Ensembl Chimpanzee

Karyotype

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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 41

Pan troglodytes News

• New chimp assembly and genebuild
  

  A new Ensembl genebuild has been completed on the latest chimpanzee assembly from the Broad Institute (PanTro 2.1).
  Read more...

• Variation databases
  

  Ensembl 41 includes the first release of variation data for chimp, to accompany the new assembly and genebuild.
  Read more...

• Compara - whole genome alignments and syntenies
  

  Whole Genome Alignments

  Chimp (Pan troglodytes)

  Owing to the new Chimp assembly and genebuild, there is a new MLAGAN primate 3-way alignment of human, chimp and macaque.
  Read more...

• RNA updates
  

  Ensembl RNA data has been updated as follows:

  • New ncRNAs for Zebrafish, Chimp, Medaka, Elephant, Rabbit, Armadillo and Tenrec
  • Updated miRNAs for all chordates.

General News

• New animated tutorials
  A selection of Ensembl tutorials are now available online as Flash-animated presentations (with popup notes instead of a soundtrack).
  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