The Apr. 2006 Drosophila melanogaster draft assembly (BDGP Release 5) was provided by the Berkeley Drosophila Genome Project (BDGP). The Release 5.12 annotations (Oct. 2008) were provided by FlyBase. For more information about this assembly, see Release 5 in the NCBI Assembly database.
A genome position can be specified by the accession number of an mRNA or EST, a chromosomal range, an Ensembl transcript ID, or keywords from the GenBank description of an mRNA. The following list provides examples of valid position queries for the Drosophila genome. Note that some position queries (e.g. "huntington") may return matches to the mRNA records of other species. In these cases, the mRNAs are mapped to their homologs in Drosophila. See the User's Guide for more information.
| Request: |
Genome Browser Response: |
|
| chr2L | Displays all of chromosome 2L (Click here for a list of chromosomes) | |
| chrYHet:1-200000 | Displays first two hundred thousand bases of chromosome Y heterochromatin | |
| FBgn0015351 | Displays region containing the gene with FlyBase ID FBgn0015351 | |
| CG6588 | Displays region containing the gene with Berkeley Drosophila Genome Project gene ID CG6588 | |
| AY122244 | Displays region containing D. melanogaster mRNA with GenBank accession number AY122244 | |
| BQ103726 | Displays region containing D. melanogaster EST with GenBank accession BQ103726 | |
| p53 | Lists mRNAs related to the p53 tumor suppressor | |
| PDZ | Lists mRNAs for PDZ domain proteins | |
| zinc finger | Lists many zinc finger mRNAs | |
| huntington | Lists mRNAs associated with Huntington's disease | |
| zahler | Lists mRNAs deposited by scientist named Zahler | |
| Celniker,S. | Lists mRNAs deposited by co-author S. Celniker | |
| Use this last format for author queries. Although GenBank requires the search format Celniker S, internally it uses the format Celniker,S.. | ||
The Release 5 D. melanogaster assembly combines euchromatic and heterochromatic sequence.
The six euchromatic arms (chr2L, chr2R, chr3L, chr3R, chr4, chrX) were sequenced and assembled by BDGP from a combination of BAC and whole genome shotgun data, and have been finished to high quality. All euchromatic sequence has been compared to the restriction digest fingerprints in multiple enzymes for validity. The details of this analysis will be described in a forthcoming publication.
4.7 Mb of heterochromatic sequence from the Drosophila Heterochromatin Genome Project (DHGP) is available on chr2LHet, chr2RHet, chr3LHet, chr3RHet, chrXHet, and chrYHet. Scaffolds that could not be unambiguously mapped to a chromosome arm have been concatenated into chrU. chrUextra contains 34,630 small scaffolds produced by the Celera shotgun assembler that could not be consistently joined with larger scaffolds. Because some of the chrUextra data are of low quality, researchers are encouraged to contact either BDGP or DHGP for further details on this resource. For more information on this assembly, see the Release 5 assembly release notes.
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. The D. melanogaster browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.