Tasmanian devil assembly and gene annotation

Assembly

This site displays the DEVIL7.0 assembly (GCA_000219685.1) of the Tasmanian devil (Sarcophilus harrisii) genome. The genome sequence and assembly are provided by the Wellcome Trust Sanger Institute and Illumina. 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 1847.19 kb and is 20.13 kb for contigs. The total number of bases in supercontigs is 3.17 Gb and in contigs is 2.93 Gb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000189315.1

Gene annotation

The Ensembl genome annotation pipeline was used to identify genes. Models built from Tasmanian devil proteins and cDNAs have been given priority over predictions from other vertebrate species. 5,663 transcript models made from paired end Illumina RNA-Seq were added into the gene set where they added a novel model or splice variant. RNA-Seq data was also used to add UTR to non species specific models. The total gene set contains 20,419 genes including pseudogenes and ncRNAs.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyDevil_ref v7.0, INSDC Assembly GCA_000189315.1, Mar 2011
Database version78.7
Base Pairs2,931,556,433
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

3,174,709,637
Genebuild byEnsembl
Genebuild methodMixed strategy build
Genebuild startedMar 2011
Genebuild releasedSep 2011
Genebuild last updated/patchedDec 2011

Gene counts

Coding genes

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

18,788
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, scRNA, snlRNA, snoRNA, snRNA, 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. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

1,490
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.

178
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.24,072

Other

Genscan gene predictions45,416