Photo: Yerkes National Primate Research Center, Emory University
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"Clint" - Pan troglodytes Photo: Yerkes National Primate Research Center, Emory University |
The October 2010 chimpanzee (Pan troglodytes) browser displays data from the 6X whole genome shotgun draft assembly (CGSC 2.1.3, GCA_000001515.3) produced by the Chimpanzee Sequencing and Analysis Consortium. This version was assembled and organized by the Genome Center at Washington University from data generated at the Washington University St. Louis School of Medicine and the Broad Institute. For more information about this assembly, see Pan_troglodytes-2.1.3 in the NCBI Assembly database.
The v2.* assemblies use a chromosomal numbering scheme that reflects orthology between the human and chimpanzee chromosomes. For details, see the Assembly details section below and the Genome Browser FAQ.
A genome position can be specified by the HUGO Gene Nomenclature Committee gene name of a human RefSeq, the accession number of an EST or mRNA, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the chimpanzee genome. See the User's Guide for more information.
| Request: |
Genome Browser Response: |
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| chr22 | Displays all of chromosome 22 | |
| chr2a:11,250,001-12,250,000 | Displays a million bases of chromosome 2a, beginning at
base 11,250,001. Note that chromosome 2 in this assembly has been split into two parts: 2a and 2b. |
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| chr2a:11,250,001+2000 | Displays a region of chr 2a that spans 2000 bases, starting at position 11,250,001 | |
| BRCA1 | Displays a list of genomic regions where human RefSeq gene BRCA1 (or features associated with BRCA1) aligns | |
| AF115459 | Displays region of genome with mRNA with GenBank accession number AF115459 | |
| 348 | Displays the region of genome with Entrez Gene identifier 348 | |
| pseudogene mRNA | Lists transcribed pseudogenes, but not cDNAs | |
| sialic acid | Lists mRNAs and RefSeqs with GenBank keywords sialic acid | |
| huntington | Lists mRNAs associated with Huntington's disease | |
| Paabo,S. | Lists mRNAs deposited by co-author S. Paabo | |
| Use this last format for author queries. Although GenBank requires the search format Paabo S, internally it uses the format Paabo,S.. | ||
This assembly covers about 97 percent of the genome and is based on 6X sequence coverage. It comprises 192,898 contigs with an N50 length of 44 kb and 33,990 supercontigs with an N50 length of 8.4 Mb. Improvements introduced with the 2.1.3 assembly include the addition of over 300,000 finishing reads and the merging in of 640 finished BACS. Approximately 49,000 additional merges were made in this assembly as compared with the 2.1 assembly.
The whole genome shotgun data were derived primarily from the donor Clint, a captive-born male chimpanzee from the Yerkes Primate Research Center in Atlanta, GA, USA. The sequence data were assembled and organized by the Genome Center at Washington University from underlying whole genome shotgun data generated at the Washington University School of Medicine and the Broad Institute. For detailed information about the assembly process, see the sequencing and analysis discussion in the GenBank accession record. To read more about the chimpanzee genome sequencing program, see the Washington University Pan troglodytes web page and the National Institutes of Health NIH News summary of the chimpanzee analysis paper.
The chromosomal numbering scheme reflects a standard that preserves orthology with human chromosomes. Proposed by E.H. McConkey in 2004, the numbering convention was subsequently endorsed by the International Chimpanzee Sequencing and Analysis Consortium. This standard assigns the identifiers "2a" and "2b" to the two chimp chromosomes that fused in the human genome to form chromosome 2. Note that the genome assembly shown in the Nov. 2003 panTro1 Genome Browser retains the older numbering scheme in which these chromosomes are numbered 12 and 13. To view a table showing the correspondence between human and chimp chromosomes, see the FAQ.
Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. The Chimp browser 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.
The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature. 2005 Sep 1;437(7055):69-87. PMID: 16136131
Huang X, Yang SP, Chinwalla AT, Hillier LW, Minx P, Mardis ER, Wilson RK. Application of a superword array in genome assembly. Nucleic Acids Res. 2006;34(1):201-5. PMID: 16397298; PMC: PMC1325203
Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes. Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. PMID: 14500911; PMC: PMC208784
McConkey EH. Orthologous numbering of great ape and human chromosomes is essential for comparative genomics. Cytogenet Genome Res. 2004;105(1):157-8. PMID: 15218271
Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC, Haussler D, Miller W. Human-mouse alignments with BLASTZ. Genome Res. 2003 Jan;13(1):103-7. PMID: 12529312; PMC: PMC430961