The Chimp chromosome numbers have been changed to the new primate standard proposed by E.H.
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The compara orthology build has been updated to include the new Opossum genome, and chimp dnafrag names have been changed to take account of the re-numbering of the Chimp chromosomes (see Chimp news for more information).
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All variation databases now include the new consequence_type 'REGULATORY_REGION'.
Features which have accompanying Gene locations, e.g. some AffyProbes, now display a table of gene names and descriptions at the top of the view page. See an example....
Click on a chromosome for a closer view
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:
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.
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.
| Assembly: | PanTro 1.0, Nov 2003 |
| Genebuild: | Ensembl, Mar 2005 |
| Database version: | 35.3 |
| Gene predictions : | 22,475 |
| 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 |
© 2009 WTSI / EBI. Ensembl is available to download for public use - please see the code licence for details.
