ArticleNucleic acids research2003
Patterns in interspecies similarity correlate with nucleotide composition in mammalian 3'UTRs.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 21 citations in OpenAlex.
- A massively parallel 3' UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization.Genome research · 2019Article
- Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera.BMC plant biology · 2014Article
- Hyper conserved elements in vertebrate mRNA 3'-UTRs reveal a translational network of RNA-binding proteins controlled by HuR.Nucleic acids research · 2013Article
- Multilevel regulation of HIF-1 signaling by TTP.Molecular biology of the cell · 2012Article
- Evolution of alternative and constitutive regions of mammalian 5'UTRs.BMC genomics · 2009Article
- Expansion of the human mu-opioid receptor gene architecture: novel functional variants.Human molecular genetics · 2009Article
- Expression patterns of protein kinases correlate with gene architecture and evolutionary rates.PloS one · 2008Article
- Identification of candidate regulatory sequences in mammalian 3' UTRs by statistical analysis of oligonucleotide distributions.BMC bioinformatics · 2007Article
- RNA expression in a cartilaginous fish cell line reveals ancient 3' noncoding regions highly conserved in vertebrates.Proceedings of the National Academy of Sciences of the United States of America · 2007Article
- Substrate dependence of conformational changes in the RNA-binding domain of tristetraprolin assessed by fluorescence spectroscopy of tryptophan mutants.Biochemistry · 2006Article
- Evidence for conservation and selection of upstream open reading frames suggests probable encoding of bioactive peptides.BMC genomics · 2006Article
- A periodic pattern of mRNA secondary structure created by the genetic code.Nucleic acids research · 2006Article
- Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals.Nucleic acids research · 2004Article
- The mammalian transcriptome and the function of non-coding DNA sequences.Genome biology · 2004Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Post-transcriptional regulation and the formation of mRNA 3' ends are crucial for gene expression in eukaryotes. Interspecies conservation of many sequences within 3'UTRs reveals selective constraint due to similar function. To study the pattern of conservation within 3'UTRs, we compiled and aligned 50 sets of complete orthologous 3'UTRs from four orders of mammals. We observed a mosaic pattern of conservation, with alternating regions of high (phylogenetic footprints) and low similarity. Conservation in 3'UTRs correlates with their base composition and also with the synonymous substitution rate in corresponding coding regions. The non-uniform distribution of conservation is more pronounced for 3'UTRs with a moderate or low level of overall conservation, where invariant nucleotides are more numerous, and their runs of lengths 4-7 occur more frequently than if conservation were random. Many runs of invariant nucleotides are AU-rich or pyrimidine-rich. Some of these runs coincide with known functional cis- elements of eukaryotic mRNAs, such as the U-rich upstream element, polyadenylation signal and DICE regulatory signal. More divergent regions of multiple alignments of 3'UTRs are often more G- and/or C-rich. Our results provide evidence on the importance of moderately conserved regions in 3'UTRs and suggest that regulatory functions of 3'UTRs might utilize gene-specific information in these regions.
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