"Clint" - Pan troglodytes
Photo: Yerkes National Primate Research Center, Emory University

The 13 Nov. 2003 chimpanzee (Pan troglodytes) Arachne assembly — NCBI Build 1 Version 1 — was produced by the Chimpanzee Sequencing and Analysis Consortium.

Sample position queries

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, a scaffold (supercontig) 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.

   Genome Browser Response:

chr23 Displays all of chromosome 23
chr6:118,000,000-119,000,000 Displays a million bases of chromosome 6, beginning at 118 million bases offset from p arm telomere
scaffold_1:1-1000000 Displays first million bases of genome positioned at scaffold 1 of the assembly
chr6:1000000+2000 Displays a region of chr 6 that spans 2000 bases, starting with position 1000000

BRCA1 Displays region of genome where human RefSeq gene BRCA1 (or features associated with BRCA1) aligns
AF115459 Displays region of genome with mRNA with GenBank accession number AF115459
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..

Assembly details

This assembly covers about 95 percent of the genome and is based on 4X sequence coverage. It is composed of 361,782 contigs with an N50 length of 15.7 kb, and 37,849 supercontigs having an N50 length of 8.6 Mb (not including gaps). The total contig length is 2.73 Gb, spanning 3.02 Gb.

Background information on the chimp genome sequencing project and the initial news release about the chimp assembly can be found on the NHGRI website. For more information about the assembly process used for this draft genome, see the Genome Browser Assembly track details page. To view a chromosome correspondence table between chimp and human chromosomes, click here. Note: this assembly does not support the new chromosomal numbering convention in which the identifiers "2a" and "2b" have been assigned to the two chimp chromosomes that align to human chromomsome 2. Instead, it retains the older numbering scheme that assigns the identifiers 12 and 13 to these chimp chromosomes. The new convention has been implemented in assemblies subsequent to panTro1. See the FAQ for a table showing the correspondence between human and chimp chromosomes.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. The complete set of sequence reads is available at the NCBI trace archive. The chimpanzee 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 the success of this release and conditions for use of the data.

Blat searches on chrUn_random are not supported at the current time, but will be available soon.

GenBank Pipeline Details

For the purposes of the GenBank alignment pipeline, this assembly is considered to be: low-coverage.