GBrowse evidence tiers help
Last Updated: 10 Aug 2009
A general description of GBrowse functionality may be found on the GBrowse page.
The sections below describe the data tiers specific to the FlyBase presentation of D. melanogaster sequence-localized stock components available from stock centers. Additional evidence and data tiers may be found in the primary GBrowse view of the D. melanogaster genome.
|Aberrations in Stock Collections|
Stock Center Aberrations: deleted segment Indicated in red. When one or more aberrations overlap the region being viewed, a darker red bar 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.
The Bloomington Deficiency Kit:
The Bloomington Deficiency Kit is a set of stocks defined by the Bloomington Drosophila Stock Center (BDSC) to provide maximal coverage of the genome with the minimal number of deficiencies having molecularly mapped breakpoints. The BDSC Deficiency Kit also includes deficiencies with breakpoints that have not been mapped molecularly, primarily to provide coverage of gaps between the molecularly defined deficiencies. Since the ends of cytologically characterized deficiencies cannot be placed on the genome map with certainty, the BDSC has defined segments of these deficiencies that fill gaps in molecularly defined coverage for GBrowse display. The endpoints of gap filling segments are derived primarily from overlapping deficiency endpoints and complementation with annotated genes.
BDSC Deficiency Kit deleted segment Molecularly defined deficiencies are indicated in red. Click the deficiency to go to the Aberration Report.
BDSC Deficiency Kit gap filling or haploinsufficiency flanking segment Segments of cytologically defined deficiencies that fill gaps between molecularly defined deficiencies or flank haploinsufficient loci are indicated in yellow. Click the segment icon to go to the Aberration Report for the full deficiency.
|Gene Model Features|
Gene Span Indicated in light blue. 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.
mRNA Indicated in peach/tan. Shows the exon (wider bars) and intron (narrow bars) structure of each annotated coding transcript, with direction of transcription indicated; introns indicated as narrow lines. Hyperlinked to Transcript Report; if label option is on, shows FlyBase symbol.
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 Sorsa polytene maps for a collection of EM micrographs of chromosome regions aligned to Bridges' maps.
Non coding RNA Indicated in peach/tan. Extent of transcribed region corresponding to an annotated non-coding RNA (intron structure not shown). Hyperlinked to Transcript Report; if label option is on, shows FlyBase symbol.
tRNA Indicated in white. Extent of transcribed region corresponding to an annotated tRNA (intron structure not shown). Hyperlinked to Transcript Report; if label option is on, shows FlyBase symbol.
|Transgene Insertions in Stock Collections|
Transgene insertion sites are indicated by blue triangles (which indicate orientation of the insertion) or diamonds (if orientation is not known). An insertion indicated by a downward-pointing triangle 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 a upward-pointing triangle 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. Hyperlinked to a FlyBase Stock Report; if label option is on, shows FlyBase symbol.
If the "Flip" option is selected, the orientations of the insertion triangles do not change and thus will be incorrect.
Insertions, Bloomington Insertions in the Bloomington Drosophila Stock Center collection.
Insertions, Harvard Insertions in the Exelixis Collection at Harvard Medical School.
Insertions, Kyoto Insertions in the Drosophila Genetic Resource Center collection.