FB2014_04, released July 21st, 2014
 
 

A Database of Drosophila Genes & Genomes

CytoSearch Query

Search Options

Genes:

  • Genes (mapped to the sequence)
  • Genes (mapped, but not to the sequence)

Insertions:

  • Insertions (sequence mapped)
  • Insertions (cytology mapped)

Aberrations:

  • Deleted segments (sequence mapped)
  • Deleted segments (cytology mapped)
  • Duplicated segments (sequence mapped)
  • Duplicated segments (cytology mapped)
  • Inversion breakpoints (cytology mapped)
  • Transposition and translocation breakpoints (cytology mapped)
  • Other breakpoints (cytology mapped)

Show only features with stocks available Group features by type
CytoSearch Help

CytoSearch lists are regional maps of the Drosophila melanogaster genome incorporating both sequence-based and cytology-based map data. Sequence-based data trumps cytology when both are available, cytology trumps meiotic data when both are available, and estimated cytology is used when only meiotic data are available. The FlyBase correspondence tables for cytological and sequence level maps are used to estimate cytology from sequence range and sequence range from cytology, for both the underlying data and the query input.

hide Examples of Search Queries
  • Category
  • Example
  • Notes
  • Cytolocation
  • 67C, 12A-D, 43, 92A1
  • Range limit is 2 Mbp, but your browser may timeout even within that range if volume of data is too large. If you encounter a page-not-found error, try narrowing the range or selecting fewer features.
  • Sequence region
  • 2R:2206427..2374251
  • All features whose directly determined or estimated sequence range overlaps this range will be returned.
  • FlyBase gene ID
  • FBgn0003174
  • All features whose directly determined or estimated sequence range overlaps the range of this gene will be returned.
  • Gene symbol
  • cnn, alphaTub67C
  • This is a case-insensitive search of valid gene symbols. If the gene symbol is unique without regard to case, all features whose sequence range overlaps the range of this gene will be returned. Use the case-sensitive option for valid symbols that are distinguished from another valid symbol only by case.
  • Gene symbol
    (case-sensitive)
  • w, W, B, b
  • Use this option for gene symbols that differ from other valid symbols only by case.
  • Gene synonym
  • CG3619, omb, ri
  • This is a case-insensitive search of both valid symbols and synonyms. If your input is not a unique symbol or synonym, a list of options with valid gene symbols will be displayed; use the valid gene symbol with the ‘Gene symbol’ menu option in a new CytoSearch query.
  • Annotation DB ID/ symbol/ synonym
    • CG3757-RA
    • FBtr0088962
    • AAF59274.2
    • CG11101-PA
    • FBpp0088036
    • FBan0011101
  • Any valid symbol or ID in the annotation database can be used with this option. This is a direct query of the chado PostgreSQL database, primarily intended for debugging use by FlyBase (but knock yourself out).
hide Other Features
  • Data on results page can be downloaded as a tab-separated-values file.
  • Sequence range on results page links to GBrowse, which provides a graphical display of annotation and
    insertions data for that region.
  • Gene, insertion and aberration symbols on results page link to their respective FlyBase reports.
hide Known Problems
  • Heterochromatic cytological locations are not supported. Heterochromatic bands will be supported when the heterochromatin sequence data are added to the annotation database.
  • Some features are present in duplicate, under different symbols (the invalid symbol is unlinked). This should be corrected with the next update of the annotation database.
  • Some transgene insertions for which FlyBase has sequence-based map data appear as cytologically mapped insertions. This should be corrected with the next update of the annotation database.
  • Only cytology-based aberration data and estimated cytology for sequence-based aberration data are currently available to CytoSearch. Observed sequence ranges will be added for the DrosDel and Exelixis deficiency collections in the near future.
  • Some genes without annotation data, e.g., Bl, are missing from the dataset. This should be corrected with the next update of the annotation database.