Ensembl Opossum

Karyotype

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About the Opossum genome

Assembly

This site presents the latest genome assembly (MonDom4) of the gray short-tailed opossum, released in January 2006.

The assembly, from the Broad Institute, has a base coverage of approximately 7.33X, constructed from 5180 supercontigs, having N50 length 59,092,948. The total contig length is 3,501,487,001, spanning 3,573,120,728 bases (including gaps).

Annotation

The gene set for Opossum was built using a modified version of the standard Ensembl genebuild pipeline. The species-specific sequence resources (opossum cDNA and protein) are very limited, so the vast majority of gene models are based on genewise alignments of proteins from other species. Most of the proteins being aligned were from species genetically distant to opossum. To improve the accuracy of models generated from these proteins, the genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. Opossum and human cDNAs were aligned and used to add UTRs to the genewise predictions where possible. The gene models were assessed by generating sets of potential orthologs to genes from other mammalian species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs, and exonerate used to build new gene models for these based on the human ortholog peptide sequence.

What's New in Ensembl 43

Monodelphis domestica News

There is no Monodelphis domestica-specific news this release.

General News

• A faster ContigView
  ContigView now displays information faster. Each open panel in ContigView is prepared in parallel, and then returned to the page when complete. This results in faster page loads.
• New - Table view
  In ContigView you can now click on the name of a feature alignment track and select 'DAS Table View' (or for DAS tracks 'view DAS reponse') from the zmenu.
  Read more...
• New search option
  It is now possible to select whether to search either the Ensembl website or the EBI site when using Ensembl search.
• Changes to Xrefs
  The following changes have been made to xrefs for Release 43:
  • We have made improvements to EntrezGene xrefs, to allow for better handling of names and synonyms
  • Incorporation of new Illumina probe data as xrefs.
    Read more...
  • API changes to ensembl-functgenomics
    A new DataSet API has been developed aimed at making web display much easier.

  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