Vegetal view of a reconstructed 128-cell Ciona gastrula. Muscle and mesenchyme are in red, endoderm in blue, notochord in orange, TLC in green, and A-line neural cells in yellow.
Image communicated by F. Robin and P. Lemaire.

(Don't hesitate to send us your own pictures with a short description !)
Major Update:
  • Aniseed v4 Final Release

    The next version of Aniseed (v4) is available. Use this legacy version (v3) at your own risks. Data won't be updated.

  • 3D Virtual Embryo

    You can access to 3D Virtual Embryo directly from the web site by clicking on 'Start 3D Virtual Embryo' in the corresponding page. It uses Java Web Start. No need to download anything.

Some updates:
  • Blast

    New version of Blast: v2.2.26+. And results are showed with 'Query' and 'Subject' corrdinates.

Aniseed is moving:
  • After moving to Montpeller

    Aniseed was completly reinstalled. 3D Virtual Embryo is up to date.

  • The ANISEED paper now available!!

    We thank all of you who contributed to the success of the system and to the publication. We have decided to include in the authors list all major contributors of unpublished data. This reward policy will be continued for subsequent releases. Do not hesitate to contribute your unpublished data: they may be crucial for someone else in the community and they will bring you authorships.

    To cite the database please use the following reference: O. Tassy, D. Dauga, F. Daian, D. Sobral F. Robin, P. Khoueiry, D. Salgado, V. Fox, D. Caillol, R. Schiappa, B. Laporte, A. Rios, G. Luxardi, T. Kusakabe, J. S. Joly, S. Darras, L. Christiaen, M. Contensin, H. Auger, C. Lamy, C. Hudson, U. Rothbächer, M. J. Gilchrist, K. W. Makabe, K. Hotta, S. Fujiwara, N. Satoh, Y. Satou and P. Lemaire (2010)The ANISEED database: digital representation, formalisation and elucidation of a chordate developmental program. Genome Research, 2010 Aug 13. [Epub ahead of print]. PMID: 20647237

ANISEED version 3:
A model organism database for Ciona intestinalis, Ciona savignyi, Halocynthia roretzi and Phallusia mammillata


Welcome to ANISEED version 3
Aniseed is a database designed to offer a representation of ascidian embryonic development at the level of the genome (cis-regulatory sequences, spatial gene expression, protein annotation), of the cell (cell shapes, fate, lineage) or of the whole embryo (anatomy, morphogenesis). Currently, the anatomy of four organism models are represented in Aniseed: Ciona intestinalis, Ciona savignyi, Halocynthia roretzi and Phallusia mammillata. Extensive molecular data can be found for Halocynthia roretzi and Ciona intestinalis. In particular, this version supports four sets of Ciona intestinalis transcript models: JGI v1.0, KyotoGrail 2005, KH and ENSEMBL, all functionally annotated, and grouped into Aniseedv3.0 gene models. You can explore gene expression profiles during normal or experimentally manipulated development, access validated cis-regulatory regions, get the molecular tools used to assay gene function, or all articles related to the function, or regulation of a given gene. Known transcriptional regulators and targets are listed for each gene, as are the gene regulatory networks acting in individual anatomical territories.
Have fun and as usual, please send us feedback on this version at
The aniseed team


If you don't know where to start ... Use anisearch to perform a keyword search on the whole database except cDNA clones, which can be accessed via the "genes/clones" menu at the top of the page.
eg. "otx" retrieves all data associated to otx. You can also combine words for example "otx 32 cell a6.5" will retrieve all in situs for otx at the 32 cell stage showing staining in the a6.5 blastomere.


OR     AND     Complete sentence
Virtual embryo
The 3D Virtual embryo is available to download in the download section of the website.
It's well supported on the majority of platform (MacOS, Windows, Linux).

All the data present in our website are now freely downloadable (Insitu data, clones, anatomical ontologies, ...) Visit our download page for more informations.

Many tutorials (text and movies) are online and may be useful ...

MISFISHIE Exchange Format
In Situs Exchange Format used by ANISEED.

Part of information found in aniseed could be also found in


Aniseed version 3.0 -     Contact:
ANISEED, NISEED Website and Database are under GPL License.    

© Tassy, Daian, Sobral, Dauga, Khoueiry, Salgado, Lemaire 2007