Ensembl mobile site help

Things to know when navigating the Ensembl mobile site

Search box

Use the search box at the top right of all Ensembl views to search for a gene, phenotype, sequence variant, and more.

Top navigation

Touch MENU button to open the main menu and touch again to close.

Touch MENU

Left hand side menu

Touch the left menu icon () or swipe right to open the side menu and touch anywhere outside the menu or touch the cross icon or swipe left to close.

The ? icon

Touch the icon to get help

And don't forget to send us your comments using the feedback link inside the main menu.

EnsemblEnsembl Home

Large yellow croaker assembly and gene annotation

Assembly

The L_crocea_2.0 assembly was submitted by BGI on November 2018. The assembly is on chromosome level, consisting of 16,979 contigs assembled into 9,998 scaffolds. From these sequences, 24 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 277,487 while the scaffold N50 is 27,037,660.

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

AssemblyL_crocea_2.0, INSDC Assembly GCA_000972845.2, Nov 2018
Base Pairs657,939,657
Golden Path Length657,939,657
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedApr 2019
Genebuild releasedMay 2019
Genebuild last updated/patchedMay 2019
Database version100.20

Gene counts

Coding genes22,929
Non coding genes770
Small non coding genes729
Long non coding genes13
Misc non coding genes28
Pseudogenes258
Gene transcripts66,805

Other

Genscan gene predictions40,548

About this species

HASH(0x22996e38)