptomes''' Small RNA-seq from larval and adult male or female tissues grouped into the four subsets below. See the [http://{{flybaseorg}}/reports/FBlc0003498 FlyAtlas2] FlyBase Dataset report and references therein for further information.
−
Extents of the amplicons are indicated with an orange bar. <br />
 
−
FBlc0000048 [http://{{SERVERNAME}}/reports/FBlc0000048.html TRiP-1] Dataset Report <br />
 
−
FBlc0000153 [http://{{SERVERNAME}}/reports/FBlc0000153.html TRiP-2] Dataset Report<br />
 
−
FBlc0000185 [http://{{SERVERNAME}}/reports/FBlc0000185.html TRiP-3] Dataset Report<br />
 
−
FBlc0000186 [http://{{SERVERNAME}}/reports/FBlc0000186.html TRiP-4] Dataset Report<br />
 
−
FBlc0000416 [http://{{SERVERNAME}}/reports/FBlc0000416.html TRiP-5] Dataset Report<br />
 
  
−
'''BKNA RNAi amplicons''' <br />
+
::'''Nervous system'''<br />
−
Extents of the amplicons are indicated with an orange bar. <br />
+
:::[http://{{flybaseorg}}/reports/FBlc0003690 microRNA-Seq_Profile_FlyAtlas2_L3_CNS] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000030.html HD2] Dataset Report (dsRNA amplicon platform) RNAi amplicons from the GenomeRNAi database. <br />
+
:::[http://{{flybaseorg}}/reports/FBlc0003659 microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Brain] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003675 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Brain] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003664.html microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Head] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003680 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Head] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003662.html microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Eye] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003678 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Eye] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003670 microRNA-Seq_Profile_FlyAtlas2_Adult_Female_ThoracicoAbdominalGanglion] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003685 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_ThoracicoAbdominalGanglion] <br />
  
−
'''HFA RNAi amplicons''' <br />
+
::'''Digestive system'''<br />
−
Extents of the amplicons are indicated with an orange bar. <br />
+
:::[http://{{flybaseorg}}/reports/FBlc0003660 microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Crop] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000031.html HFA] Datset Report.
+
:::[http://{{flybaseorg}}/reports/FBlc0003676 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Crop] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003694 microRNA-Seq_Profile_FlyAtlas2_L3_Midgut] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003666 microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Midgut] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003682 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Midgut] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003692 microRNA-Seq_Profile_FlyAtlas2_L3_Hindgut] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003665 microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Hindgut] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003681 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Hindgut] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003668 microRNA-Seq_Profile_FlyAtlas2_Adult_Female_RectalPad] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003683 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_RectalPad] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003695 microRNA-Seq_Profile_FlyAtlas2_L3_SalivaryGland] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003669 microRNA-Seq_Profile_FlyAtlas2_Adult_Female_SalivaryGland] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003684 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_SalivaryGland] <br />
  
−
'''NIG-Fly RNAi amplicons''' <br />
+
::'''Reproductive system'''<br />
−
Extents of the amplicons are indicated with an orange bar. <br />
+
:::[http://{{flybaseorg}}/reports/FBlc0003667 microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Ovary] <br />
−
[http://{{SERVERNAME}}/reports/FBlc0000491.html NIG_RNAi_Fly-1] Datset Report.
+
:::[http://{{flybaseorg}}/reports/FBlc0003673 microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Virgin_Spermathecum] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003672 microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Mated_Spermathecum] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003687 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Testis] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003688 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_AccessoryGland] <br />
  
−
==Aberrations==
+
::'''Other systems and whole organism'''<br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003696 microRNA-Seq_Profile_FlyAtlas2_L3_Trachea] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003691 microRNA-Seq_Profile_FlyAtlas2_L3_FatBody] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003663 microRNA-Seq_Profile_FlyAtlas2_Adult_Female_FatBody] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003679 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_FatBody] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003693 microRNA-Seq_Profile_FlyAtlas2_L3_MalpighianTubule] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003671 microRNA-Seq_Profile_FlyAtlas2_Adult_Female_MalpighianTubule] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003686 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_MalpighianTubule] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003697 microRNA-Seq_Profile_FlyAtlas2_L3_Carcass] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003661 microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Carcass] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003677 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Carcass] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003698 microRNA-Seq_Profile_FlyAtlas2_L3_Whole] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003674 microRNA-Seq_Profile_FlyAtlas2_Adult_Female_Whole] <br />
 +
:::[http://{{flybaseorg}}/reports/FBlc0003689 microRNA-Seq_Profile_FlyAtlas2_Adult_Male_Whole] <br />
  
−
'''Deleted segment'''. 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.
+
==Gene Predictions==
  
−
==Expression Levels: RNA-Seq==
+
'''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 [https://www.ncbi.nlm.nih.gov/genome/annotation_euk/gnomon/ NCBI Gnomon Description Page] for more information.
  
