(Photo courtesy of Genoscope)
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Tetraodon nigroviridis (Photo courtesy of Genoscope) |
The Tetraodon nigroviridis V8 assembly (March 2007) was provided by Genoscope, Evry, France, in collaboration with the Broad Institute, Cambridge, MA, USA. The project was supported by the Consortium National de Recherche en Genomique and the National Human Genome Research Institute (NHGRI). For more information about this assembly, see ASM18073v1 in the NCBI Assembly database.
A genome position can be specified by the accession number of an mRNA or EST, a chromosome range, or keywords from the GenBank description of an mRNA. The following list provides examples of various types of position queries for the Tetraodon 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 Tetraodon. See the User Guide for more information.
| Request: |
Genome Browser Response: | |
| chr1 | Displays all of chromosome 1 | |
| chr1:1-200000 | Displays first two hundred thousand bases of chromosome 1 | |
| chr1:100000+2000 | Displays a region of chromosome 1 that spans 2000 bases, starting with position 100000 | |
| CR731623 | Displays region containing Tetraodon mRNA with GenBank accession number CR731623 | |
| BC083244 | Displays region containing Other mRNA with GenBank accession BC083244 | |
| IL11 | Lists mRNAs related to IL11 (interleukin-11) | |
| T-cell receptor | Lists mRNAs for T-cell receptor genes in GenBank | |
| kinase | Lists many kinase mRNAs | |
| tyrosine kinase | Lists only tyrosine kinases | |
| breast cancer | Lists mRNAs associated with breast cancer | |
| abkevich | Lists mRNAs deposited by scientist named Abkevich | |
| Hashimoto,H. | Lists mRNAs deposited by co-author H. Hashimoto | |
| Use this last format for author queries. Although GenBank requires the search format Hashimoto H, internally it uses the format Hashimoto,H. | ||
The Tetraodon was sequenced through a collaboration between Genoscope and the Broad Institute using a whole genome sequencing strategy. The sequence data were assembled using Arachne, resulting in a sequence coverage of about 7.9X. This assembly, which has been improved from the v7 assembly by using a new fosmid library of around 6x of clone coverage, contains 1,849 placed scaffolds (N50 size 1349163) and 15,296 unplaced scaffolds (N50 size 54038) covering more than 90% of the genome. For detailed sequencing and assembly information, see the Genoscope Tetraodon nigroviridis assembly page.
Downloads of the Tetraodon data and annotations may be obtained from the UCSC FTP site or Downloads page. These data have been freely provided by Genoscope for use in the UCSC Genome Browser with specific conditions for use. For more information about the Tetraodon nigroviridis project, see the Genoscope website.
The tetNig2 annotation tracks were generated by UCSC and its collaborators. See the credits page for a detailed list of the organizations and individuals who contributed to this release.