Ensembl Chimp

Karyotype

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About the Chimp genome

Assembly

This site provides a data set based on the November 13th 2003 4x shotgun assembly from the Chimpanzee Sequencing Consortium headed by the GSC (St. Louis) and The Broad Institute (MIT).

The assembly is a merge of a "modified de novo" (MDN) assembly from the ARACHNE group, which used the human genome to establish that particular inserts were not chimeric, and a separate "validated chimp-on-human" (VCH) assembly which took the chimp reads which align uniquely to human, formed them into contigs via this alignment, and removed contigs which failed a two-haplotype consistency check.

Shared reads were used to align the two assemblies to each other, and where they were consistent, the VCH sequence was transferred to the MDN, resulting in the released merged assembly.

This release of the assembly has the following properties:

• 361782 contigs, having N50 length 15.7 Kb
• contig length total 2.73 Gb, spanning 3.02 Gb
• 37849 supercontigs, having N50 length 8.6 Mb (not including gaps).

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 by UCSC using BLASTz. These alignments were used to transfer human gene structures (Human Build 34d) to chimpanzee. Owing to the low coverage commensurate with a 4x shotgun, there will inevitably be some mis-assemblies and mis-placements; however with better data it is expected that most chimpanzee genes will align with near-identical human genes.

• More information about the chimpanzee gene build.

What's New in Ensembl 39

Pan troglodytes News

• Updated miRNA sets
  Micro-RNA data sets have been updated in a wide range of Ensembl species, including Chicken, Dog, Cow, Chimp, Macaque, Rat, Tetraodon, Fugu, Xenopus, and Ciona intestinalis.

General News

• Bug fixes
  In order to fix some problems with the store() method in Gene and Transcript, DBEntryAdaptor and AttributeAdaptor now require a gene/transcript/translation dbID rather than object as one of their arguments (please see POD for details).
• Multiple versions of genes
  The schema and API have been changed to allow multiple versions of genes, transcripts and exons, for better integration with Otter (the Ensembl-based database schema used as a backend for Havana).
  Read more...
• New MLAGAN groups
  A new 3-way MLAGAN Primate group has been created, containing Human, Chimp and macaque.
  Read more...
• Compara - whole genome alignments, syntenies and families
  

  Whome Genome Alignments.
  Read more...

More news...

Statistics

Assembly:	PanTro 1.0, Nov 2003
Genebuild:	Ensembl, Mar 2005
Database version:	39.3c
Known genes:	15,032
Projected genes:	5,191
Novel genes:	2,252
RNA genes:	3,725
Genscan gene predictions:	129,588
Gene exons:	226,066
Gene transcripts:	43,000
Base Pairs:	2,733,948,177
Golden Path Length:	2,733,223,211
Most common InterPro domains:	Top 40 Top 500