Photo courtesy of USDA (Agricultural Research Service)
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Meleagris gallopavo Photo courtesy of USDA (Agricultural Research Service) |
The Dec. 2009 Meleagris gallopavo draft assembly (TGC Turkey_2.01 (NCBI project 62397, GCA_000003025.2)) was produced by the Turkey Genome Consortium. For more information about this assembly, see Turkey_2.01 in the NCBI Assembly database.
A genome position can be specified by the accession number of a sequenced genomic supercontig, 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 turkey genome. See the User's Guide for more information.
| Request: | Genome Browser Response: | |
|---|---|---|
| chrZ | Displays all of chromosome Z | |
| chr3:1-1000000 | Displays first million bases of chr 3 | |
| chr3:23000+4000 | Displays a region of chr 3 that spans 4000 bases, starting with position 23,000 | |
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| BX950328 | Displays region of mRNA with GenBank accession number BX950328 | |
| BU335953 | Displays region of EST with GenBank accession AF070471 on chr 9 | |
| CWNT-8C | Displays region of genome with gene symbol CWNT-8C | |
| NM_204735 | Displays the region of genome with RefSeq identifier NM_204735 | |
| 374180 | Displays the region of genome with Entrez Gene identifier 374180 | |
| EU177006;AY873804 | Displays region between genome landmarks, such as the mRNA markers EU177006 and AY873804. This syntax may also be used for other range queries, such as between uniquely determined ESTs, STSs, refSeqs, etc. | |
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| homeobox caudal | Lists mRNAs for caudal homeobox genes | |
| zinc finger | Lists many zinc finger mRNAs | |
| kruppel zinc finger | Lists only kruppel-like zinc fingers | |
| jarvis | Lists mRNAs deposited by scientist named Jarvis | |
| Taguchi,T. | Lists mRNAs deposited by co-author T. Taguchi | |
| Use this last format for author queries. Although GenBank requires the search format Taguchi T, internally it uses the format Taguchi,T.. | ||
This assembly sequenced DNA from a female turkey "Nici" on two next-generation sequencing platforms, Roche 454 and Illumina GAII. The draft assembly has approximately 1.1 GB with 917 MB assigned to 32 specific chromosomes: chr1-30, chrW, and chrZ. The mitochondrial sequence chrM was obtained from GenBank accession NC_010195. This assembly covers about 90 percent of the genome and is based on approximate 5X genome coverage in 454 reads and 25X coverage in GAII reads. The total sequence length is approximately 1.1 Gb, of which about 0.12 Gb are 'N' bases in gaps, resulting in approximately 1.08 Gb of ACGT bases.
For more information about the techniques and the assembly process used to produce this assembly, see the GenBank accession record and the paper:
Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Blomberg Le Ann, Bouffard P, Burt DW, Crasta O, Crooijmans RP et al. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol. 2010 Sep 7;8(9). PMID: 20838655; PMC: PMC2935454
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The turkey 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 the success of this release.