New Release: FB2015_02, released May 4th, 2015
FB2015_02, released May 4, 2015
 
 

A Database of Drosophila Genes & Genomes

GBrowse Gene Disruptions, Stocks and Reagents view help

 

Gene Disruptions, Stocks, and Reagents contains information relevant to mutations which have been localized to the sequence, reagents such as RNAi amplicons, and stock center data. Stock center data includes both the Bloomington Deficiency Kit lines as well as transgene insertions available from the various stock centers.

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
Aberrations
Deleted segment Indicated in red. 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.
Available in these data source views:
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
Duplicated segment. Indicated in blue. When one or more aberrations cover the region being viewed, a darker blue bar labeled "Spanning aberration(s)" will be seen. When moused-over, a pop-up box containing all the aberrations that cover the region being viewed will appear. Click one of the aberration symbols to go to the Aberration Report.
Available in these data source views:
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
Stock Center Data: Aberrations
Stock center aberration: 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.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Stock center aberration: duplicated segment Indicated in blue. When one or more aberrations cover the region being viewed, a darker blue bar labelled "Spanning aberration(s)" will be seen. When moused-over, a pop-up box containing all the aberrations that cover the region being viewed will appear. Click one of the aberration symbols to go to the Aberration Report.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
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.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
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.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Transgene insertions in Stock Collections
Insertions, Bloomington Insertions in the Bloomington Drosophila Stock Center collection.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Insertions, Harvard Insertions in the Exelixis Collection at Harvard Medical School.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Insertions, Kyoto Insertions in the Drosophila Genetic Resource Center collection.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Clones
Tiling BACs Tiling BAC Indicated by narrow gray bar. BAC genomic clones used by the Berkeley Drosophila Genome Project as part of the minimal tiling path used for determination of the D. melanogaster genomic sequence (FBrf0155823).
Available in these data source views:
  • MegaView
  • Gene Disruptions, Stocks, and Reagents
Aligned cDNAs cDNA and other aligned sequences Indicated in dark green. D. melanogaster cDNA sequences submitted to the sequence databases; shows the exon (wider bars) and intron (narrow bars) structure, and direction of transcription. Sequences submitted prior to 2003 aligned using sim4 (FBrf0105376) or sim4tandem (sim4 modified by S. Shu, BDGP) to Release 3 by the BDGP and promoted to Releases 4 and 5 by FlyBase. Sequences submitted since 2003 aligned to Releases 4 and 5 by NCBI and submitted to FlyBase.
Available in these data source views:
  • Gene Models/Evidence (under track grouping, 'Aligned Evidence')
  • Expression/Regulation (under track grouping, 'Aligned Evidence')
  • Gene Disruptions, Stocks, and Reagents
Reagents and Data
DRSC RNAi amplicons FBlc0000026 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 DGRC-1 library collection report.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
VDRC RNAi reagent FBlc0000041, FBlc0000055 Segment used to create inverted repeat in RNAi construct from the Vienna Drosophila RNAi Center (FBrf0200327). Corresponding allele and construct symbols share the alphanumeric identifier.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
TRiP RNAi amplicons FBlc0000048 FBlc0000153 FBlc0000185 FBlc0000186 FBlc0000416 Segment used to create inverted repeat in RNAi construct from the DRSC TRiP project. Corresponding allele and construct symbols share the alphanumeric identifier.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
NIG-Fly RNAi amplicons FBlc0000491 Segment used to create inverted repeat in RNAi construct from the Japanese National Institute of Genetics. Corresponding allele and construct symbols share the alphanumeric identifier.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
BKNAmplicons FBlc0000030 RNAi amplicons from the GenomeRNAi database. Extents of the amplicons are indicated with an orange bar.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
HFAAmplicons FBlc0000031 RNAi amplicons from the GenomeRNAi database. Extents of the amplicons are indicated with an orange bar.
Available in these data source views:
  • Gene Disruptions, Stocks, and Reagents
Putative brain enhancers (Pfeiffer et al) FBlc0000201
Available in these data source views:
  • Expression/Regulation (under track grouping 'Noncoding Features')
  • 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