Click on a chromosome for a closer view
This site provides a data set based on the March
2006 Pan_troglodytes-2.1 6x shotgun assembly from the Chimpanzee Sequencing
Consortium headed by the GSC (St. Louis) and The Broad Institute (MIT).
The chimpanzee 2.1 assembly is a merge of the initial 4X made in collaboration with the Broad Institute at MIT and Harvard and an additional (2X) whole genome coverage from the WUGSC (St. Louis) utilizing a combination of whole genome plasmid reads as well as fosmid and BAC end sequences.
This release of the assembly has the following properties:
As of Release 35 we have changed the chimpanzee chromosome numbering to match the new primate standard proposed by E.H. McConkey (Cytogenetics and Genome Research, 105:157-158) and endorsed by the International Chimpanzee Genome Consortium.
The genome was aligned to human NCBI36 by UCSC using BLASTz. These alignments were used to transfer human ensembl gene structures (Human Build 36f) to chimpanzee. 92% of the chimp-specific proteins were aligned to the chimp genome in a first layer of annotation. The 8% missing correspond to fragments or proteins that contain stop codons in the assembled genome
The following changes have been made to the Ensembl API.
Read more...
| Assembly: | CHIMP2.1, Mar 2006 |
| Genebuild: | Ensembl, May 2007 |
| Database version: | 46.21e |
| Known genes: | 2,585 |
| Projected genes: | 16,558 |
| Novel genes: | 1,429 |
| Pseudogenes: | 872 |
| RNA genes: | 4,034 |
| Genscan gene predictions: | 126,540 |
| Gene exons: | 239,056 |
| Gene transcripts: | 34,039 |
| SNPs: | 1,520,077 |
| Base Pairs*: | 2,928,563,828 |
| Golden Path Length**: | 3,350,417,645 |
| Most common InterPro domains: | Top 40 Top 500 |
* Total number of base pairs = sum of lengths of DNA table
** Reference assembly (Golden path) length = sum of non-redundant top level seq regions
© 2008 WTSI / EBI. Ensembl is available to download for public use - please see the code licence for details.
