Ensembl Chimpanzee

Karyotype

Click on a chromosome for a closer view

About the Chimp genome

Assembly

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:

• 246876 contigs, having N50 length 30.8 Kb
• contig length total 2.92 Gb
• chromosome length total 3.35 Gb

Chromosome numbering

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.

• More information about the chimp chromosome numbering scheme.

Annotation

The genome was aligned to human NCBI36 by UCSC using BLASTz. These alignments were used to transfer human ensembl gene structures (Human Build 36b) to chimpanzee. 94% of the genes were mapped by direct projection while only 0,1% of the human ensembl genes were not mapped, the remaining 5.9% were aligned directly into the chimpanzee genome by using Exonerate (G. Slater et al., BMC Bioinformatics. 2005 6:31).

• More information about the chimpanzee gene build.

What's New in Ensembl 43

Pan troglodytes News

There is no Pan troglodytes-specific news this release.

General News

• A faster ContigView
  ContigView now displays information faster. Each open panel in ContigView is prepared in parallel, and then returned to the page when complete. This results in faster page loads.
• New - Table view
  In ContigView you can now click on the name of a feature alignment track and select 'DAS Table View' (or for DAS tracks 'view DAS reponse') from the zmenu.
  Read more...
• New search option
  It is now possible to select whether to search either the Ensembl website or the EBI site when using Ensembl search.
• Changes to Xrefs
  The following changes have been made to xrefs for Release 43:
  • We have made improvements to EntrezGene xrefs, to allow for better handling of names and synonyms
  • Incorporation of new Illumina probe data as xrefs.
    Read more...
  • API changes to ensembl-functgenomics
    A new DataSet API has been developed aimed at making web display much easier.

  More news...

Statistics

* Total number of base pairs = sum of lengths of DNA table

** Reference assembly (Golden path) length = sum of non-redundant top level seq regions