This release of Loxodonta africana data is assembled into scaffolds, so there are no chromosomes available to browse.
A few example data points :
This is the first release of the low-coverage 2X assembly of the Elephant (Loxodonta africana). The genome sequencing and assembly is provided by the Broad Institute.
The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for supercontigs is 41 kb and is 2.8 kb for contigs. The total number of bases in supercontigs is 3.69 Gb and in contigs is 2.30 Gb.
Owing to the fragmentary nature of this preliminary assembly, it was necessary to arrange some scaffolds into "gene-scaffold" super-structures, in order to present complete genes. There are 7883 such gene-scaffolds, with identifiers of the form "GeneScaffold_1".
Loxodonta africana is one of 16 mammals that will be sequenced as part of the Mammalian Genome Project, funded by the National Institutes of Health (NIH). A group of species were chosen to maximise the branch length of the evolutionary tree while representing the diversity of mammalian species. Low-coverage 2X assemblies will be produced for these mammals and used in alignments for cross-species comparison. The aim is to increase our understanding of functional elements, especially in the human genome.
The multiple alignments are being extended with new species and 2X genomes.
Read more...
The Blastz-net alignments have been updated for the following species.
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Canonical transcripts have been defined for all genes in the core databases.
Read more...
| Assembly: | BROAD E1, May 2005 |
| Genebuild: | Ensembl, Aug 2006 |
| Database version: | 50.1e |
| Known protein-coding genes: | 17 |
| Projected protein-coding genes: | 12,874 |
| Novel protein-coding genes: | 2,826 |
| Pseudogenes: | 3,030 |
| RNA genes: | 1,570 |
| Genscan gene predictions: | 107,250 |
| Gene exons: | 216,909 |
| Gene transcripts: | 18,747 |
| Base Pairs: | 2,295,548,473 |
| Golden Path Length: | 3,717,990,240 |
| Most common InterPro domains: | Top 40 Top 500 |
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