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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 multiple alignments are being extended with new species and 2X genomes.
Canonical transcripts have been defined for all genes in the core databases.
|Assembly:||CHIMP2.1, Mar 2006|
|Genebuild:||Ensembl, Feb 2008|
|Known protein-coding genes:||2,647|
|Projected protein-coding genes:||15,906|
|Novel protein-coding genes:||1,276|
|Genscan gene predictions:||126,539|
|Golden Path Length:||3,350,417,645|
|Most common InterPro domains:||Top 40 Top 500|