ArticleGenome research2009
Conserved introns reveal novel transcripts in Drosophila melanogaster.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed.
- Bi-alignments with affine gaps costs.Algorithms for molecular biology : AMB · 2022Article
- Identification of Regulatory Functions of LncRNAs Associated WithFrontiers in genetics · 2021Article
- The roles of long noncoding RNAs in breast cancer metastasis.Cell death & disease · 2020Review
- A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers.GigaScience · 2020Article
- Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis.RNA biology · 2019Article
- Genome-wide identification and developmental expression profiling of long noncoding RNAs during Drosophila metamorphosis.Scientific reports · 2016Article
- Evolution of the unspliced transcriptome.BMC evolutionary biology · 2015Article
- Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.G3 (Bethesda, Md.) · 2015Article
- Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved.RNA (New York, N.Y.) · 2015Article
- Characteristics and significance of intergenic polyadenylated RNA transcription in Arabidopsis.Plant physiology · 2013Article
- Hidden treasures in unspliced EST data.Theory in biosciences = Theorie in den Biowissenschaften · 2012Article
- Article
- Molecular mechanisms and function prediction of long noncoding RNA.TheScientificWorldJournal · 2012Review
- Identification and properties of 1,119 candidate lincRNA loci in the Drosophila melanogaster genome.Genome biology and evolution · 2012Article
- "Hypothesis for the modern RNA world": a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity.Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life · 2011Article
- The reality of pervasive transcription.PLoS biology · 2011Article
- Enrichment of mRNA-like noncoding RNAs in the divergence of Drosophila males.Molecular biology and evolution · 2011Article
- The Drosophila melanogaster transcriptome by paired-end RNA sequencing.Genome research · 2011Article
- Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome.Nucleic acids research · 2010Article
- De novo prediction of structured RNAs from genomic sequences.Trends in biotechnology · 2010Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Noncoding RNAs that are-like mRNAs-spliced, capped, and polyadenylated have important functions in cellular processes. The inventory of these mRNA-like noncoding RNAs (mlncRNAs), however, is incomplete even in well-studied organisms, and so far, no computational methods exist to predict such RNAs from genomic sequences only. The subclass of these transcripts that is evolutionarily conserved usually has conserved intron positions. We demonstrate here that a genome-wide comparative genomics approach searching for short conserved introns is capable of identifying conserved transcripts with a high specificity. Our approach requires neither an open reading frame nor substantial sequence or secondary structure conservation in the surrounding exons. Thus it identifies spliced transcripts in an unbiased way. After applying our approach to insect genomes, we predict 369 introns outside annotated coding transcripts, of which 131 are confirmed by expressed sequence tags (ESTs) and/or noncoding FlyBase transcripts. Of the remaining 238 novel introns, about half are associated with protein-coding genes-either extending coding or untranslated regions or likely belonging to unannotated coding genes. The remaining 129 introns belong to novel mlncRNAs that are largely unstructured. Using RT-PCR, we verified seven of 12 tested introns in novel mlncRNAs and 11 of 17 introns in novel coding genes. The expression level of all verified mlncRNA transcripts is low but varies during development, which suggests regulation. As conserved introns indicate both purifying selection on the exon-intron structure and conserved expression of the transcript in related species, the novel mlncRNAs are good candidates for functional transcripts.
Indexed as
Identifiers
What OpenQuestion holds
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.