ArticleBMC research notes2017
Consideration of non-canonical splice sites improves gene prediction on the Arabidopsis thaliana Niederzenz-1 genome sequence.
Article in BMC research notes, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed.
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- NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction.PLoS computational biology · 2025Article
- DRANetSplicer: A Splice Site Prediction Model Based on Deep Residual Attention Networks.Genes · 2024Article
- Identification of annotation artifacts concerning the chalcone synthase (CHS).BMC research notes · 2023Article
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- Mapping-by-Sequencing Reveals Genomic Regions Associated with Seed Quality Parameters inGenes · 2022Article
- Spliceator: multi-species splice site prediction using convolutional neural networks.BMC bioinformatics · 2021Article
- Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp.BMC biology · 2021Article
- Characterization of theFrontiers in plant science · 2021Article
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- A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set.PloS one · 2019Article
- Genome-wide analyses supported by RNA-Seq reveal non-canonical splice sites in plant genomes.BMC genomics · 2018Article
- A major QTL on chromosome C05 significantly reduces acid detergent lignin (ADL) content and increases seed oil and protein content in oilseed rape (Brassica napus L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2018Article
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3 authors.
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Abstract
objectiveThe Arabidopsis thaliana Niederzenz-1 genome sequence was recently published with an ab initio gene prediction. In depth analysis of the predicted gene set revealed some errors involving genes with non-canonical splice sites in their introns. Since non-canonical splice sites are difficult to predict ab initio, we checked for options to improve the annotation by transferring annotation information from the recently released Columbia-0 reference genome sequence annotation Araport11.
resultsIncorporation of hints generated from Araport11 enabled the precise prediction of non-canonical splice sites. Manual inspection of RNA-Seq read mapping and RT-PCR were applied to validate the structural annotations of non-canonical splice sites. Predictions of untranslated regions were also updated by harnessing the potential of Araport11's information, which was generated by using high coverage RNA-Seq data. The improved gene set of the Nd-1 genome assembly (GeneSet_Nd-1_v1.1) was evaluated via comparison to the initial gene prediction (GeneSet_Nd-1_v1.0) as well as against Araport11 for the Col-0 reference genome sequence. GeneSet_Nd-1_v1.1 contains previously missed non-canonical splice sites in 1256 genes. Reciprocal best hits for 24,527 (89.4%) of all nuclear Col-0 genes against the GeneSet_Nd-1_v1.1 indicate a high gene prediction quality.
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