ArticleDevelopment genes and evolution2005
Cataloging transcription factor and major signaling molecule genes for functional genomic studies in Ciona intestinalis.
Article in Development genes and evolution, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 25 citations in OpenAlex.
- Single-cell Transcriptomic Studies Unveil Potential Nodes of the Notochord Gene Regulatory Network.Integrative and comparative biology · 2024Review
- Actin Filament in the First Cell Cycle Contributes to the Determination of the Anteroposterior Axis in Ascidian Development.Journal of developmental biology · 2022Article
- Dynamic changes in the association between maternal mRNAs and endoplasmic reticulum during ascidian early embryogenesis.Development genes and evolution · 2022Article
- The notochord gene regulatory network in chordate evolution: Conservation and divergence from Ciona to vertebrates.Current topics in developmental biology · 2020Review
- A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona.Genome biology and evolution · 2019Article
- Repertoires of G protein-coupled receptors forProceedings of the National Academy of Sciences of the United States of America · 2019Article
- Gene regulatory systems that control gene expression in the Ciona embryo.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2015Review
- Comparative cytogenetic mapping of Sox2 and Sox14 in cichlid fishes and inferences on the genomic organization of both genes in vertebrates.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2011Article
- The identification of transcription factors expressed in the notochord of Ciona intestinalis adds new potential players to the brachyury gene regulatory network.Developmental dynamics : an official publication of the American Association of Anatomists · 2011Article
- Evolution of non-coding regulatory sequences involved in the developmental process: reflection of differential employment of paralogous genes as highlighted by Sox2 and group B1 Sox genes.Proceedings of the Japan Academy. Series B, Physical and biological sciences · 2009Review
- Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations.Genome biology · 2008Article
- Logic of gene regulatory networks.Current opinion in biotechnology · 2007Review
- PlanTAPDB, a phylogeny-based resource of plant transcription-associated proteins.Plant physiology · 2007Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ascidian Ciona intestinalis provides an excellent experimental system for functional genomic studies because (1) its genome has been sequenced, (2) the transcription factor genes and genes for major signal transduction molecules have been extensively screened and annotated on a genome-wide scale using the molecular phylogenetical method, and (3) their embryonic expression profiles have been almost completely determined. However, the entire genetic structure, including the 5' and 3' untranslated regions and the protein-coding regions, of most gene models used in these prior studies is not always supported by cDNA evidence, and thus, these gene models are potentially imprecise. To facilitate functional genomic studies based on precise gene structures, our present study determined 406 cDNA sequences for 357 transcription factor genes and 112 cDNA sequences for 107 signal transduction molecule genes, greatly improving the previous gene models and revealing transcript variants for 44 genes. Considering these data alongside those of previously characterized genes deposited in the DNA Data Bank of Japan/European Molecular Biology Laboratory/GENBANK databases, 95.6% of the catalogued transcription factor genes (373/390) and 98.3% of the catalogued signal transduction molecule genes (117/119) have now been verified by cDNA sequences. Thus, the present study greatly improves the resources available for functional genomic studies in C. intestinalis.
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