−
'''Developmental stage subsets, unique reads (modENCODE)'''[http://{{SERVERNAME}}/reports/FBlc0000085.html modENCODE_mRNA-Seq_U] Dataset report. These tracks contain RNA-Seq expression data for several different stages of development.
+
'''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: [http://{{flybaseorg}}/reports/FBrf0202906.html Lin MF, Carlson, JW et al. (2007)], [http://{{flybaseorg}}/reports/FBrf0213957.html Lin MF, Jungreis I, and Kellis M. (2011)] for more information.

Latest revision as of 09:36, 22 February 2024

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 span 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 displays a pop-up window containing an automated gene summary when moused over and links to the FlyBase Gene Report when clicked.

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. Each transcript summary glyph is hyperlinked to a pop-up window containing an automated gene summary; 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.

Aberrations

Aberration junctions Location of aberration breakpoint reported in the literature. Often the exact breakpoint location is unknown and the feature indicates a range within which the breakpoint has been mapped.

Deficiencies (formerly Deleted segment) Glyphs correspond to the extent of deleted sequences. For convenience, labels for deficiencies without stocks available at Drosophila stock centers are red. Hover over each glyph to view a pop-up window with stock center availability. Click on each glyph to expand the pop-up window with a list of affected genes and a link to the relevant FlyBase Aberration Report with further information including links to the relevant Stock Report with stock ordering information. For tracks displaying only deficiencies with stocks available, please see the 'Deficiency Stocks' and 'Deficiency Kit' tracks in this section.

Duplications Glyphs correspond to the extent of duplicated sequences. For convenience, labels for duplications without stocks available at Drosophila stock centers are red. Hover over each glyph to view a pop-up window with stock center availability. Click on each glyph to expand the pop-up window with a list of affected genes and a link to the relevant FlyBase Aberration Report with further information including links to the relevant Stock Report with stock ordering information. Many of these duplications were generated by transgenic methods and belong to several curated collections. See the Dps(X)DC_set1, Dps_BAC_Retrofit, Dps_GenetiVision, and Dps(X)BSC_set1 FlyBase Dataset Reports for more details on these collections. For tracks displaying only duplications with stocks available, please see the 'Duplication Stocks' track in this section.

Deficiency 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. Click on each glyph to view a pop-up window with a list of affected genes and a link to the relevant FlyBase Aberration Report with further information including links to the relevant Stock Report with stock ordering information.

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. The BDSC Deficiency Kit includes deficiencies with molecularly mapped breakpoints as well as deficiencies with breakpoints that have not been mapped molecularly, primarily to provide coverage of gaps between the molecularly defined deficiencies. These two classes of deficiencies are separated into the following two tracks.

BDSC Deficiency Kit: deleted segment Molecularly defined deficiencies. Click on each glyph to view a pop-up window with a list of affected genes and a link to the relevant FlyBase Aberration Report with further information including links to the relevant Stock Report with stock ordering information.
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. 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 JBrowse display. The endpoints of gap filling segments are derived primarily from overlapping deficiency endpoints and complementation with annotated genes. Each glyph is hyperlinked to a FlyBase Aberration Report with further information including links to the relevant Stock Report with stock ordering information.

Duplication Stocks in Bloomington, Kyoto (formerly Stock Center Aberrations: duplicated segment) This track contains only duplications available from the Bloomington or Kyoto Stock Centers. Click on each glyph to view a pop-up window with a list of affected genes and a link to the relevant FlyBase Aberration Report with further information including links to the relevant Stock Report with stock ordering information.

Transgenic Insertions

Transgenic Insertions(formerly Transgenic insertion site) Insertions are indicated by blue diamonds with an arrow indicating orientation if known. An arrow pointing to the right indicates a transposable element 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 arrow pointing to the left indicates a transposable element 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, a dotted line represents the region of uncertainty. Hover over each insertion glyph to view a pop-up window with basic information and click to go to its FlyBase Insertion Report with further information including links to the relevant Stock Report with stock ordering information.

