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 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

• More information about the chimpanzee gene build.

What's New in Ensembl 50

Pan troglodytes News

• New variation databases
  Ensembl 50 includes a new orangutan variation database, with SNPs called by Ensembl using ssaha2/pileup from reference assembly reads, plus remapping of SNPs to the new assemblies for tetraodon and cow.
  Read more...
• Non-coding genes
  These have been updated for most species, including an miRNA update and HGNC names where possible.
• Chimp
  The new release of Ensembl Chimp includes additional chimp-specific genes and the latest human gene set.
• Multiple alignments
  

  The multiple alignments are being extended with new species and 2X genomes.
  Read more...

General News

• Canonical Transcripts
  

  Canonical transcripts have been defined for all genes in the core databases.
  Read more...

More news...

Statistics

Assembly:	CHIMP2.1, Mar 2006
Genebuild:	Ensembl, Feb 2008
Database version:	50.21i
Known protein-coding genes:	2,647
Projected protein-coding genes:	15,906
Novel protein-coding genes:	1,276
Pseudogenes:	471
RNA genes:	4,633
Genscan gene predictions:	126,539
Gene exons:	234,984
Gene transcripts:	34,623
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

How the statistics are calculated