ArticleGenome research2012
Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
77 citing papers in PubMed, 171 citations in OpenAlex.
- Genomic and Structural Analysis of Gamete Recognition Proteins in a Broadcast Spawning Echinoderm Mesocentrotus franciscanus.Journal of molecular evolution · 2026Article
- An ancient evolutionary origin for IL-1 cytokines.Nature ecology & evolution · 2026Article
- SpEchinoidin, a C-type lectin and a member of an expanded CTL family, is up-regulated by phagocytes in sea urchins responding to immune challenge.Developmental and comparative immunology · 2026Article
- Detection of ExpressedBiology · 2025Article
- Expression of Hox Genes in Early Development of Irregular Sea Urchin Scaphechinus mirabilis (Echinodermata, Echinoidea).Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections · 2025Article
- Microbial communities experienced during early development shape the host immune system and epigenome.iScience · 2025Article
- Ultrafiltration and Fluid Excretion in Echinoids Involves the Axial Organ with Elimination via the Intestine.Life (Basel, Switzerland) · 2025Article
- Expression of HOX Cluster Genes in Early Larval Development of Sea Urchin Strongylocentrotus intermedius (Echinodermata, Echinoidea).Doklady biological sciences : proceedings of the Academy of Sciences of the USSR, Biological sciences sections · 2025Article
- Single-cell omics: experimental workflow, data analyses and applications.Science China. Life sciences · 2025Review
- Combinatorial regulatory states define cell fate diversity during embryogenesis.Nature communications · 2024Article
- Active DNA demethylation of developmentalScience advances · 2022Article
- Twinkle twinkle brittle star: the draft genome of Ophioderma brevispinum (Echinodermata: Ophiuroidea) as a resource for regeneration research.BMC genomics · 2022Article
- Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla.Genomics · 2022Article
- Review
- An approach to quantitate maternal transcripts localized in sea urchin egg cortex using RT-qPCR with accurate normalization.PloS one · 2022Article
- Different sea urchin RAG-like genes were domesticated to carry out different functions.Frontiers in immunology · 2022Article
- Pattern of Repetitive Element Transcription Segregate Cell Lineages during the Embryogenesis of Sea UrchinBiomedicines · 2021Article
- Dynamically expressed single ELAV/Hu orthologue elavl2 of bees is required for learning and memory.Communications biology · 2021Article
- Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling.Genome research · 2021Article
- A nomenclature for echinoderm genes.Database : the journal of biological databases and curation · 2021Article
17 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
A comprehensive transcriptome analysis has been performed on protein-coding RNAs of Strongylocentrotus purpuratus, including 10 different embryonic stages, six feeding larval and metamorphosed juvenile stages, and six adult tissues. In this study, we pooled the transcriptomes from all of these sources and focused on the insights they provide for gene structure in the genome of this recently sequenced model system. The genome had initially been annotated by use of computational gene model prediction algorithms. A large fraction of these predicted genes were recovered in the transcriptome when the reads were mapped to the genome and appropriately filtered and analyzed. However, in a manually curated subset, we discovered that more than half the computational gene model predictions were imperfect, containing errors such as missing exons, prediction of nonexistent exons, erroneous intron/exon boundaries, fusion of adjacent genes, and prediction of multiple genes from single genes. The transcriptome data have been used to provide a systematic upgrade of the gene model predictions throughout the genome, very greatly improving the research usability of the genomic sequence. We have constructed new public databases that incorporate information from the transcriptome analyses. The transcript-based gene model data were used to define average structural parameters for S. purpuratus protein-coding genes. In addition, we constructed a custom sea urchin gene ontology, and assigned about 7000 different annotated transcripts to 24 functional classes. Strong correlations became evident between given functional ontology classes and structural properties, including gene size, exon number, and exon and intron size.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.