Transgenic Insertion Stocks in Bloomington, Kyoto This track contains only insertions available from the Bloomington and Kyoto Stock Centers. Insertions are indicated by blue diamonds with an arrow indicating orientation if known. An arrow pointing to the right indicates a transposable element 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 arrow pointing to the left indicates a transposable element 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, a dotted line represents the region of uncertainty. Hover over each insertion glyph to view a pop-up window with basic information and click to go to its FlyBase Insertion Report with further information including links to the relevant Stock Report with stock ordering information.

Mutations & Sequence Variants

Mutations & Experimentally Induced Variants

Substitutions Substitutions include point mutations in which a single nucleotide has been changed into another nucleotide as well as multiple nucleotide variants (MNV) in which the inserted sequence is the same length as the replaced sequence. The location of the mutation is indicated with a vertical bar and labeled with the FlyBase allele symbol. Point mutations are labeled in blue while MNVs are labeled in red to allow the user to easily distinguish substitution types. Each feature glyph is hyperlinked to the related FlyBase Allele Report.
Insertions, Deletions This track shows insertions or deletions of one or more nucleotides as well as delins, alterations which include both an insertion and a deletion of 2 or more nucleotides. In the case of deletions and delins, the extent of the lesion is indicated by a yellow bar. In the case of nucleotide insertions, the location of the insertion is indicated by a vertical line. Mutations are labeled with the FlyBase allele symbol, insertions in green, deletions in red and delins in black. Each feature glyph is hyperlinked to the related FlyBase Allele Report.
Complex Substitutions 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. Each feature glyph is hyperlinked to the related FlyBase Allele Report.
Roughly Mapped Mutations (formerly Uncharacterized change in nucleotide sequence) The mutation has only been roughly mapped molecularly, e.g. to a restriction fragment. The location of the mutation is indicated with a red bar and labeled with the FlyBase allele symbol. Each feature glyph is hyperlinked to the related FlyBase Allele Report.
FlyBase Mutations/Variants on Alliance These represent the portion of FlyBase curated mutation data shared with the Alliance of Genome Resources. The same data is contained in the other tracks in this section, as well as in the Transgenic Insertions track, and can be viewed separately by mutation type therein. Here, the differently-shaped glyphs represent mutation type- deletions are rectangles, insertions are inverted triangles and point mutations are diamonds. Hovering over each glyph brings up a window with further information.

Polymorphisms & Natural Population 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.

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.
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.

Misc. Reagents

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. Each feature glyph is hyperlinked to a FlyBase Sequence Feature Report with supporting data and links to the relevant Stock Report with stock ordering information. See the GMR_Brain_exp_1 FlyBase Dataset Report and references therein for more information on this collection.
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 FlyBase Dataset Report and references therein for more information on this collection.

sgRNA Reagents

TRiP-OE-VPR 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 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 and TRiP-OE-flySAM.dCas9 FlyBase Dataset Reports 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 fragments reported in the literature. Labeled with FlyBase allele symbol designation. Each feature glyph is linked to the related FlyBase Allele Report which contains 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.

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. The 5-state model track legend is as follows.
5 state.png
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. The 9-state model track legend is as follows.
9 state.png
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.
ChIP-seq_H3K4me1_E6-8h_mesoderm
ChIP-seq_H3K27Ac_E6-8h_mesoderm
ChIP-seq_H3K4me3_E6-8h_mesoderm
ChIP-seq_RpII33_E6-8h_mesoderm
ChIP-seq_H3K79me3_E6-8h_mesoderm
ChIP-seq_H3K36me3_E6-8h_mesoderm
ChIP-seq_H3K27me3_E6-8h_mesoderm

