ArticleCurrent genetics2010
Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature.
Article in Current genetics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 60 citations in OpenAlex.
- Mitochondrial genome ofFrontiers in plant science · 2025Article
- Conservation of the moss RNA editing factor PPR78 despite the loss of its known cytidine-to-uridine editing sites is explained by a hidden extra target.The Plant cell · 2024Article
- Insights into the multi-chromosomal mitochondrial genome structure of the xero-halophytic plant Haloxylon Ammodendron (C.A.Mey.) Bunge ex Fenzl.BMC genomics · 2024Article
- A Bibliometric Study for Plant RNA Editing Research: Trends and Future Challenges.Molecular biotechnology · 2023Review
- Beyond a PPR-RNA recognition code: Many aspects matter for the multi-targeting properties of RNA editing factor PPR56.PLoS genetics · 2023Article
- Rickettsial DNA and a trans-splicing rRNA group I intron in the unorthodox mitogenome of the fern Haplopteris ensiformis.Communications biology · 2023Article
- Revisiting chloroplast genomic landscape and annotation towards comparative chloroplast genomes of Rhamnaceae.BMC plant biology · 2023Article
- Comparative analysis of mitochondrial genomes ofFrontiers in plant science · 2023Article
- Plant mitochondrial RNA editing factors can perform targeted C-to-U editing of nuclear transcripts in human cells.Nucleic acids research · 2022Article
- Mitochondrial phylogenomics of Cuscuta (Convolvulaceae) reveals a potentially functional horizontal gene transfer from the host.Genome biology and evolution · 2022Article
- Sequencing of Complete Chloroplast Genomes.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Potential of Transcript Editing Across Mitogenomes of Early Land Plants Shows Novel and Familiar Trends.International journal of molecular sciences · 2019Article
- Plant-type pentatricopeptide repeat proteins with a DYW domain drive C-to-U RNA editing inCommunications biology · 2019Article
- Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0.BMC bioinformatics · 2018Article
- The complete plastid genomes of Ophrys iricolor and O. sphegodes (Orchidaceae) and comparative analyses with other orchids.PloS one · 2018Article
- Convergent Evolution of Fern-Specific Mitochondrial Group II Intron atp1i361g2 and Its Ancient Source Paralogue rps3i249g2 and Independent Losses of Intron and RNA Editing among Pteridaceae.Genome biology and evolution · 2016Article
- Reverse U-to-C editing exceeds C-to-U RNA editing in some ferns - a monilophyte-wide comparison of chloroplast and mitochondrial RNA editing suggests independent evolution of the two processes in both organelles.BMC evolutionary biology · 2016Article
- Frequent chloroplast RNA editing in early-branching flowering plants: pilot studies on angiosperm-wide coexistence of editing sites and their nuclear specificity factors.BMC evolutionary biology · 2016Article
- Analyses of the complete genome and gene expression of chloroplast of sweet potato [Ipomoea batata].PloS one · 2015Article
- Chloroplast RNA editing going extreme: more than 3400 events of C-to-U editing in the chloroplast transcriptome of the lycophyte Selaginella uncinata.RNA (New York, N.Y.) · 2014Article
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transcripts in mitochondria and chloroplasts of land plants are modified through RNA editing, the exchanges of pyrimidines-a post-transcriptional process that may affect more than 1,000 sites in the mitochondrial transcriptomes of some plant species. RNA editing mainly acts as a correcting mechanism to re-create evolutionary conserved coding sequences on mRNA level and can be reasonably well predicted in new plant organelle gene sequence data. Identification and annotation of RNA editing sites is cumbersome and error-prone for larger data sets or organelle sequences subject to highly frequent RNA editing. We here present PREPACT, WWW-accessible at http://www.prepact.de , which allows prediction, analysis, annotation and graphical display of RNA editing sites for both directions of pyrimidine exchanges, using the recently proposed RNA editing nomenclature. PREPACT offers prediction of RNA editing, analysis of partial editing in cDNA pools and a BLASTX mode for simultaneous prediction of genes and RNA editing sites in novel sequences. Output options include (i) lists and annotations of RNA editing sites, (ii) sequence alignments with user-controlled color highlighting of editings, (iii) graphical displays of RNA editing in sequences and alignments. Finally, binary matrices of editing positions can be produced that may be used for downstream (e.g. phylogenetic) analyses.
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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 Socratic graph.