Fruitfly assembly and gene annotation

Assembly

The data displayed on the Ensembl Fruitfly Drosophila melanogaster site is a compendium of data from the Berkeley Drosophila Genome Project (BDGP), FlyBase and the Drosophila Heterochromatin Genome Project (DHGP). The genomic sequence is the BDGP assembly, release 5 (April 2006).

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000001215.1

Gene annotation

The annotations are imported from FlyBase release 5.46 (FB2012_04, dated 6 July 2012). No additional gene build has been carried out, however BLAST hits and protein features have been computed, and cross-references to other data sources were updated in Ensembl release 70 (January 2013).

Variation Data

The Ensembl Fruitfly Drosophila melanogaster variation database has been produced using data from release 1.0 of the "50 genomes" data set from the Drosophila Population Genome Project. The data set contains over 6.7 million SNPs from two populations, one comprising 37 lines from north Carolina and the other comprising 15 lines from Malawi.

This species (and other invertebrates, including 11 other drosophilid species) are also available from our sister site, Ensembl Metazoa

References

The genome sequence of Drosophila melanogaster
Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF et al.
Science. 2000. 287(5461):2185-95

Evolution of genes and genomes on the Drosophila phylogeny
Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W et al.
Nature. 2007 Nov 8. 450(7167):203-18

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyBDGP 5, INSDC Assembly GCA_000001215.1, Apr 2006
Database version76.546
Base Pairs168,736,537
Golden Path Length168,736,537
Genebuild byFlyBase
Genebuild methodImport
Genebuild startedApr 2012
Genebuild releasedApr 2012
Genebuild last updated/patchedApr 2012

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

13,937
Small non coding genes1,331
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

175
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.29,173

Other

Genscan gene predictions19,451
Snap gene prediction21,795
Short Variants6,794,867