Photo courtesy of J.R. Kaplan
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Macaca mulatta Photo courtesy of J.R. Kaplan |
The Jan. 2006 rhesus macaque (Macaca mulatta) draft assembly — v.1.0, Mmul_051212 — was obtained from the Baylor College of Medicine Human Genome Sequencing Center (BCM HGSC). The sequencing and assembly of the rhesus macaque genome is a project of the Macaque Genome Sequencing Consortium led by the BCM HGSC, in collaboration with the Genome Sequencing Center at Washington University School of Medicine in St. Louis and the J. Craig Venter Institute Joint Technology Center. For more information about this assembly, see Mmul_051212 in the NCBI Assembly database.
This assembly, rheMac2, is based on the genome of an Indian-origin female. The rheMac3 assembly is based on the genome of a five-year old female originating from the South-West of China.
A genome position can be specified by the accession number of a sequenced mRNA or EST, a scaffold coordinate range, a gene identifier, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the rhesus genome. See the User's Guide for more information.
| Request: |
Genome Browser Response: |
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| chr19 | Displays all of chromosome 19 | |
| chr19:1-100000 | Displays the first 100,000 bases of chromosome 19 | |
| chr19:100000+2000 | Displays a region of chr 19 that spans 2000 bases, starting with position 100000 | |
| CO582753 | Displays EST with GenBank accession CO582753 | |
| BT019700 | Displays human mRNA with GenBank accession BT019700 aligning to rheMac2 assembly | |
| PRNP | Lists PRNP genes in other species aligned to rheMac2 chromosome 10 | |
| leptin | Lists mRNAs associated with leptin receptors | |
| zinc finger | Lists many zinc finger mRNAs | |
| kruppel zinc finger | Lists only kruppel-like zinc fingers | |
| Scinicariello,F. | Lists mRNAs deposited by co-author F. Scinicariello | |
| Use this last format for author queries. Although GenBank requires the search format Scinicariello F, internally it uses the format Scinicariello,F.. | ||
The groups in the Macaque Genome Sequencing Consortium carried out preliminary assemblies of the genome data using different and complementary approaches. The resulting data were combined into a single, high-density "melded" assembly by a team at J. Craig Venter Institute. This collaboration made use of published macaque maps (Rogers, 2006; Murphy, 2005), the BAC fingerprint map from the Michael Smith Genome Sciences Centre, and the human genome reference sequence.
Several whole genome shotgun (WGS) libraries, with inserts of 2-4 kb and 10 kb, fosmids with ~35 kb inserts, and BACs with 180 kb inserts were used to produce the clone-end sequence data. Approximately 20.1 million reads were used in the assembly, representing about 14.9 Gb of sequence and about 5.1X coverage of the (clonable) macaque genome. The assemblers produced a set of contigs and scaffolds. Scaffolds include sequence contigs that could be ordered and oriented with respect to each other as well as isolated contigs that could not be linked (single contig scaffolds or singletons). The N50 of the contigs is 25.7 kb and the N50 of the scaffolds is 5.87 Mb. (The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.) The total length of all contigs is 2.87 Gb. When the gaps between contigs in scaffolds are included, the total span of the assembly is 3.01 Gb.
For general information about the rhesus monkey sequencing project, see the Baylor Rhesus Monkey Project web page.
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The rheMac2 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.