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 37

Pan troglodytes News

• Projected gene names
  

  Gene names have been projected across orthologues in the form.
  Read more...

• SSAHA2
  Transcript-based SSAHA2 servers are now available for all species. Go to BlastView and select SSAHA2 from the Search Tool box.
• UniProt updates
  Support has been added for variable splice UniProt records by adding an external db with a display label of "UniprotKB/SpliceVariant" to the external_db table on all databases.
  Read more...
• GeneSeqalignView
  This new view is based on GeneSeqView, with the added ability to align the given sequence with one or more species.
  Read more...
• Bug fix to Transcript.pm
  Transcript.pm; is_known() was returning true if the transcript had a display_xref set, which is both incorrect and inconsistent with the is_known() method in Gene.pm. The new behaviour is to return true if the transcript's status is KNOWN.

More news...

Statistics

Assembly:	PanTro 1.0, Nov 2003
Genebuild:	Ensembl, Mar 2005
Database version:	37.3a
Known genes:	19,838
Novel genes:	2,637
RNA genes:	3,476
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