The November 2004 Drosophila pseudoobscura genome assembly is based on the FlyBase Release 1.0 assembly. A list of the 17 chromosome/linkage group sequences can be found here.

Sample position queries

A genome position can be specified by a chromosome/group coordinate range, the accession number of an mRNA or RefSeq entry, a gene name, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the D. pseudoobscura 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 D. pseudoobscura. See the User's Guide for more information.

Request:
    Genome Browser Response:
chr4_group3 Displays all of linkage group chr4_group3.
chr2:1-50,000 Displays first 50,000 bases of chromosome 2.

AF025805 Displays region of genome aligning to mRNA with GenBank accession AF025805
dock Displays region of genome aligning to gene with identifier dock (a D. melanogaster gene)
NM_057677 Displays region of genome aligning to RefSeq accession with identifier NM_057677 (a D. melanogaster RefSeq entry)

zinc finger Lists zinc finger mRNAs
kruppel zinc finger Lists only kruppel-like zinc fingers
huntington Lists candidate genes associated with Huntington's disease
zahler Lists mRNAs deposited by scientist named Zahler
Zeng,L.W. Lists mRNAs deposited by co-author L.W. Zeng

Use this last format for author queries. Although GenBank requires the search format Zeng LW, internally it uses the format Zeng,L.W.

Assembly details

The Flybase Release 1.0 assembly contains complete chromosome sequences (chr2 and chr3), linkage groups (chr4_group*, chrXL_group* and chrXR_group*), and a concatenation of unplaced contigs (chrU). A list of all 17 sequences can be found here. For more details about the Release 1.0 assembly and the annotations provided by FlyBase, see the release notes.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. The dp3 annotation tracks were generated by UCSC, Flybase and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to the success of this release.

GenBank Pipeline Details

For the purposes of the GenBank alignment pipeline, this assembly is considered to be: well-ordered.