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

Zebra mbuna assembly and gene annotation

Assembly

The M_zebra_UMD2a assembly was submitted by Broad Institute on April 2018. The assembly is on chromosome level, consisting of 2,331 contigs assembled into 1,690 scaffolds. From these sequences, 22 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 1,407,748 while the scaffold N50 is 32,660,920.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000238955.5

Gene annotation

The zebra mbuna (Maylandia zebra) is a species of cichlid endemic to Lake Malawi in Africa. This species can reach a length of 11.3 cm (4.4 in). It feeds on aufwuchs, a surface layer of mostly algal material that grows on rocks. This cichlid is a mouthbrooder and the female broods the eggs in her mouth for about three weeks. This fish can sometimes be found in the aquarium trade.

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

AssemblyM_zebra_UMD2a, INSDC Assembly GCA_000238955.5, Apr 2018
Base Pairs957,485,262
Golden Path Length957,485,262
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.2

Gene counts

Coding genes27,187
Non coding genes1,386
Small non coding genes1,324
Long non coding genes3
Misc non coding genes59
Pseudogenes49
Gene transcripts39,681

Other

Genscan gene predictions45,513

About this species