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Elephant shark assembly and gene annotation

Assembly

The Callorhinchus_milii-6.1.3 assembly was submitted by Institute of Molecular and Cell Biology, Singapore on December 2013. The assembly is on scaffold level, consisting of 67,421 contigs assembled into 21,204 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 46,577 while the scaffold N50 is 4,521,921.

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

AssemblyCallorhinchus_milii-6.1.3, INSDC Assembly GCA_000165045.2, Dec 2013
Base Pairs974,498,586
Golden Path Length974,498,586
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedSep 2018
Genebuild releasedJun 2019
Genebuild last updated/patchedMar 2019
Database version100.613

Gene counts

Coding genes19,415
Non coding genes380
Small non coding genes358
Long non coding genes1
Misc non coding genes21
Pseudogenes289
Gene transcripts49,990

Other

Genscan gene predictions45,388

About this species

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