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 diamond-shaped feature glyph displays a pop-up window with basic information when hovered over and links to a FlyBase Sequence Feature Report with further 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 diamond-shaped feature glyph displays a pop-up window with basic information when hovered over and links to a FlyBase Sequence Feature Report with further 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-chip_Mef2_E2-4h_organism
ChIP-chip_sna_E2-4h_organism
ChIP-chip_tin_E2-4h_organism
ChIP-chip_twi_E2-4h_organism
ChIP (embryo, 4-6h) - Doc2 pMad Mef2 pan pnr slp1 tin twi
ChIP-chip_Doc2_E4-6h_organism
ChIP-chip_pMad_E4-6h_organism
ChIP-chip_Mef2_E4-6h_organism
ChIP-chip_pan_E4-6h_organism
ChIP-chip_pnr_E4-6h_organism
ChIP-chip_slp1_E4-6h_organism
ChIP-chip_tin_E4-6h_organism
ChIP-chip_twi_E4-6h_organism
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 (embryo, 8-10h) - bin Mef2
ChIP-chip_bin_E8-10h_organism
ChIP-chip_Mef2_E8-10h_organism
ChIP (embryo, 10-12h) - bin Mef2
ChIP-chip_bin_E10-12h_organism
ChIP-chip_Mef2_E10-12h_organism
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.
mE1_TFBS_disco
mE1_TFBS_ftz-f1
mE1_TFBS_GATAe
BDTNP1_TFBS_hb
mE1_TFBS_hkb
BDTNP1_TFBS_kni
mE1_TFBS_Kr
mE1_TFBS_sbb
mE1_TFBS_sens
BDTNP1_TFBS_shn
BDTNP1_TFBS_sna
BDTNP1_TFBS_tll
mE1_TFBS_zfh1
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.
BDTNP1_TFBS_bcd
mE1_TFBS_cad
mE1_TFBS_Dll
mE1_TFBS_en
mE1_TFBS_eve
BDTNP1_TFBS_ftz
mE1_TFBS_inv
BDTNP1_TFBS_prd
mE1_TFBS_Ubx
BDTNP1_TFBS_z
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.
BDTNP1_TFBS_da
mE1_TFBS_h
mE1_TFBS_kn
BDTNP1_TFBS_twi
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.
mE1_TFBS_bab1
mE1_TFBS_chinmo
mE1_TFBS_Trl
mE1_TFBS_ttk
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.
mE1_TFBS_cnc
mE1_TFBS_D
BDTNP1_TFBS_dl
BDTNP1_TFBS_gt
mE1_TFBS_jumu
BDTNP1_TFBS_Mad
BDTNP1_TFBS_Med
mE1_TFBS_run
BDTNP1_TFBS_slp1
mE1_TFBS_Stat92E

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 Mostly 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. A few genomic DNA submissions, including third party submissions, are included in this tier.
Inferred transcript sequences Mostly D. melanogaster sequences designated as Third Party Annotation:Inferential. 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 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 are dotted lines with TSS peak profile overlaid. The arrow points in the direction of transcription. Hover over glyph for a pop-up window with basic information, click to go 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.
Known bug.

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. The portion of exons confirmed by RNA-Seq reads are represented by blue bars while introns are represented as lines. Hover over each exon junction glyph to view a pop-up window containing read counts from modENCODE and/or Baylor datasets and click to go to a FlyBase exon junction Sequence Feature Report. 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 Proteomes Alignment of peptide sequences identified in various developmental proteomes to the reference genome. Each peptide glyph is hyperlinked to a FlyBase Sequence Feature Report with the peptide sequence. Data obtained from: Casas-Vila et al., 2017, Cao et al., 2020.
Peptide Atlas Alignment of peptide sequences determined by mass spectroscopy, derived from polypeptides isolated from the sequenced strain at various developmental stages and from various tissues. 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

Expression

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.

modENCODE transcriptomes
Developmental stages, unique reads modENCODE_mRNA-Seq_U Dataset report. These tracks contain RNA-Seq expression data for several different stages of development.
Tissues
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.
Knoblich lab- L3 CNS transcriptomes
L3 CNS neuron
Knoblich_mRNA_L3_CNS_neuron
L3 CNS neuroblast
Knoblich_mRNA_L3_CNS_neuroblast
Oliver lab- SRA Aggregated RNA-Seq
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 transcriptomes 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

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.

Lai lab transcriptomes
Developmental stages, stranded small RNA-Seq (Lai lab) See Lai_shortRNA-Seq_profiles_development Dataset Report.
Tissues, stranded small RNA-Seq (Lai lab) See Lai_shortRNA-Seq_profiles_tissues Dataset Report.
Cell lines
Schneider and embryonic-derivedSee Lai_shortRNA-Seq_profiles_cells Dataset Report.
Imaginal disc-derived See Lai_shortRNA-Seq_profiles_cells Dataset Report.
CNS-, ovary- and blood-derived See Lai_shortRNA-Seq_profiles_cells Dataset Report.
FlyAtlas2 transcriptomes 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.

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