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Northern spotted owl assembly and gene annotation

Assembly

The Soccid_v01 assembly was submitted by California Academy of Sciences on September 2017. The assembly is on scaffold level, consisting of 28,713 contigs assembled into 8,108 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 159,062 while the scaffold N50 is 3,983,020.

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

AssemblySoccid_v01, INSDC Assembly GCA_002372975.1, Sep 2017
Base Pairs1,255,541,132
Golden Path Length1,255,541,132
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedFeb 2020
Genebuild releasedMay 2020
Genebuild last updated/patchedFeb 2020
Database version101.1

Gene counts

Coding genes16,814
Non coding genes479
Small non coding genes410
Long non coding genes66
Misc non coding genes3
Pseudogenes108
Gene transcripts24,189

Other

Genscan gene predictions57,944

About this species

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