Photo courtesy of Dr. Art Arnold (UCLA Department of Physiological Science)
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Taeniopygia guttata Photo courtesy of Dr. Art Arnold (UCLA Department of Physiological Science) |
The Jul. 2008 Taeniopygia guttata draft assembly was produced by the Genome Sequencing Center at the Washington University in St. Louis (WUSTL) School of Medicine. UCSC's version taeGut1 corresponds to the WUSTL v3.2.4 assembly.
A genome position can be specified by the accession number of a sequenced genomic region, an mRNA or EST, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the Zebra finch genome. See the User's Guide for more information.
| Request: | Genome Browser Response: | |
|---|---|---|
| chrZ | Displays all of chromosome Z | |
| chr3:1-500,000 | Displays first 500,000 bases of chr 3 | |
| chr3:228,000+30000 | Displays a region of chr 3 that spans 30,000 bases, starting with position 228,000 | |
| | ||
| DQ216330 | Displays region of mRNA with GenBank accession number DQ216330 | |
| CK308913 | Displays region of EST with GenBank accession CK308913 on chr Z | |
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| pseudogene mRNA | Lists transcribed pseudogenes, but not cDNAs | |
| zinc finger | Lists many zinc finger mRNAs | |
| kruppel zinc finger | Lists only kruppel-like zinc fingers | |
| jarvis | Lists mRNAs deposited by scientist named Jarvis | |
| Wada,K. | Lists mRNAs deposited by co-author K. Wada | |
| Use this last format for author queries. Although GenBank requires the search format Wada K, internally it uses the format Wada,K.. | ||
The zebra finch DNA used for the shotgun sequencing and the BAC and cosmid libraries was derived from a single male domesticated zebra finch. The initial assembly was generated using PCAP with approximately 6X coverage. About 1.0 Gb of the 1.2-Gb genome has been ordered and oriented along 33 chromosomes and one linkage group. The chromosome names are based on their homologous chromosomes in the chicken (Gallus gallus). For more assembly details, as well as a cross reference table of zebra finch and chicken chromosome names, see the WUSTL assembly page.
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or Downloads page. These data have specific conditions for use.
The zebra finch browser annotations 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.