New Release: FB2015_03, released June 26th, 2015
FB2015_03, released June 26, 2015
 
 

A Database of Drosophila Genes & Genomes

GBrowse MegaView help

 

MegaView contains tracks which require a very ‘zoomed out’ view. With MegaView, entire chromosome arms can be viewed at once, allowing large features such as aberrations and duplications to be viewed in their entirety.

Links to other views:

Reference Genome Annotations
Gene Span Shows the total extent of the transcribed region of an annotated gene (including non-coding genes), with direction of transcription indicated. No transcript substructure is shown; corresponds to the entire extent defined by all annotated transcripts. Hyperlinked to Gene Report; label shows FlyBase gene symbol.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
Transcript SO:0000673 Shows the exon (wider bars) and intron (black line) structure of each annotated coding transcript, with direction of transcription indicated. Hyperlinked to Transcript Report; if label option is on, shows FlyBase symbol.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
CDS Shows extent of sequence encoding each specific polypeptide, with direction of transcription indicated; introns indicated as narrow lines. Hyperlinked to Polypeptide Report; if label option is on, shows FlyBase symbol.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
Natural TE 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; if label option is on, shows FlyBase symbol.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
Repeat region Regions of genomic repeats and low complexity DNA sequences, as computed using RepeatMasker and RepeatRunner (FBrf0194515)
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
General
Estimated Cytological band Approximate extent of the classical cytological chromosome bands described by Bridges. See Computed cytological data for a detailed description of how this computed cytological location is calculated. See Sorsa polytene maps for a collection of EM micrographs of chromosome regions aligned to Bridges' maps.
Available in these data source views:
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
3-frame translation (forward) If zoomed out (greater than 400bp), shows ticks at sites of stop codons for the three frames on the forward strand. If zoomed in (400bp or less), shows predicted translations for each frame, using single-letter amino acid code.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
3-frame translation (reverse) If zoomed out (greater than 400bp), shows ticks at sites of stop codons for the three frames on the reverse strand. If zoomed in (400bp or less), shows predicted translations for each frame, using single-letter amino acid code.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
DNA/GC Content If zoomed out (greater than 100bp) shows a graphic of GC content calculated over 10bp intervals. If zoomed in (100bp or less), shows the double-stranded DNA sequence.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
Mapped Mutations
Transgene insertion site SO:0000368 Indicated by blue triangles with an arrow or diamonds with no arrow. An insertion indicated by a downward-pointing triangle and 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 by an upward-pointing triangle and 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 indicated with a blue diamond has an unknown orientation. For all insertions, if the estimated insertion site is larger than 10 nucleotides, there are short dashes on either side of the triangle or diamond. In those cases, see the Insertion Report for more information about localization. Insertions are hyperlinked to their respective Insertion Report. NOTE: If the "Flip" option is selected, the orientations of the insertion triangles do not change and thus will be incorrect. For a guide on how to work out the orientation of an insertion relative to a transcript of interest, see this short powerpoint presentation.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
Point mutation SO:1000008 A single nucleotide has been changed into another nucleotide. Location of mutation is indicated with a grey bar and labeled with the FlyBase allele symbol.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Sequence variant 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 grey bar and labeled with the FlyBase allele symbol.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Uncharacterized change in nucleotide sequence SO:1000007 The nature of the nucleotide substitution is either uncharacterized or only partially characterized. The location of the mutation is indicated with grey bar and labeled with the FlyBase allele symbol.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Aberration junction 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). Generally the exact breakpoint location is unknown and the feature indicates a range within which the breakpoint has been mapped. References and supporting information available in the "Mapped features and mutations" section of the Gene Report for a nearby gene; genetic data available in the Aberration Report.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Complex substitution SO:1000005 The mutation occurred from a mutation event that cannot be determined from the observed DNA change. Location of mutation is indicated with a grey bar and labeled with the FlyBase allele symbol.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Indels SO:1000032 The junction where an insertion or deletion of one or more nucleotides occurred. Location of mutation is indicated with a grey bar and labeled with the FlyBase allele symbol. In the case of deletions, the extent of the deletion is indicated by a grey bar. In the case of insertions, the location of the nucleotide(s) insertion is indicated by a vertical grey line.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Rescue fragment SO:0000411 Locations of transgenic rescue fragment reported in the literature. Labeled with FlyBase allele symbol designation. Reference and supporting information available in the "Mapped features and mutations" section of the Gene Report; genetic data available in the Allele Report.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Blast Hit
BLAST HSP If entry into GBrowse was via a linked hit using the FlyBase BLAST tool, the extent of the aligned region is shown as a vertical grey bar that extends through all the GBrowse tiers.
Available in these data source views:
  • Gene Models/Evidence
  • Expression/Regulation
  • MegaView
  • Gene Disruptions, Stocks, and Reagents