ArticleRNA (New York, N.Y.)2006
The disparate nature of "intergenic" polyadenylation sites.
Article in RNA (New York, N.Y.), 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 50 citations in OpenAlex.
- Transposons disrupt genomic stability and trigger cancers.Frontiers in cellular and infection microbiology · 2025Review
- GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing.bioRxiv : the preprint server for biology · 2024Article
- CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing.Nature communications · 2024Article
- ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms.Nature communications · 2020Article
- Genome-Wide Profiling of Polyadenylation Events in Maize Using High-Throughput Transcriptomic Sequences.G3 (Bethesda, Md.) · 2019Article
- Towards a complete map of the human long non-coding RNA transcriptome.Nature reviews. Genetics · 2018Review
- Genome-wide dynamics of alternative polyadenylation in rice.Genome research · 2016Article
- Structural Variation ofGenomics & informatics · 2016Review
- Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana.BMC genomics · 2015Article
- Evaluation of two statistical methods provides insights into the complex patterns of alternative polyadenylation site switching.PloS one · 2015Article
- Bioinformatics analysis of alternative polyadenylation in green alga Chlamydomonas reinhardtii using transcriptome sequences from three different sequencing platforms.G3 (Bethesda, Md.) · 2014Article
- IB4-binding sensory neurons in the adult rat express a novel 3' UTR-extended isoform of CaMK4 that is associated with its localization to axons.The Journal of comparative neurology · 2014Article
- A multiplex RNA-seq strategy to profile poly(A+) RNA: application to analysis of transcription response and 3' end formation.Genomics · 2011Article
- Poly(A) signals located near the 5' end of genes are silenced by a general mechanism that prevents premature 3'-end processing.Molecular and cellular biology · 2011Article
- Article
- POLYAR, a new computer program for prediction of poly(A) sites in human sequences.BMC genomics · 2010Article
- Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.BMC genomics · 2009Article
- Identification of gene 3' ends by automated EST cluster analysis.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Genome level analysis of rice mRNA 3'-end processing signals and alternative polyadenylation.Nucleic acids research · 2008Article
- Beyond the 3' end: experimental validation of extended transcript isoforms.Nucleic acids research · 2007Article
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
No grant is acknowledged in the PubMed record.
Abstract
The termination of mature eukaryotic mRNAs occurs at specific polyadenylation sites located downstream from stop codons in the 3'-untranslated region (UTR). An accurate delineation of these sites is essential for the study of 3'-UTR-based gene regulation and for the design of pertinent probes for transcriptome analysis. Although typical poly(A) sites are located between 0 and 2 kb from the stop codon, EST sequence analyses have identified sites located at unexpectedly long ranges (5-10 kb) in a number of genes. Here we perform a complete mapping of EST and full-length cDNA sequences on the mouse and human genome to observe putative poly(A) sites extending beyond annotated 3'-ends and into the intergenic regions. We introduce several quality parameters for poly(A) site prediction and train a classification tree to associate P-values to predicted sites. We observe a higher than background level of high-scoring sites up to 12-15 kb past the stop codon, both in human and mouse. This leads to an estimate of about 5000 human genes having unreported 3'-end extensions and about 3500 novel polyadenylated transcripts lying in present "intergenic" regions. These high-scoring, long-range poly(A) sites corresponding to novel transcripts and gene extensions should be incorporated into current human and mouse gene repositories.
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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.