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:
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.
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.
There is no Xenopus tropicalis-specific news this release.
Ensembl release 50 will occur in July (rather than in April as originally scheduled).
Read more...
We are now using the new enredo-pecan-ortheus (EPO) pipeline for 7-way alignments (placental mammals).
Read more...
| Assembly: | JGI 4.1, Aug 2005 |
| Genebuild: | Ensembl, Nov 2005 |
| Database version: | 49.41i |
| Known protein-coding genes: | 5,440 |
| Projected protein-coding genes: | 8,165 |
| Novel protein-coding genes: | 4,418 |
| RNA genes: | 946 |
| Genscan gene predictions: | 66,517 |
| Gene exons: | 192,682 |
| Gene transcripts: | 27,711 |
| Base Pairs: | 1,510,886,836 |
| Golden Path Length: | 1,510,886,836 |
| Most common InterPro domains: | Top 40 Top 500 |
© 2008 WTSI / EBI. Ensembl is available to download for public use - please see the code licence for details.
