C.intestinalis assembly and gene annotation


The Ciona intestinalis genome is the smallest of any experimentally manipulable chordate, and thus provides a good system for exploring vertebrate evolutionary origins. This Ensembl website presents the sequence data provided by the Kyoto University, with additional Ensembl genebuild (see below).

The current size of the assembly (which includes unmapped scaffolds) is 115Mb, with 78Mb of the assembly mapped to chromosome arms The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 size of scaffolds is 98.07 kb.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000224145.1

Other assemblies

  • JGI2 (Ensembl release 54)

Gene annotation

The standard Ensembl mammalian pipeline was modified for annotation of the Ciona genome, owing to the lack of genomic information from closely related species. Thus, in addition to aligning known Ciona proteins to the genome sequence (as per the standard pipeline), the large quantities of Ciona-specific cDNA and EST sequences were aligned against the genome and then protein data from other species was used to build additional gene models.

In addition to the coding transcript models, non-coding RNAs and pseudogenes were annotated.

More information

General information about this species can be found in Wikipedia.



AssemblyKH, INSDC Assembly GCA_000224145.1, Apr 2011
Base Pairs112,164,198
Golden Path Length115,227,500
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2011
Genebuild releasedMar 2012
Genebuild last updated/patchedMar 2014
Database version90.3

Gene counts

Coding genes16,671
Non coding genes455
Small non coding genes442
Misc non coding genes13
Gene transcripts17,784


Genscan gene predictions10,697

About this species