Coelacanth assembly and gene annotation


This is the preliminary display of the Coelacanth (Latimeria chalumnae) genome produced by the Broad Institute. Illumina techology was used to produced this high quality draft. The whole genome shotgun data was assembled with Allpaths. The genome is 2.9gb in length;,composed of 291,828 contigs with an N50 value of 12.6kb and 22,818 scaffolds with an N50 value of 765kb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000225785.1

Gene annotation

The Ensembl genome annotation pipeline was used to identify genes. Models built from Coelacanth proteins and cDNAs have been given priority over predictions from other vertebrate species. 6,671 transcript models made from paired end Illumina RNA-Seq were added into the gene set where they added a novel model or splice variant. RNA-Seq data was also used to add UTR to non species specific models. The total gene set contains 19,697 protein coding genes with a further 2,894 ncRNAs and 141 pseudogenes.

More information

General information about this species can be found in Wikipedia.



AssemblyLatCha1, INSDC Assembly GCA_000225785.1, Sep 2011
Database version80.1
Base Pairs2,183,592,768
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedSep 2011
Genebuild releasedOct 2011
Genebuild last updated/patchedNov 2012

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

Non coding genes2,918
Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

Misc non coding genes59

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.26,660


Genscan gene predictions103,879