The October 2004 frog (Xenopus tropicalis) whole genome shotgun (WGS) assembly version 3.0 was sequenced and assembled by the DOE Joint Genome Institute (JGI).

Sample position queries

A genome position can be specified by the accession number of a sequenced genomic clone, an mRNA or EST, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list provides examples of various types of position queries for the frog genome. See the User's Guide for more information.

   Genome Browser Response:

scaffold_3 Displays all of scaffold 3
scaffold_3:1-2000000 Displays first 2 million bases of scaffold_3
scaffold_3:100000+2000 Displays a region of scaffold_3 that spans 2000 bases, starting with position 100000
CR848332 Displays location of mRNA with GenBank accession CR848332
AL680330 Displays location of EST with GenBank accession AL680330
scaffold_1001.8 Displays location of Genscan gene prediction with identifier scaffold_1001.8

dazl Lists dazl mRNAs
zinc finger Lists zinc finger mRNAs
asashima Lists mRNAs deposited by scientists named Asashima
Papalopulu,N. Lists mRNAs deposited by co-author N. Papalopulu

Use this last format for author queries. Although GenBank requires the search format Papalopulu N, internally it uses the format Papalopulu,N..

Assembly Details

Assembly version 3.0 of WGS reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 7.4X. After trimming for vector and quality, 19.1 million reads assembled into 27,064 scaffolds totaling 1.63 Gbp. Roughly half the genome is contained in 392 scaffolds, each of at least 1.2 Mb in length. For more information about this assembly, see the JGI X. tropicalis website.

The xenTro1 sequence and annotation data can be downloaded from the UCSC Genome Browser FTP server or downloads page. These data have specific conditions for use.

Many thanks to JGI and the other institutions who contributed to the sequencing and mapping effort for this release. The xenTro1 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.