About the Drosophila melanogaster (Fruit fly) assembly

The D. melanogaster Release 3.1 (Jan. 2003) annotated genome sequence was provided by the Berkeley Drosophila Genome Project (BDGP). The 116.8 Mb euchromatic sequence - which is virtually gap-free and of high accuracy - contains 6 euchromatic chromosome arms represented by 13 scaffolds with a total of 37 sequence gaps. The sequence quality of this release has an estimated error rate of less than one in 100,000 base pairs in the unique portion of the sequence, and less than one in 10,000 base pairs in the repetitive portion. The Release 3.1 sequence was reannotated using the Apollo Genome Annotation and Curation Tool.

For more information about Release 3.1, see the assembly release notes and a list of online refereed articles from Genome Biology.

Downloads of the Drosophila data and annotations may be obtained from the UCSC Genome Browser FTP site.

Sample position queries

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 various types of 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 help.

Request:
   Genome Browser Response:

chr2L Displays all of chromosome 2L
chrYh:1-200000 Displays first two hundred thousand bases of chromosome Yh (h = heterochromatin random reads)

FBgn0058440 Displays region containing the gene with FlyBase ID FBgn0058440
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 entry authors -- even though Genbank searches require Celniker S format, GenBank entries themselves use Celniker,S. internally.