Kangaroo rat assembly and gene annotation

Assembly

This is the first release of the low-coverage 1.85X assembly of the kangaroo rat (dipodomys ordii). The genome sequencing is provided by the Human Genome Sequencing Center, Baylor College of Medicine and assembly is provided by the Broad Institute.

The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for supercontigs is 31.47 kb and is 4.29 kb for contigs. The total number of bases in supercontigs is 2.05 Gb and in contigs is 1.84 Gb.

Gene annotation

Owing to the fragmentary nature of this preliminary assembly, it was necessary to arrange some scaffolds into "gene-scaffold" super-structures, in order to present complete genes. There are 6907 such gene-scaffolds, with identifiers of the form "GeneScaffold_1".

Mammalian Genome Project

Dipodomys ordii is one of 24 mammals that will be sequenced as part of the Mammalian Genome Project, funded by the National Institutes of Health (NIH). A group of species were chosen to maximise the branch length of the evolutionary tree while representing the diversity of mammalian species. Low-coverage 2X assemblies will be produced for these mammals and used in alignments for cross-species comparison. The aim is to increase our understanding of functional elements, especially in the human genome.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblydipOrd1, Jul 2008
Database version76.1
Base Pairs1,844,961,421
Golden Path Length2,165,294,802
Genebuild byEnsembl
Genebuild methodProjection build
Genebuild startedNov 2008
Genebuild releasedFeb 2009
Genebuild last updated/patchedMay 2010

Gene counts

Coding genes

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

15,798
Small non coding genes

Small 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 small non coding genes: miRNA, miscRNA, rRNA, tRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.

3,036
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.

1,010
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.19,899

Other

Genscan gene predictions143,756