Monodelphis domestica Photo courtesy of Paul Samollow, Southwest Foundation for Biomedical Research, San Antonio. (NHGRI Press Photos)

The January 2006 opossum (Monodelphis domestica) draft assembly was produced by The Broad Institute.

Sample position queries

A genome position can be specified by a scaffold coordinate range, an mRNA or EST, or keywords from the GenBank description of an mRNA. The following list provides examples of various types of position queries for the opossum genome. See the User's Guide for more information.

Request:		Genome Browser Response:
chrX		Displays all of chromosome X
chr2:1-1000000		Displays first 1,000,000 bases of chr 2
chr2:1000000+2000		Displays a region of chr 2 that spans 2000 bases, starting with position 1,000,000
AF049761		Displays region of mRNA with GenBank accession number AF049761
CLOCK		Displays a list of genomic regions showing tBLASTn alignment of peptides from human CLOCK gene
EC091554		Displays region of EST with GenBank accession EC091554
NM_001033969		Displays the region of genome with RefSeq identifier NM_001033969, the BCRA1 gene
immunoglobulin		Lists immunoglobulin regions
immunoglobulin light chain kappa		Lists only immunoglobulin light chain kappa mRNAs
miller		Lists mRNAs deposited by scientists named Miller
Miska,K.B.		Lists mRNAs deposited by co-author K.B. Miska

Use this last format for author queries. Although GenBank requires the search format Miska KB, internally it uses the format Miska,K.B.

Assembly Details

This draft of the opossum genome has approximately 6.5X coverage. The assembly length is nearly 3.57 billion bp including gaps (3.50 billion bp without gaps) contained on chromosomes 1-8, X, and Un. The N50 of the scaffolds including gaps is 59,775,228 bp; the N50 without gaps is 107,990. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer.

The Broad Institute reports the following statistics for the monDom4 assembly:

• Total number of contigs in assembly: 72,811
• Total number of supercontigs in assembly: 5,344
• Placed contigs: 62,871
• Placed supercontigs: 207
• Unplaced contigs: 9,940
• Total bases in chromosomes 1 thru 8 and X: 3,431,385,331
• Total bases in chromosome Un: 174,229,318
• Number of gap bases (==N) in chromosomes 1 thru 8 and X: 88,330,281
• GC/AT ratio in chromosomes 1 thru 8 and X: 1,258,733,983/2,084,321,067 = 0.6039
• GC/AT ratio in chromosome Un: 65,676,956/92,911,214 = .7069

The monDom4 sequence and annotation data can be downloaded from the Genome Browser FTP server or Downloads page. These data have specific conditions for use.

Many thanks to The Broad Institute for the opossum assembly data. The monDom4 annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to this release.

GenBank Pipeline Details