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Mmul_1 is a preliminary assembly of the rhesus monkey, Macaca
mulatta using whole genome shotgun (WGS) reads from small and medium
insert clones.
Several WGS libraries, with
inserts of 2-4 kb and 10 kb, fosmids with ~35kb inserts, and BACs with 180kb inserts were used to produce the data.
The release was produced by the Macaque Genome Sequencing Consortium, led by the Baylor College of Human Medicine, melding three separate complementary assemblies (created using the Atlas, Celera and PCAP systems). This involved iteratively splitting likely chimeric scaffolds and joining together existing scaffolds where possible. Chimeric scaffolds (<100 total) were identified by breaks in synteny with the human genome, which were confirmed to be artefacts by the other assemblies.
This is a draft sequence and may contain errors so users should exercise caution. Typical errors in draft genome sequences include misassemblies of repeated sequences, collapses of repeated regions, and unmerged overlaps (e.g. due to polymorphisms) creating artificial duplications. However base accuracy in contigs (contiguous blocks of sequence) is usually very high with most errors near the ends of contigs. [More about the assembly].
The gene set for macaque was built using the ensembl pipeline. The species-specific resources for macaque are relatively limited, so we decided to take a combined approach utilizing macaque's great similarity to human to aid our annotation efforts. The gene structures are mainly based on alignments to human and macaque protein data. Both macaque and human cDNAs were used to add UTR structures, and finally gene predictions based on Uniprot proteins and human cdnas were used to fill gaps in the annotation.
The multiple alignments are being extended with new species and 2X genomes.
Read more...
Canonical transcripts have been defined for all genes in the core databases.
Read more...
| Assembly: | MMUL 1.0, Feb 2006 |
| Genebuild: | Ensembl, Jan 2006 |
| Database version: | 50.10i |
| Known protein-coding genes: | 874 |
| Projected protein-coding genes: | 17,505 |
| Novel protein-coding genes: | 3,526 |
| Pseudogenes: | 1,762 |
| RNA genes: | 4,224 |
| Genscan gene predictions: | 125,893 |
| Gene exons: | 246,943 |
| Gene transcripts: | 38,146 |
| Base Pairs: | 3,093,871,206 |
| Golden Path Length: | 3,097,179,960 |
| 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. This is a mirror site of Ensembl from BGI-SZ.
