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Ensembl data and displays for A. gambiae are made possible through a joint effort by the Ensembl Group and VectorBase, a NIAID Bioinformatics Resource Center. Further details, as well as additional A. gambiae and other vector-specific data, can be found at VectorBase.org.
The genome assembly presented here (AgamP3, February 2006) is a revised assembly based on the whole genome shotgun assembly of the PEST strain of Anopheles gambiae produced by the The International Anopheles Genome Project and described in Holt et al (October 2002) and Mongin et al. AgamP3 incorporates improvements to the placement of scaffolds on chromosomes, the designation of some scaffolds and scaffold segments as alternative assemblies ("haplotypes") and the designation of some scaffolds as probable bacterial contaminants (details at VectorBase).
The total length of scaffold sequence in the AgamP3 genome assembly is 264 Mbp of which 87% has been assigned to and ordered on chromosomes. Chromosome arms 2L, 2R, 3L, 3R, and X are represented by 12, 23, 22, 10, and 13 large scaffolds respectively. Two 'artificial chromosomes' have been made with scaffolds concatenated together in size order: 'Y_unplaced' with 55 small scaffolds assigned to the Y chromosome, and 'UNKN' with the remaining 8029 unplaced scaffolds.
The annotation of AgamP3 has been carried out by VectorBase using the Ensembl system. Gene prediction utilised updated mappings of protein sets and Anopheles ESTs to the genome together with data provided by the research community, a limited number of models manually annotated by VectorBase, and selected ab initio predictions. 'Known' genes are those which could be named using entries from the community gene symbol database or from Uniprot.
misc_* tables and updates of xrefs (including GO).The following non-schema changes have been made to the core database.
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Protein/Protein
Updates of orthologues/paralogues and families to include the new species and gene sets announced.
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| Assembly: | AgamP3, Feb 2006 |
| Genebuild: | VectorBase, Oct 2005 |
| Database version: | 40.3c |
| Known genes: | 1,163 |
| Novel genes: | 12,114 |
| tRNA genes: | 450 |
| miRNA genes: | 38 |
| Gene exons: | 53,338 |
| Gene transcripts: | 14,089 |
| Base Pairs: | 278,253,050 |
| Golden Path Length: | 273,093,681 |
| Most common InterPro domains: | Top 40 Top 500 |
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