Opossum assembly and gene annotation

Assembly

This site presents the latest genome assembly (MonDom5) of the grey short-tailed opossum, released in October 2006. Scaffold and contigs remain the same as the previous release; only mapping changes have been made.

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).

The genome assembly represented here corresponds to GCF_000002295.2

Gene annotation

The current gene set for Opossum is projected from the MonDom4 geneset, which 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.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblymonDom5, INSDC Assembly GCF_000002295.2, Oct 2006
Database version75.5
Base Pairs3,501,660,299
Golden Path Length3,605,631,728
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedFeb 2007
Genebuild releasedApr 2007
Genebuild last updated/patchedAug 2012

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

21,327
Short non coding genes

Short non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as short non coding genes: miRNA, miscRNA, rRNA, tRNA, ncRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the short non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.

1,850
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

722
Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.24,882

Other

Genscan gene predictions109,135
Short Variants1,398,945

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