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Three-toed box turtle assembly and gene annotation

Assembly

The T_m_triunguis-2.0 assembly was submitted by McDonnell Genome Institute - Washington University School of Medicine on September 2018. The assembly is on scaffold level, consisting of 106,051 contigs assembled into 52,260 scaffolds. 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 76,614 while the scaffold N50 is 24,249,581.

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

AssemblyT_m_triunguis-2.0, INSDC Assembly GCA_002925995.2, Sep 2018
Base Pairs2,571,267,249
Golden Path Length2,571,267,249
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJul 2019
Genebuild releasedSep 2019
Genebuild last updated/patchedSep 2019
Database version100.2

Gene counts

Coding genes22,095
Non coding genes1,002
Small non coding genes850
Long non coding genes139
Misc non coding genes13
Pseudogenes135
Gene transcripts33,673

Other

Genscan gene predictions89,767

About this species

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