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Tasmanian devil assembly and gene annotation

Assembly

The mSarHar1.11 assembly was submitted by SC on November 2019. The assembly is on chromosome level, consisting of 445 contigs assembled into 106 scaffolds. From these sequences, 8 chromosomes have been built. 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 the contigs is 62,339,597 while the scaffold N50 is 611,347,268.

Gene annotation

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments.
Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold.
Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.
lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement, please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblymSarHar1.11, INSDC Assembly GCA_902635505.1, Nov 2019
Base Pairs3,086,657,325
Golden Path Length3,086,657,325
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2019
Genebuild releasedJun 2020
Genebuild last updated/patchedJun 2020
Database version104.1

Gene counts

Coding genes19,228
Non coding genes4,336
Small non coding genes984
Long non coding genes3,330
Misc non coding genes22
Pseudogenes228
Gene transcripts43,475

Other

Genscan gene predictions40,469

About this species

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