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Example Data Points

This release of X.tropicalis data is assembled into scaffolds, so there are no chromosomes available to browse. Use the BLAST and SSAHA buttons in the menu bar, left, to locate data.

A few example data points:

• Scaffold: Scaffold_1
• Scaffold: Scaffold_20
• Scaffold: Scaffold_40

About the X. tropicalis genome

Assembly

The Xenopus tropicalis genome assembly version 4.1 [August 2005] is the fourth of a series of preliminary assembly releases by the JGI that are planned as part of the ongoing X. tropicalis genome project. This Ensembl website presents the sequence data provided by the JGI.

The reads were assembled using JAZZ, the JGI assembler, producing a genome of approximately 1.5 Gb. The assembly contains 19,501 scaffolds with an average coverage of 7.65X. Roughly half of the genome is contained in 272 scaffolds, all at least 1.56 Mb in length. In this update to the 4.0 assembly, some scaffolds showing homology to a known prokaryotic contaminant as well as non-cellular or vector contamination have been removed - see the JGI website (above) for more information.

Annotation

The gene set for Xenopus tropicalis was built using a modified version of the standard Ensembl pipeline. Both Xenopus tropicalis and Xenopus laevis proteins were used to predict gene structures. cDNAs from both species were used to add UTRs. Gene predictions were also based on Xenopus tropicalis cDNAs manually annotated in the July 2005 jamboree. Finally, gene predictions based on UniProt proteins were used to fill gaps in the annotation.

What's New in Ensembl 50

Xenopus tropicalis News

• Non-coding genes
  These have been updated for most species, including an miRNA update and HGNC names where possible.

General News

• Canonical Transcripts
  

  Canonical transcripts have been defined for all genes in the core databases.
  Read more...

• SSAHA
  From release 50 we will no longer be providing SSAHA sequence search. If you wish to run your own SSAHA sequence search you can download the files to generate the search hashes from our FTP site.
• Projections of gene names and GO terms
  These have been done as usual, between a variety of species.
• Stored peptide stats
  In order to improve efficiency on ProtView, peptide statistics are now calculated in advance and stored as translation attributes, instead of being calculated on the fly.

More news...

Statistics

How the statistics are calculated