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 44

Pan troglodytes News

• Variation updates
  All species with variation data now have a failed_variation table. Also, in species that have duplicate variations (with the same mapping but different IDs), these have been put into the variation_synonym table.

General News

• ncRNAs for Ensembl chordates
  All Ensembl genebuild databases (i.e. excluding the imported invertebrate databases for mosquitoes, fruit fly, worm and yeast) have been updated with new ncRNA data.
• Compara updates
  

  Pairwise alignments

  • Platypus (Ornithorhynchus anatinus) OANA5 BLASTZ_NET vs Mus musculus (NCBIM36)
  • Cat (Felis catus) BLASTZ_NET vs Canis familiaris (BROADD2)
  • Treeshrew (Tupaia belangeri) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Hedgehog (Erinaceus europaeus) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Opossum (Monodelphis domestica) BROAD5 (new assembly) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Bushbaby (Otolemur garnetti) (2X genome, new species) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Ground squirrel (Spermophilus tridecemlineatus) (2X genome, new species) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Little brown bat (Myotis lucifugus) (2X genome, new species) BLASTZ_NET vs Homo sapiens (NCBI36)

  Multiple alignments

  PECAN (vertebrates) 10 ways.
  Read more...

• Schema changes
  There have been no major schema changes this release, however we are starting to systematically work through the schema to make sure that all column types are appropriate for the data they are likely to hold.
  Read more...
• 
  

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