ArticleNucleic acids research2013
UCNEbase--a database of ultraconserved non-coding elements and genomic regulatory blocks.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers, 1 of them a synthesis that pooled it.
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Who cites it
78 citing papers in PubMed, 1 synthesis or guideline pooled it, 129 citations in OpenAlex.
- The landscape of long noncoding RNAs in the human transcriptome.Nature genetics · 2015Pooled it
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- Non-Random Association of Ultraconserved Genomic Elements (UCE) with Human Genes.International journal of molecular sciences · 2026Article
- Non-coding structural variants disrupt FOXG1 transcriptional regulation in early neurodevelopment.Nature communications · 2026Article
- Federated learning for the pathogenicity annotation of genetic variants in multi-site clinical settings.Bioinformatics (Oxford, England) · 2025Article
- Long-term evolutionary persistence of a cryptic color polymorphism in frogs.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Dissecting the Emerging Regulatory and Mechanistic Paradigms of Transcribed Conserved Non-Coding Elements in Breast Cancer.Biomolecules · 2025Article
- Rare germline structural variants increase risk for pediatric solid tumors.Science (New York, N.Y.) · 2025Article
- GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing.bioRxiv : the preprint server for biology · 2024Article
- Phylogenomic analysis of the Lake Kronotskoe species flock of Dolly Varden charr reveals genetic and developmental signatures of sympatric radiation.Development (Cambridge, England) · 2024Article
- Computational identification of ultra-conserved elements in the human genome: a hypothesis on homologous DNA pairing.NAR genomics and bioinformatics · 2024Article
- Genome-wide Cas9-mediated screening of essential non-coding regulatory elements via libraries of paired single-guide RNAs.Nature biomedical engineering · 2024Article
- Paired CRISPR screening libraries for studying the function of the non-coding genome at scale.Nature biomedical engineering · 2024Article
- An epigenetic toolbox for conservation biologists.Evolutionary applications · 2024Article
- Phylogenomic analysis of the Lake Kronotskoe species flock of Dolly Varden charr reveals genetic and developmental signatures of sympatric radiation.bioRxiv : the preprint server for biology · 2024Article
- Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci.Nature communications · 2024Article
- Genetic marker: a genome mapping tool to decode genetic diversity of livestock animals.Frontiers in genetics · 2024Review
- Topological structures and syntenic conservation in sea anemone genomes.Nature communications · 2023Article
- Profound Non-Randomness in Dinucleotide Arrangements within Ultra-Conserved Non-Coding Elements and the Human Genome.Biology · 2023Article
- Convergent genomics of longevity in rockfishes highlights the genetics of human life span variation.Science advances · 2023Article
18 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
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
UCNEbase (http://ccg.vital-it.ch/UCNEbase) is a free, web-accessible information resource on the evolution and genomic organization of ultra-conserved non-coding elements (UCNEs). It currently covers 4351 such elements in 18 different species. The majority of UCNEs are supposed to be transcriptional regulators of key developmental genes. As most of them occur as clusters near potential target genes, the database is organized along two hierarchical levels: individual UCNEs and ultra-conserved genomic regulatory blocks (UGRBs). UCNEbase introduces a coherent nomenclature for UCNEs reflecting their respective associations with likely target genes. Orthologous and paralogous UCNEs share components of their names and are systematically cross-linked. Detailed synteny maps between the human and other genomes are provided for all UGRBs. UCNEbase is managed by a relational database system and can be accessed by a variety of web-based query pages. As it relies on the UCSC genome browser as visualization platform, a large part of its data content is also available as browser viewable custom track files. UCNEbase is potentially useful to any computational, experimental or evolutionary biologist interested in conserved non-coding DNA elements in vertebrates.
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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.