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Burton's mouthbrooder assembly and gene annotation

Assembly

The AstBur1.0 assembly was submitted by Broad Institute on December 2011. The assembly is on scaffold level, consisting of 69,074 contigs assembled into 8,001 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 21,886 while the scaffold N50 is 1,194,190.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000239415.1

Gene annotation

Astatotilapia burtoni is a species of fish in the family Cichlidae.It is found in Burundi, Rwanda, Tanzania, and Zambia.Its natural habitats are rivers, intermittent rivers, swamps, freshwater lakes, freshwater marshes, intermittent freshwater marshes, and inland deltas.Astatotilapia burtoni has been used as a model organism to study the behaviors and physical systems of cichlids, including their development and embryogenesis. Moreover, the phylogenetic position of this particular species makes it an ideal model system for comparative genomic research. A. burtoni belongs under the haplochromines, which is the lineage of cichlids with the most species, and has been discovered to be a sister group to both the Lake Victoria region superflock (which has about 600 species) and the species flock of Lake Malawi (which has about 1,000 species).

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

AssemblyAstBur1.0, INSDC Assembly GCA_000239415.1, Dec 2011
Base Pairs831,411,547
Golden Path Length831,411,547
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedMay 2018
Genebuild releasedJul 2018
Genebuild last updated/patchedJul 2018
Database version94.1

Gene counts

Coding genes23,079
Non coding genes781
Small non coding genes762
Long non coding genes3
Misc non coding genes16
Pseudogenes23
Gene transcripts36,423

Other

Genscan gene predictions36,654

About this species