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 59)

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
Database version80.3
Base Pairs112,164,198
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 startedAug 2011
Genebuild releasedMar 2012
Genebuild last updated/patchedMar 2014

Gene counts

Coding genes

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

Non coding genes455
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 genes13

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.17,784


Genscan gene predictions10,697